[{"quality_controlled":"1","citation":{"short":"I. Vercellino, L.A. Sazanov, Nature Reviews Molecular Cell Biology 23 (2022) 141–161.","ama":"Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. <i>Nature Reviews Molecular Cell Biology</i>. 2022;23:141–161. doi:<a href=\"https://doi.org/10.1038/s41580-021-00415-0\">10.1038/s41580-021-00415-0</a>","apa":"Vercellino, I., &#38; Sazanov, L. A. (2022). The assembly, regulation and function of the mitochondrial respiratory chain. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41580-021-00415-0\">https://doi.org/10.1038/s41580-021-00415-0</a>","ieee":"I. Vercellino and L. A. Sazanov, “The assembly, regulation and function of the mitochondrial respiratory chain,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 23. Springer Nature, pp. 141–161, 2022.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 23, Springer Nature, 2022, pp. 141–161, doi:<a href=\"https://doi.org/10.1038/s41580-021-00415-0\">10.1038/s41580-021-00415-0</a>.","ista":"Vercellino I, Sazanov LA. 2022. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 23, 141–161.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41580-021-00415-0\">https://doi.org/10.1038/s41580-021-00415-0</a>."},"type":"journal_article","pmid":1,"abstract":[{"lang":"eng","text":"The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases."}],"department":[{"_id":"LeSa"}],"volume":23,"corr_author":"1","publisher":"Springer Nature","date_created":"2021-10-24T22:01:35Z","publication_status":"published","external_id":{"isi":["000705697100001"],"pmid":["34621061"]},"_id":"10182","scopus_import":"1","month":"02","date_published":"2022-02-01T00:00:00Z","intvolume":"        23","day":"01","doi":"10.1038/s41580-021-00415-0","year":"2022","publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"article_type":"original","isi":1,"publication":"Nature Reviews Molecular Cell Biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","page":"141–161","date_updated":"2024-10-09T21:01:03Z","title":"The assembly, regulation and function of the mitochondrial respiratory chain","author":[{"first_name":"Irene","orcid":" 0000-0001-5618-3449","full_name":"Vercellino, Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public"},{"volume":22,"department":[{"_id":"MaMo"}],"publisher":"Springer","citation":{"short":"M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics 22 (2022) 1513–1566.","mla":"Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” <i>Foundations of Computational Mathematics</i>, vol. 22, no. 5, Springer, 2022, pp. 1513–66, doi:<a href=\"https://doi.org/10.1007/s10208-021-09531-x\">10.1007/s10208-021-09531-x</a>.","ista":"Mondelli M, Thrampoulidis C, Venkataramanan R. 2022. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. 22(5), 1513–1566.","chicago":"Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” <i>Foundations of Computational Mathematics</i>. Springer, 2022. <a href=\"https://doi.org/10.1007/s10208-021-09531-x\">https://doi.org/10.1007/s10208-021-09531-x</a>.","ama":"Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear and spectral estimators for generalized linear models. <i>Foundations of Computational Mathematics</i>. 2022;22(5):1513-1566. doi:<a href=\"https://doi.org/10.1007/s10208-021-09531-x\">10.1007/s10208-021-09531-x</a>","ieee":"M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination of linear and spectral estimators for generalized linear models,” <i>Foundations of Computational Mathematics</i>, vol. 22, no. 5. Springer, pp. 1513–1566, 2022.","apa":"Mondelli, M., Thrampoulidis, C., &#38; Venkataramanan, R. (2022). Optimal combination of linear and spectral estimators for generalized linear models. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-021-09531-x\">https://doi.org/10.1007/s10208-021-09531-x</a>"},"type":"journal_article","abstract":[{"text":"We study the problem of recovering an unknown signal 𝑥𝑥 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator 𝑥𝑥^L and a spectral estimator 𝑥𝑥^s. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine 𝑥𝑥^L and 𝑥𝑥^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of 𝑥𝑥^L and 𝑥𝑥^s, given the limiting distribution of the signal 𝑥𝑥. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form 𝜃𝑥𝑥^L+𝑥𝑥^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s), we design and analyze an approximate message passing algorithm whose iterates give 𝑥𝑥^L and approach 𝑥𝑥^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately.","lang":"eng"}],"quality_controlled":"1","_id":"10211","month":"10","issue":"5","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-11-03T10:59:08Z","external_id":{"arxiv":["2008.03326"],"isi":["000685721000001"]},"isi":1,"publication":"Foundations of Computational