[{"article_number":"L061304","quality_controlled":"1","oa":1,"month":"06","publication":"Physical Review A","publisher":"American Physical Society","date_updated":"2023-08-02T06:31:52Z","doi":"10.1103/PhysRevA.107.L061304","article_processing_charge":"No","oa_version":"Preprint","external_id":{"arxiv":["2302.01022"],"isi":["001019748000005"]},"article_type":"letter_note","volume":107,"type":"journal_article","date_published":"2023-06-20T00:00:00Z","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"department":[{"_id":"MiLe"},{"_id":"OnHo"}],"year":"2023","language":[{"iso":"eng"}],"publication_status":"published","day":"20","date_created":"2023-07-16T22:01:10Z","arxiv":1,"author":[{"last_name":"Agafonova","full_name":"Agafonova, Sofya","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","_id":"13233","title":"Finite-range bias in fitting three-body loss to the zero-range model","abstract":[{"lang":"eng","text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.01022"}],"intvolume":"       107","citation":{"ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>","mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>.","chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>.","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","apa":"Agafonova, S., Lemeshko, M., &#38; Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023."},"ec_funded":1,"status":"public","isi":1,"scopus_import":"1","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"issue":"6"},{"_id":"13234","title":"Into the unknown: Active monitoring of neural networks (extended version)","abstract":[{"lang":"eng","text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, by DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS.","ec_funded":1,"status":"public","has_accepted_license":"1","intvolume":"        25","citation":{"ieee":"K. Kueffner, A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: Active monitoring of neural networks (extended version),” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25. Springer Nature, pp. 575–592, 2023.","short":"K. Kueffner, A. Lukina, C. Schilling, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 25 (2023) 575–592.","ista":"Kueffner K, Lukina A, Schilling C, Henzinger TA. 2023. Into the unknown: Active monitoring of neural networks (extended version). International Journal on Software Tools for Technology Transfer. 25, 575–592.","apa":"Kueffner, K., Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2023). Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>","chicago":"Kueffner, Konstantin, Anna Lukina, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>.","ama":"Kueffner K, Lukina A, Schilling C, Henzinger TA. Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. 2023;25:575-592. doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>","mla":"Kueffner, Konstantin, et al. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25, Springer Nature, 2023, pp. 575–92, doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>."},"isi":1,"scopus_import":"1","file_date_updated":"2024-01-30T12:06:07Z","publication_identifier":{"eissn":["1433-2787"],"issn":["1433-2779"]},"publication":"International Journal on Software Tools for Technology Transfer","doi":"10.1007/s10009-023-00711-4","publisher":"Springer Nature","date_updated":"2024-01-30T12:06:57Z","article_processing_charge":"Yes (in subscription journal)","oa":1,"file":[{"relation":"main_file","creator":"dernst","file_id":"14903","date_created":"2024-01-30T12:06:07Z","content_type":"application/pdf","file_size":13387667,"date_updated":"2024-01-30T12:06:07Z","checksum":"3c4b347f39412a76872f9a6f30101f94","access_level":"open_access","file_name":"2023_JourSoftwareTools_Kueffner.pdf","success":1}],"quality_controlled":"1","month":"08","volume":25,"type":"journal_article","date_published":"2023-08-01T00:00:00Z","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"article_type":"original","oa_version":"Published Version","external_id":{"arxiv":["2009.06429"],"isi":["001020160000001"]},"language":[{"iso":"eng"}],"ddc":["000"],"year":"2023","related_material":{"record":[{"status":"public","relation":"shorter_version","id":"10206"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"ToHe"}],"page":"575-592","author":[{"orcid":"0000-0001-8974-2542","last_name":"Kueffner","first_name":"Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","full_name":"Kueffner, Konstantin"},{"last_name":"Lukina","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","first_name":"Anna","full_name":"Lukina, Anna"},{"orcid":"0000-0003-3658-1065","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Schilling, Christian"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"}],"publication_status":"published","day":"01","date_created":"2023-07-16T22:01:11Z","arxiv":1},{"article_processing_charge":"No","publication":"ACS Nano","doi":"10.1021/acsnano.3c03541","publisher":"American Chemical Society","date_updated":"2023-08-02T06:29:55Z","month":"06","quality_controlled":"1","volume":17,"date_published":"2023-06-13T00:00:00Z","type":"journal_article","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"oa_version":"None","article_type":"original","external_id":{"isi":["001008564800001"],"pmid":["37310395"]},"year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"author":[{"first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740"},{"first_name":"Mingquan","full_name":"Li, Mingquan","last_name":"Li"},{"last_name":"Wan","first_name":"Shanhong","full_name":"Wan, Shanhong"},{"last_name":"Lim","full_name":"Lim, Khak Ho","first_name":"Khak Ho"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"},{"last_name":"Hong","full_name":"Hong, Min","first_name":"Min"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"page":"11923–11934","date_created":"2023-07-16T22:01:11Z","publication_status":"published","day":"13","abstract":[{"lang":"eng","text":"AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13235","title":"Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance","pmid":1,"acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (Grant No. 22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","status":"public","citation":{"chicago":"Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li, Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” <i>ACS Nano</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsnano.3c03541\">https://doi.org/10.1021/acsnano.3c03541</a>.","ama":"Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. <i>ACS Nano</i>. 2023;17(12):11923–11934. doi:<a href=\"https://doi.org/10.1021/acsnano.3c03541\">10.1021/acsnano.3c03541</a>","mla":"Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” <i>ACS Nano</i>, vol. 17, no. 12, American Chemical Society, 2023, pp. 11923–11934, doi:<a href=\"https://doi.org/10.1021/acsnano.3c03541\">10.1021/acsnano.3c03541</a>.","ieee":"Y. Liu <i>et al.</i>, “Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance,” <i>ACS Nano</i>, vol. 17, no. 12. American Chemical Society, pp. 11923–11934, 2023.","short":"Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong, A. Cabot, ACS Nano 17 (2023) 11923–11934.","ista":"Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 17(12), 11923–11934.","apa":"Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023). Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c03541\">https://doi.org/10.1021/acsnano.3c03541</a>"},"intvolume":"        17","isi":1,"scopus_import":"1","issue":"12","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]}},{"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031327254"],"issn":["0302-9743"]},"scopus_import":"1","citation":{"mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” <i>International Conference on Integer Programming and Combinatorial Optimization</i>, vol. 13904, Springer Nature, 2023, pp. 453–65, doi:<a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">10.1007/978-3-031-32726-1_32</a>.","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. In: <i>International Conference on Integer Programming and Combinatorial Optimization</i>. Vol 13904. Springer Nature; 2023:453-465. doi:<a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">10.1007/978-3-031-32726-1_32</a>","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” In <i>International Conference on Integer Programming and Combinatorial Optimization</i>, 13904:453–65. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">https://doi.org/10.1007/978-3-031-32726-1_32</a>.","apa":"Zheng, D. W., &#38; Henzinger, M. H. (2023). Multiplicative auction algorithm for approximate maximum weight bipartite matching. In <i>International Conference on Integer Programming and Combinatorial Optimization</i> (Vol. 13904, pp. 453–465). Madison, WI, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">https://doi.org/10.1007/978-3-031-32726-1_32</a>","ista":"Zheng DW, Henzinger MH. 2023. Multiplicative auction algorithm for approximate maximum weight bipartite matching. International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 13904, 453–465.","ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” in <i>International Conference on Integer Programming and Combinatorial Optimization</i>, Madison, WI, United States, 2023, vol. 13904, pp. 453–465.","short":"D.W. Zheng, M.H. Henzinger, in:, International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2023, pp. 453–465."},"intvolume":"     13904","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.09217","open_access":"1"}],"status":"public","ec_funded":1,"acknowledgement":"The first author thanks to Chandra Chekuri for useful discussions about this paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges.","lang":"eng"}],"title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","_id":"13236","date_created":"2023-07-16T22:01:11Z","arxiv":1,"day":"22","publication_status":"published","author":[{"first_name":"Da Wei","full_name":"Zheng, Da Wei","last_name":"Zheng"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H"}],"conference":{"end_date":"2023-06-23","location":"Madison, WI, United States","name":"IPCO: Integer Programming and Combinatorial Optimization","start_date":"2023-06-21"},"alternative_title":["LNCS"],"page":"453-465","department":[{"_id":"MoHe"}],"year":"2023","language":[{"iso":"eng"}],"external_id":{"arxiv":["2301.09217"]},"oa_version":"Preprint","project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"type":"conference","date_published":"2023-05-22T00:00:00Z","volume":13904,"month":"05","quality_controlled":"1","oa":1,"article_processing_charge":"No","doi":"10.1007/978-3-031-32726-1_32","publisher":"Springer Nature","date_updated":"2023-07-18T07:08:51Z","publication":"International Conference on Integer Programming and Combinatorial Optimization"},{"publication_identifier":{"eissn":["2522-5820"]},"scopus_import":"1","isi":1,"citation":{"mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>, vol. 5, Springer Nature, 2023, pp. 379–397, doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>.","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. 2023;5:379–397. doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &#38; Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>","ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.","short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” <i>Nature Reviews Physics</i>, vol. 5. Springer Nature, pp. 379–397, 2023."},"intvolume":"         5","status":"public","acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases."}],"title":"Amyloid formation as a protein phase transition","_id":"13237","date_created":"2023-07-16T22:01:12Z","day":"01","publication_status":"published","author":[{"first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T.","last_name":"Michaels"},{"full_name":"Qian, Daoyuan","first_name":"Daoyuan","last_name":"Qian"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"last_name":"Linse","first_name":"Sara","full_name":"Linse, Sara"},{"full_name":"Knowles, Tuomas P.J.","first_name":"Tuomas P.J.","last_name":"Knowles"}],"page":"379–397","department":[{"_id":"AnSa"}],"year":"2023","language":[{"iso":"eng"}],"article_type":"original","external_id":{"isi":["001017539800001"]},"oa_version":"None","type":"journal_article","date_published":"2023-07-01T00:00:00Z","volume":5,"month":"07","quality_controlled":"1","article_processing_charge":"No","doi":"10.1038/s42254-023-00598-9","publisher":"Springer Nature","date_updated":"2023-08-02T06:28:38Z","publication":"Nature Reviews Physics"},{"quality_controlled":"1","oa":1,"month":"05","doi":"10.1007/978-3-031-32733-9_26","date_updated":"2025-07-14T09:09:53Z","publisher":"Springer Nature","publication":"SIROCCO 2023: Structural Information and Communication Complexity ","article_processing_charge":"No","oa_version":"Preprint","external_id":{"arxiv":["2204.13459"]},"date_published":"2023-05-25T00:00:00Z","type":"conference","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"volume":13892,"department":[{"_id":"KrPi"},{"_id":"KrCh"}],"related_material":{"record":[{"id":"14506","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"year":"2023","day":"25","publication_status":"published","arxiv":1,"date_created":"2023-07-16T22:01:12Z","conference":{"location":"Alcala de Henares, Spain","end_date":"2023-06-09","start_date":"2023-06-06","name":"SIROCCO: Structural Information and Communication Complexity"},"alternative_title":["LNCS"],"page":"576-594","author":[{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"},{"full_name":"Svoboda, Jakub","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267","last_name":"Svoboda"},{"last_name":"Yeo","orcid":"0009-0001-3676-4809","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","full_name":"Yeo, Michelle X"}],"acknowledgement":"We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful discussions about different variants of the problem. This work is supported by the European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025, the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant 470029389 (FlexNets), 2021–2024.","title":"Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation","_id":"13238","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n.","lang":"eng"}],"citation":{"chicago":"Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” In <i>SIROCCO 2023: Structural Information and Communication Complexity </i>, 13892:576–94. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">https://doi.org/10.1007/978-3-031-32733-9_26</a>.","ama":"Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In: <i>SIROCCO 2023: Structural Information and Communication Complexity </i>. Vol 13892. Springer Nature; 2023:576-594. doi:<a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">10.1007/978-3-031-32733-9_26</a>","mla":"Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” <i>SIROCCO 2023: Structural Information and Communication Complexity </i>, vol. 13892, Springer Nature, 2023, pp. 576–94, doi:<a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">10.1007/978-3-031-32733-9_26</a>.","ieee":"S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation,” in <i>SIROCCO 2023: Structural Information and Communication Complexity </i>, Alcala de Henares, Spain, 2023, vol. 13892, pp. 576–594.","short":"S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information and Communication Complexity , Springer Nature, 2023, pp. 576–594.","ista":"Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023: Structural Information and Communication Complexity . SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 576–594.","apa":"Schmid, S., Svoboda, J., &#38; Yeo, M. X. (2023). Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In <i>SIROCCO 2023: Structural Information and Communication Complexity </i> (Vol. 13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">https://doi.org/10.1007/978-3-031-32733-9_26</a>"},"intvolume":"     13892","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.13459"}],"status":"public","ec_funded":1,"scopus_import":"1","publication_identifier":{"isbn":["9783031327322"],"issn":["0302-9743"],"eissn":["1611-3349"]}},{"issue":"27","publication_identifier":{"eissn":["1948-7185"]},"isi":1,"file_date_updated":"2023-07-19T06:55:39Z","status":"public","ec_funded":1,"citation":{"short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","ieee":"Y. Wei <i>et al.</i>, “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., &#38; Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>.","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>.","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. 2023;14(27):6309-6314. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>"},"intvolume":"        14","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.","lang":"eng"}],"title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","_id":"13251","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","author":[{"orcid":"0000-0001-8913-9719","last_name":"Wei","first_name":"Yujing","id":"0c5ff007-2600-11ee-b896-98bd8d663294","full_name":"Wei, Yujing"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525"},{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","last_name":"Lorenc"},{"last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A.","first_name":"Ayan A."},{"last_name":"Bakr","full_name":"Bakr, Osman M.","first_name":"Osman M."