Mathematics","arxiv":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"ddc":["510"],"oa":1,"file":[{"content_type":"application/pdf","checksum":"9ea12dd8045a0678000a3a59295221cb","relation":"main_file","date_updated":"2021-12-13T15:47:54Z","file_id":"10542","access_level":"open_access","creator":"alisjak","file_size":2305731,"file_name":"2021_Springer_Mondelli.pdf","date_created":"2021-12-13T15:47:54Z","success":1}],"day":"01","doi":"10.1007/s10208-021-09531-x","date_published":"2022-10-01T00:00:00Z","intvolume":"        22","article_type":"original","year":"2022","acknowledgement":"M. Mondelli would like to thank Andrea Montanari for helpful discussions. All the authors would like to thank the anonymous reviewers for their helpful comments.","publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"title":"Optimal combination of linear and spectral estimators for generalized linear models","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco"},{"first_name":"Christos","last_name":"Thrampoulidis","full_name":"Thrampoulidis, Christos"},{"first_name":"Ramji","full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan"}],"page":"1513-1566","date_updated":"2025-04-15T06:53:08Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2021-12-13T15:47:54Z","oa_version":"Published Version","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computational Mathematics","Analysis"]},{"oa":1,"doi":"10.1111/nph.17792","day":"01","date_published":"2022-01-01T00:00:00Z","intvolume":"       233","acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","year":"2022","article_type":"original","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"isi":1,"publication":"New Phytologist","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","author":[{"first_name":"Ivan","last_name":"Kashkan","full_name":"Kashkan, Ivan"},{"first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katarzyna","last_name":"Retzer","full_name":"Retzer, Katarzyna"},{"first_name":"Jana","last_name":"Humpolíčková","full_name":"Humpolíčková, Jana"},{"first_name":"Aswathy","last_name":"Jayasree","full_name":"Jayasree, Aswathy"},{"first_name":"Roberta","full_name":"Filepová, Roberta","last_name":"Filepová"},{"last_name":"Vondráková","full_name":"Vondráková, Zuzana","first_name":"Zuzana"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741"},{"first_name":"Debbie","last_name":"Rombaut","full_name":"Rombaut, Debbie"},{"first_name":"Thomas B.","full_name":"Jacobs, Thomas B.","last_name":"Jacobs"},{"first_name":"Mikko J.","full_name":"Frilander, Mikko J.","last_name":"Frilander"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Růžička","full_name":"Růžička, Kamil","first_name":"Kamil"}],"page":"329-343","date_updated":"2024-05-22T11:33:15Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","citation":{"short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2022) 329–343.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 233, no. 1, Wiley, 2022, pp. 329–43, doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>.","chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>.","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2022. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233(1), 329–343.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. 2022;233(1):329-343. doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2022). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>","ieee":"I. Kashkan <i>et al.</i>, “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 233, no. 1. Wiley, pp. 329–343, 2022."},"abstract":[{"lang":"eng","text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development."}],"pmid":1,"type":"journal_article","quality_controlled":"1","volume":233,"department":[{"_id":"JiFr"}],"publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}],"publication_status":"published","date_created":"2021-11-14T23:01:24Z","external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"_id":"10282","month":"01","scopus_import":"1","issue":"1"},{"oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"13061","status":"public"}]},"date_updated":"2025-04-14T13:55:31Z","page":"89-100","author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E"},{"first_name":"Christopher","full_name":"Pull, Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982"},{"first_name":"Filip","last_name":"Naiser","full_name":"Naiser, Filip"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth"},{"first_name":"Jiri","last_name":"Matas","full_name":"Matas, Jiri"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia"}],"title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2022-02-03T13:37:11Z","language":[{"iso":"eng"}],"status":"public","date_published":"2022-01-01T00:00:00Z","intvolume":"        25","oa":1,"file":[{"content_type":"application/pdf","checksum":"0bd4210400e9876609b7c538ab4f9a3c","relation":"main_file","date_updated":"2022-02-03T13:37:11Z","file_id":"10721","access_level":"open_access","creator":"cchlebak","file_size":700087,"success":1,"file_name":"2021_EcologyLetters_CasillasPerez.pdf","date_created":"2022-02-03T13:37:11Z"}],"day":"01","doi":"10.1111/ele.13907","acknowledgement":"The