},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"orcid":"0000-0002-7183-5203","last_name":"Alpichshev","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek"}],"keyword":["General Materials Science","Physical and Theoretical Chemistry"],"page":"6309-6314","date_created":"2023-07-18T11:13:17Z","arxiv":1,"day":"05","publication_status":"published","language":[{"iso":"eng"}],"year":"2023","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"date_published":"2023-07-05T00:00:00Z","project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"type":"journal_article","volume":14,"article_type":"original","external_id":{"arxiv":["2304.14198"],"isi":["001022811500001"]},"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","doi":"10.1021/acs.jpclett.3c01158","date_updated":"2023-07-19T06:59:19Z","publisher":"American Chemical Society","publication":"The Journal of Physical Chemistry Letters","month":"07","file":[{"date_updated":"2023-07-19T06:55:39Z","file_size":2121252,"success":1,"access_level":"open_access","file_name":"2023_JourPhysChemistry_Wei.pdf","checksum":"c0c040063f06a51b9c463adc504f1a23","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2023-07-19T06:55:39Z","file_id":"13253"}],"quality_controlled":"1","oa":1},{"has_accepted_license":"1","citation":{"apa":"GOSWAMI, B. B., &#38; An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>Npj Climate and Atmospheric Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” <i>npj Climate and Atmospheric Science</i>, vol. 6. Springer Nature, 2023.","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>, vol. 6, 82, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>.","ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>npj Climate and Atmospheric Science</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>."},"intvolume":"         6","status":"public","acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","abstract":[{"text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13256","title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","publication_identifier":{"eissn":["2397-3722"]},"file_date_updated":"2023-07-31T08:00:01Z","isi":1,"scopus_import":"1","article_type":"original","external_id":{"isi":["001024920300002"]},"oa_version":"Published Version","volume":6,"type":"journal_article","date_published":"2023-07-08T00:00:00Z","month":"07","article_number":"82","file":[{"date_updated":"2023-07-31T08:00:01Z","file_size":1750712,"access_level":"open_access","file_name":"2023_npjclimate_Goswami.pdf","success":1,"checksum":"e9967d436a83b8ffcc6f58782e1f7500","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"13326","date_created":"2023-07-31T08:00:01Z"}],"quality_controlled":"1","oa":1,"article_processing_charge":"Yes","publication":"npj Climate and Atmospheric Science","doi":"10.1038/s41612-023-00411-5","date_updated":"2023-08-02T06:38:07Z","publisher":"Springer Nature","date_created":"2023-07-23T22:01:10Z","publication_status":"published","day":"08","author":[{"last_name":"Goswami","first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"Goswami, Bidyut B"},{"last_name":"An","full_name":"An, Soon Il","first_name":"Soon Il"}],"department":[{"_id":"CaMu"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2023","language":[{"iso":"eng"}],"ddc":["550"]},{"volume":108,"type":"journal_article","date_published":"2023-07-15T00:00:00Z","external_id":{"isi":["001062708600002"],"arxiv":["2208.10038"]},"article_type":"original","oa_version":"Preprint","article_processing_charge":"No","publication":"Physical Review B","date_updated":"2023-12-13T11:58:57Z","publisher":"American Physical Society","doi":"10.1103/PhysRevB.108.035111","month":"07","article_number":"035111","oa":1,"quality_controlled":"1","author":[{"last_name":"Shekhter","full_name":"Shekhter, A.","first_name":"A."},{"last_name":"Mcdonald","first_name":"R. D.","full_name":"Mcdonald, R. D."},{"first_name":"B. J.","full_name":"Ramshaw, B. J.","last_name":"Ramshaw"},{"orcid":"0000-0001-9760-3147","last_name":"Modic","full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A"}],"date_created":"2023-07-23T22:01:10Z","arxiv":1,"publication_status":"published","day":"15","year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"KiMo"}],"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.10038"}],"citation":{"mla":"Shekhter, A., et al. “Magnetotropic Susceptibility.” <i>Physical Review B</i>, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>.","ama":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. <i>Physical Review B</i>. 2023;108(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>","chicago":"Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>.","apa":"Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., &#38; Modic, K. A. (2023). Magnetotropic susceptibility. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>","ista":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111.","short":"A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023).","ieee":"A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” <i>Physical Review B</i>, vol. 108, no. 3. American Physical Society, 2023."},"intvolume":"       108","abstract":[{"text":"The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13257","title":"Magnetotropic susceptibility","acknowledgement":"We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784.","issue":"3","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"isi":1,"scopus_import":"1"},{"department":[{"_id":"KrCh"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2023","ddc":["000"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13336"}]},"publication_status":"published","day":"12","date_created":"2023-07-23T22:01:11Z","author":[{"last_name":"Kleshnina","first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X"},{"last_name":"Simsa","orcid":"0000-0001-6687-1210","first_name":"Stepan","id":"409d615c-2f95-11ee-b934-90a352102c1e","full_name":"Simsa, Stepan"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"article_number":"4153","quality_controlled":"1","file":[{"access_level":"open_access","file_name":"2023_NatureComm_Kleshnina.pdf","success":1,"checksum":"5aceefdfe76686267b93ae4fe81899f1","date_updated":"2023-07-31T11:32:36Z","file_size":1601682,"content_type":"application/pdf","file_id":"13337","date_created":"2023-07-31T11:32:36Z","relation":"main_file","creator":"dernst"}],"oa":1,"month":"07","publication":"Nature Communications","publisher":"Springer Nature","date_updated":"2025-07-14T09:09:53Z","doi":"10.1038/s41467-023-39625-9","article_processing_charge":"Yes","external_id":{"pmid":["37438341"],"isi":["001029450400031"]},"article_type":"original","oa_version":"Published Version","volume":14,"date_published":"2023-07-12T00:00:00Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","file_date_updated":"2023-07-31T11:32:36Z","isi":1,"scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","pmid":1,"_id":"13258","title":"The effect of environmental information on evolution of cooperation in stochastic games","abstract":[{"text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","intvolume":"        14","citation":{"ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023).","apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., &#38; Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>","ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153.","chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>.","mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>, vol. 14, 4153, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>.","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>"},"ec_funded":1,"status":"public"},{"author":[{"last_name":"De Castro Barbosa Rodrigues Barata","first_name":"Carolina","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","full_name":"De Castro Barbosa Rodrigues Barata, Carolina"},{"last_name":"Snook","full_name":"Snook, Rhonda R.","first_name":"Rhonda R."},{"last_name":"Ritchie","full_name":"Ritchie, Michael G.","first_name":"Michael G."},{"last_name":"Kosiol","full_name":"Kosiol, Carolin","first_name":"Carolin"}],"publication_status":"published","day":"01","date_created":"2023-07-23T22:01:11Z","ddc":["570"],"language":[{"iso":"eng"}],"year":"2023","related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"BeVi"}],"volume":15,"date_published":"2023-07-01T00:00:00Z","type":"journal_article","oa_version":"Published Version","article_type":"original","external_id":{"isi":["001023444700003"],"pmid":["37341535"]},"publication":"Genome biology and evolution","date_updated":"2023-08-02T06:42:35Z","doi":"10.1093/gbe/evad113","publisher":"Oxford Academic","article_processing_charge":"Yes","article_number":"evad113","oa":1,"quality_controlled":"1","file":[{"date_updated":"2023-08-01T06:58:34Z","file_size":2382587,"access_level":"open_access","file_name":"2023_GBE_Barata.pdf","success":1,"checksum":"70de3c4878de6efe00dc56de2df8812f","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"13339","date_created":"2023-08-01T06:58:34Z"}],"month":"07","issue":"7","publication_identifier":{"eissn":["1759-6653"]},"isi":1,"scopus_import":"1","file_date_updated":"2023-08-01T06:58:34Z","status":"public","has_accepted_license":"1","citation":{"ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38; Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol. 15, no. 7. Oxford Academic, 2023.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>.","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>."},"intvolume":"        15","_id":"13260","title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","abstract":[{"text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","pmid":1},{"year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"author":[{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","orcid":"0000-0001-7205-2975"},{"last_name":"Chen","full_name":"Chen, Hongtao","first_name":"Hongtao"},{"full_name":"Barinov, Lev","first_name":"Lev","last_name":"Barinov"},{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"}],"page":"1357-1362","date_created":"2023-07-23T22:01:12Z","day":"29","publication_status":"published","article_processing_charge":"No","date_updated":"2023-12-13T11:41:07Z","doi":"10.1126/science.adf5568","publisher":"American Association for the Advancement of Science","publication":"Science","month":"06","quality_controlled":"1","oa":1,"date_published":"2023-06-29T00:00:00Z","type":"journal_article","project":[{"grant_number":"343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"volume":380,"external_id":{"isi":["001106405600028"]},"article_type":"original","oa_version":"Preprint","scopus_import":"1","isi":1,"issue":"6652","publication_identifier":{"eissn":["1095-9203"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.","lang":"eng"}],"title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","_id":"13261","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","status":"public","citation":{"short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362.","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>."