authors are grateful to G. Tkačik and V. Mireles for advice on data analyses and to A. Schloegl for help using the IST Austria HPC cluster for data processing. The authors thank J. Eilenberg for providing the fungal strain and A.V. Grasse for support with the molecular analysis. The authors also thank the Social Immunity group at IST Austria, in particular B. Milutinović, for discussions throughout and comments on the manuscript.","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"article_type":"original","year":"2022","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"publication":"Ecology Letters","ddc":["573"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2021-11-14T23:01:25Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"pmid":["34725912"],"isi":["000713396100001"]},"_id":"10284","issue":"1","scopus_import":"1","month":"01","quality_controlled":"1","citation":{"chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>.","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2022. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Ecology Letters. 25(1), 89–100.","mla":"Casillas Perez, Barbara E., et al. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>, vol. 25, no. 1, Wiley, 2022, pp. 89–100, doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>.","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies,” <i>Ecology Letters</i>, vol. 25, no. 1. Wiley, pp. 89–100, 2022.","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. 2022;25(1):89-100. doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &#38; Cremer, S. (2022). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, Ecology Letters 25 (2022) 89–100."},"pmid":1,"abstract":[{"text":"Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing ‘superorganisms’––incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.","lang":"eng"}],"type":"journal_article","department":[{"_id":"SyCr"}],"volume":25,"corr_author":"1","publisher":"Wiley"},{"date_created":"2021-11-25T13:49:16Z","publication_status":"published","external_id":{"arxiv":["1907.05055"],"isi":["000798210100003"]},"_id":"10335","scopus_import":"1","month":"12","quality_controlled":"1","citation":{"short":"V. Kaluza, M. Tancer, Combinatorica 42 (2022) 1317–1345.","chicago":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” <i>Combinatorica</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00493-021-4443-7\">https://doi.org/10.1007/s00493-021-4443-7</a>.","ista":"Kaluza V, Tancer M. 2022. Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. 42, 1317–1345.","mla":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” <i>Combinatorica</i>, vol. 42, Springer Nature, 2022, pp. 1317–45, doi:<a href=\"https://doi.org/10.1007/s00493-021-4443-7\">10.1007/s00493-021-4443-7</a>.","ama":"Kaluza V, Tancer M. Even maps, the Colin de Verdière number and representations of graphs. <i>Combinatorica</i>. 2022;42:1317-1345. doi:<a href=\"https://doi.org/10.1007/s00493-021-4443-7\">10.1007/s00493-021-4443-7</a>","ieee":"V. Kaluza and M. Tancer, “Even maps, the Colin de Verdière number and representations of graphs,” <i>Combinatorica</i>, vol. 42. Springer Nature, pp. 1317–1345, 2022.","apa":"Kaluza, V., &#38; Tancer, M. (2022). Even maps, the Colin de Verdière number and representations of graphs. <i>Combinatorica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00493-021-4443-7\">https://doi.org/10.1007/s00493-021-4443-7</a>"},"abstract":[{"text":"Van der Holst and Pendavingh introduced a graph parameter σ, which coincides with the more famous Colin de Verdière graph parameter μ for small values. However, the definition of a is much more geometric/topological directly reflecting embeddability properties of the graph. They proved μ(G) ≤ σ(G) + 2 and conjectured σ(G) ≤ σ(G) for any graph G. We confirm this conjecture. As far as we know, this is the first topological upper bound on σ(G) which is, in general, tight.\r\nEquality between μ and σ does not hold in general as van der Holst and Pendavingh showed that there is a graph G with μ(G) ≤ 18 and σ(G) ≥ 20. We show that the gap appears at much smaller values, namely, we exhibit a graph H for which μ(H) ≥ 7 and σ(H) ≥ 8. We also prove that, in general, the gap can be large: The incidence graphs Hq of finite projective planes of order q satisfy μ(Hq) ∈ O(q3/2) and σ(Hq) ≥ q2.","lang":"eng"}],"type":"journal_article","department":[{"_id":"UlWa"}],"volume":42,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1907.05055","open_access":"1"}],"publisher":"Springer Nature","corr_author":"1","oa_version":"Preprint","page":"1317-1345","date_updated":"2024-10-09T20:53:51Z","author":[{"first_name":"Vojtech","last_name":"Kaluza","full_name":"Kaluza, Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","orcid":"0000-0002-2512-8698"},{"first_name":"Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer","full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"}],"title":"Even maps, the Colin de