},"intvolume":"       380","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adf5568"}]},{"article_processing_charge":"Yes (in subscription journal)","publisher":"Association for Computing Machinery","doi":"10.1145/3558481.3591082","date_updated":"2023-07-31T10:54:32Z","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","month":"06","oa":1,"file":[{"creator":"dernst","relation":"main_file","date_created":"2023-07-31T10:53:08Z","file_id":"13334","content_type":"application/pdf","file_size":2087937,"date_updated":"2023-07-31T10:53:08Z","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1,"file_name":"2023_SPAA_Fedorov.pdf","access_level":"open_access"}],"quality_controlled":"1","type":"conference","date_published":"2023-06-17T00:00:00Z","oa_version":"Published Version","external_id":{"arxiv":["2304.09331"]},"year":"2023","language":[{"iso":"eng"}],"ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"author":[{"last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","full_name":"Fedorov, Alexander"},{"last_name":"Hashemi","full_name":"Hashemi, Diba","first_name":"Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"},{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"conference":{"end_date":"2023-06-19","location":"Orlando, FL, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2023-06-17"},"page":"261-271","arxiv":1,"date_created":"2023-07-23T22:01:12Z","day":"17","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"title":"Provably-efficient and internally-deterministic parallel Union-Find","_id":"13262","status":"public","citation":{"ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., &#38; Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Orlando, FL, United States, 2023, pp. 261–271.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2023:261-271. doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2023, pp. 261–71, doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>.","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 261–71. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>."},"has_accepted_license":"1","scopus_import":"1","file_date_updated":"2023-07-31T10:53:08Z","publication_identifier":{"isbn":["9781450395458"]}},{"scopus_import":"1","isi":1,"file_date_updated":"2023-07-31T11:09:05Z","issue":"Supplement_1","publication_identifier":{"eissn":["1367-4811"],"issn":["1367-4803"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models.","lang":"eng"}],"title":"Trap spaces of multi-valued networks: Definition, computation, and applications","_id":"13263","pmid":1,"acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","status":"public","ec_funded":1,"citation":{"chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>.","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>, vol. 39, no. Supplement_1, Oxford Academic, 2023, pp. i513–22, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>.","ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. 2023;39(Supplement_1):i513-i522. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>","ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” <i>Bioinformatics</i>, vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.","short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522.","apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., &#38; Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522."},"intvolume":"        39","has_accepted_license":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/giang-trinh/trap-mvn"}]},"language":[{"iso":"eng"}],"ddc":["000"],"year":"2023","department":[{"_id":"ToHe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Trinh","full_name":"Trinh, Van Giang","first_name":"Van Giang"},{"full_name":"Benhamou, Belaid","first_name":"Belaid","last_name":"Benhamou"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"orcid":"0000-0003-1993-0331","last_name":"Pastva","first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel"}],"page":"i513-i522","date_created":"2023-07-23T22:01:12Z","day":"30","publication_status":"published","article_processing_charge":"Yes","doi":"10.1093/bioinformatics/btad262","date_updated":"2023-12-13T11:41:52Z","publisher":"Oxford Academic","publication":"Bioinformatics","month":"06","quality_controlled":"1","oa":1,"file":[{"success":1,"access_level":"open_access","file_name":"2023_Bioinformatics_Trinh.pdf","checksum":"ba3abe1171df1958413b7c7f957f5486","date_updated":"2023-07-31T11:09:05Z","file_size":641736,"content_type":"application/pdf","date_created":"2023-07-31T11:09:05Z","file_id":"13335","relation":"main_file","creator":"dernst"}],"type":"journal_article","date_published":"2023-06-30T00:00:00Z","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"volume":39,"oa_version":"Published Version","article_type":"original","external_id":{"isi":["001027457000060"],"pmid":["37387165"]}},{"oa_version":"Preprint","article_type":"original","external_id":{"arxiv":["2206.05746"],"isi":["001012022600004"]},"type":"journal_article","date_published":"2023-06-09T00:00:00Z","volume":19,"month":"06","oa":1,"quality_controlled":"1","article_number":"064032","article_processing_charge":"No","doi":"10.1103/PhysRevApplied.19.064032","date_updated":"2023-11-30T10:56:03Z","publisher":"American Physical Society","publication":"Physical Review Applied","date_created":"2023-07-23T22:01:12Z","arxiv":1,"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"day":"09","publication_status":"published","author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","full_name":"Phan, Duc T","last_name":"Phan"},{"last_name":"Falthansl-Scheinecker","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","first_name":"Paul","full_name":"Falthansl-Scheinecker, Paul"},{"full_name":"Mishra, Umang","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","first_name":"Umang","last_name":"Mishra"},{"last_name":"Strickland","full_name":"Strickland, W. M.","first_name":"W. M."},{"full_name":"Langone, D.","first_name":"D.","last_name":"Langone"},{"last_name":"Shabani","full_name":"Shabani, J.","first_name":"J."},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"}],"department":[{"_id":"AnHi"},{"_id":"OnHo"}],"related_material":{"record":[{"id":"14547","relation":"dissertation_contains","status":"public"}]},"year":"2023","language":[{"iso":"eng"}],"intvolume":"        19","citation":{"chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>.","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>.","ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>","ieee":"D. T. Phan <i>et al.</i>, “Gate-tunable superconductor-semiconductor parametric amplifier,” <i>Physical Review Applied</i>, vol. 19, no. 6. American Physical Society, 2023.","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., &#38; Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>","ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032."},"main_file_link":[{"url":"https://arxiv.org/abs/2206.05746","open_access":"1"}],"status":"public","acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n","lang":"eng"}],"title":"Gate-tunable superconductor-semiconductor parametric amplifier","_id":"13264","publication_identifier":{"eissn":["2331-7019"]},"issue":"6","scopus_import":"1","isi":1},{"isi":1,"scopus_import":"1","issue":"3","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"_id":"13265","title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","abstract":[{"text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.02374","open_access":"1"}],"citation":{"short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).","ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3. Association for Computing Machinery, 2023.","apa":"Zhong, F., Xu, Y., Zhao, H., &#38; Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>","ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>.","mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>.","ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>"},"intvolume":"        42","year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"BeBi"}],"author":[{"full_name":"Zhong, Fanchao","first_name":"Fanchao","last_name":"Zhong"},{"last_name":"Xu","full_name":"Xu, Yonglai","first_name":"Yonglai"},{"last_name":"Zhao","orcid":"0000-0002-6389-1045","full_name":"Zhao, Haisen","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","first_name":"Haisen"},{"first_name":"Lin","full_name":"Lu, Lin","last_name":"Lu"}],"publication_status":"published","day":"17","date_created":"2023-07-23T22:01:13Z","arxiv":1,"publication":"ACM Transactions on Graphics","date_updated":"2023-12-13T11:34:59Z","publisher":"Association for Computing Machinery","doi":"10.1145/3575859","article_processing_charge":"No","article_number":"26","quality_controlled":"1","oa":1,"month":"03","volume":42,"date_published":"2023-03-17T00:00:00Z","type":"journal_article","oa_version":"Preprint","article_type":"original","external_id":{"arxiv":["2201.02374"],"isi":["001018739600002"]}},{"date_created":"2023-07-23T22:01:13Z","publication_status":"published","day":"01","author":[{"first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"page":"489-495","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"JiFr"}],"year":"2023","ddc":["580"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_type":"original","external_id":{"isi":["001026321500001"],"pmid":["37434303"]},"volume":240,"date_published":"2023-10-01T00:00:00Z","project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123","name":"Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"type":"journal_article","month":"10","oa":1,"file":[{"creator":"dernst","relation":"main_file","file_id":"14898","date_created":"2024-01-29T11:21:43Z","content_type":"application/pdf","file_size":974464,"date_updated":"2024-01-29T11:21:43Z","checksum":"6d9bbd45b8e7bb3ceee2586d447bacb2","file_name":"2023_NewPhytologist_Qi.pdf","access_level":"open_access","success":1}],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publication":"New Phytologist","date_updated":"2024-01-29T11:21:55Z","doi":"10.1111/nph.19123","publisher":"Wiley","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"issue":"2","file_date_updated":"2024-01-29T11:21:43Z","isi":1,"scopus_import":"1","has_accepted_license":"1","citation":{"ama":"Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. 2023;240(2):489-495. doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>","mla":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>.","chicago":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>.","ista":"Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495.","apa":"Qi, L., &#38; Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>","short":"L. Qi, J. Friml, New Phytologist 240 (2023) 489–495.","ieee":"L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” <i>New Phytologist</i>, vol. 240, no. 2. Wiley, pp. 489–495, 2023."},"intvolume":"       240","status":"public","pmid":1,"acknowledgement":"We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.","abstract":[{"lang":"eng","text":"The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13266","title":"Tale of cAMP as a second messenger in auxin signaling and beyond"},{"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"isi":1,"scopus_import":"1","ec_funded":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-023-01936-6"}],"intvolume":"        20","citation":{"mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023."},"_id":"13267","title":"Dense 4D nanoscale reconstruction of living brain tissue","abstract":[{"text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","pmid":1,"page":"1256-1265","author":[{"full_name":"Velicky, Philipp","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","orcid":"0000-0001-5665-0430"},{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","orcid":"0000-0003-3862-1235","last_name":"Michalska"},{"last_name":"Lyudchik","full_name":"Lyudchik, Julia","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wei, Donglai","first_name":"Donglai","last_name":"Wei"},{"first_name":"Zudi","full_name":"Lin, Zudi","last_name":"Lin"},{"orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake"},{"first_name":"Jakob","full_name":"Troidl, Jakob","last_name":"Troidl"},{"first_name":"Johanna","full_name":"Beyer, Johanna","last_name":"Beyer"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","full_name":"Ben Simon, Yoav","last_name":"Ben Simon"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","last_name":"Cenameri"},{"last_name":"Broichhagen","first_name":"Johannes","full_name":"Broichhagen, Johannes"},{"last_name":"Grant","full_name":"Grant, Seth G.N.","first_name":"Seth G.N."},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"publication_status":"published","day":"01","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"date_created":"2023-07-23T22:01:13Z","language":[{"iso":"eng"}],"year":"2023","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}],"record":[{"relation":"research_data","status":"public","id":"12817"},{"status":"public","relation":"shorter_version","id":"14770"}]},"department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"volume":20,"type":"journal_article","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"},{"grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"date_published":"2023-08-01T00:00:00Z","external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"oa_version":"Published Version","article_type":"original","publication":"Nature Methods","date_updated":"2024-01-10T08:37:48Z","publisher":"Springer Nature","doi":"10.1038/s41592-023-01936-6","article_processing_charge":"Yes","oa":1,"quality_controlled":"1","month":"08"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations.","lang":"eng"}],"title":"On type II degenerations of hyperkähler manifolds","_id":"13268","acknowledgement":"The first author is supported by the ERC Synergy Grant HyperK. The second author is supported by the Max Planck Institute for Mathematics and the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","status":"public","ec_funded":1,"citation":{"ieee":"D. Huybrechts and M. Mauri, “On type II degenerations of hyperkähler manifolds,” <i>Mathematical Research Letters</i>, vol. 30, no. 1. International Press, pp. 125–141, 2023.","short":"D. Huybrechts, M. Mauri, Mathematical Research Letters 30 (2023) 125–141.","apa":"Huybrechts, D., &#38; Mauri, M. (2023). On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. International Press. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>","ista":"Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 30(1), 125–141.","chicago":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>. International Press, 2023. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>.","mla":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>, vol. 30, no. 1, International Press, 2023, pp. 125–41, doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>.","ama":"Huybrechts D, Mauri M. On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. 2023;30(1):125-141. doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>"},"intvolume":"        30","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.01587","open_access":"1"}],"scopus_import":"1","isi":1,"issue":"1","publication_identifier":{"eissn":["1945-001X"],"issn":["1073-2780"]},"article_processing_charge":"No","date_updated":"2024-01-16T12:00:47Z","publisher":"International Press","doi":"10.4310/mrl.2023.v30.n1.a6","publication":"Mathematical Research Letters","month":"06","quality_controlled":"1","oa":1,"date_published":"2023-06-21T00:00:00Z","type":"journal_article","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"volume":30,"external_id":{"isi":["001027656000006"],"arxiv":["2108.01587"]},"article_type":"original","oa_version":"Preprint","year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"TaHa"}],"author":[{"full_name":"Huybrechts, D.","first_name":"D.","last_name":"Huybrechts"},{"last_name":"Mauri","full_name":"Mauri, Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130","first_name":"Mirko"}],"page":"125-141","date_created":"2023-07-23T22:01:14Z","arxiv":1,"day":"21","publication_status":"published"},{"publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"issue":"10","isi":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.01427","open_access":"1"}],"citation":{"apa":"Polyanskii, N., &#38; Zhang, Y. (2023). Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>","ista":"Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on Information Theory. 69(10), 6340–6357.","ieee":"N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10. Institute of Electrical and Electronics Engineers, pp. 6340–6357, 2023.","short":"N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 6340–6357.","mla":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10, Institute of Electrical and Electronics Engineers, 2023, pp. 6340–57, doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>.","ama":"Polyanskii N, Zhang Y. Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. 2023;69(10):6340-6357. doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>","chicago":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>."},"intvolume":"        69","status":"public","acknowledgement":"Nikita Polyanskii’s research was conducted in part during October 2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute of Science and Technology. His work was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang is supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","_id":"13269","title":"Codes for the Z-channel","abstract":[{"text":"This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","day":"04","date_created":"2023-07-23T22:01:14Z","arxiv":1,"page":"6340-6357","author":[{"full_name":"Polyanskii, Nikita","first_name":"Nikita","last_name":"Polyanskii"},{"orcid":"0000-0002-6465-6258","last_name":"Zhang","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan"}],"department":[{"_id":"MaMo"}],"language":[{"iso":"eng"}],"year":"2023","article_type":"original","oa_version":"Preprint","external_id":{"arxiv":["2105.01427"],"isi":["001069680100011"]},"volume":69,"type":"journal_article","date_published":"2023-07-04T00:00:00Z","quality_controlled":"1","oa":1,"month":"07","publication":"IEEE Transactions on Information Theory","date_updated":"2024-01-29T11:10:54Z","doi":"10.1109/TIT.2023.3292219","publisher":"Institute of Electrical and Electronics Engineers","article_processing_charge":"No"}]