Verdière number and representations of graphs","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_published":"2022-12-01T00:00:00Z","intvolume":"        42","oa":1,"doi":"10.1007/s00493-021-4443-7","day":"01","publication_identifier":{"issn":["0209-9683"]},"year":"2022","article_type":"original","acknowledgement":"V. K. gratefully acknowledges the support of Austrian Science Fund (FWF): P 30902-N35. This work was done mostly while he was employed at the University of Innsbruck. During the early stage of this research, V. K. was partially supported by Charles University project GAUK 926416. M. T. is supported by the grant no. 19-04113Y of the Czech Science Foundation(GA ˇCR) and partially supported by Charles University project UNCE/SCI/004.","isi":1,"arxiv":1,"publication":"Combinatorica","ddc":["514","516"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"arxiv":1,"publication":"IEEE Transactions on Wireless Communications","isi":1,"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1109/TWC.2021.3125626","day":"01","oa":1,"intvolume":"        21","date_published":"2022-06-01T00:00:00Z","acknowledgement":"S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC) and by Huawei. M. Mondelli is partially\r\nsupported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by\r\nthe National Science Foundation under Grant CCF-1764104.","year":"2022","article_type":"original","publication_identifier":{"eissn":["1558-2248"],"issn":["1536-1276"]},"title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","author":[{"first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi"},{"first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"first_name":"Arman","full_name":"Fazeli, Arman","last_name":"Fazeli"},{"first_name":"Alexander","full_name":"Vardy, Alexander","last_name":"Vardy"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"last_name":"Goldsmith","full_name":"Goldsmith, Andrea","first_name":"Andrea"}],"related_material":{"record":[{"status":"public","id":"10053","relation":"earlier_version"}]},"date_updated":"2025-04-15T07:50:11Z","page":"3909-3920","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Preprint","volume":21,"department":[{"_id":"MaMo"}],"publisher":"Institute of Electrical and Electronics Engineers","main_file_link":[{"url":"https://arxiv.org/abs/2012.13378","open_access":"1"}],"type":"journal_article","abstract":[{"text":"This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1-1/μ + N/P log2 log2 N/P), where N is the block length of the code and μ is the scaling exponent of the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P = N/2, the latency of SSC decoding is O(N1-1/μ), which is sublinear in the block length. This recovers a result from our earlier work. Second, in a fully-serial implementation where P = 1, the latency of SSC decoding scales as O(N log2 log2 N). The multiplicative constant is also calculated: we show that the latency of SSC decoding when P = 1 is given by (2 + o(1))N log2 log2 N. Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P = N1/μ. The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations.","lang":"eng"}],"citation":{"short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 21 (2022) 3909–3920.","ista":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2022. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 21(6), 3909–3920.","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>.","mla":"Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6, Institute of Electrical and Electronics Engineers, 2022, pp. 3909–20, doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>.","apa":"Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., &#38; Goldsmith, A. (2022). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>","ama":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2022;21(6):3909-3920. doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>","ieee":"S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6. Institute of Electrical and Electronics Engineers, pp. 3909–3920, 2022."},"quality_controlled":"1","_id":"10364","month":"06","scopus_import":"1","issue":"6","publication_status":"published","date_created":"2021-11-28T23:01:29Z","external_id":{"isi":["000809406400028"],"arxiv":["2012.13378"]}},{"external_id":{"isi":["000791838800012"]},"date_created":"2021-12-05T23:01:44Z","publication_status":"published","scopus_import":"1","month":"03","_id":"10413","quality_controlled":"1","citation":{"short":"D. Dikranjan, A. Giordano Bruno, H.P. Künzi, N. Zava, D. Toller, Topology and Its Applications 309 (2022).","ista":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. 2022. Generalized quasi-metric semilattices. Topology and its Applications. 309, 107916.","chicago":"Dikranjan, Dikran, Anna Giordano Bruno, Hans Peter Künzi, Nicolò Zava, and Daniele Toller. “Generalized Quasi-Metric Semilattices.” <i>Topology and Its Applications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.topol.2021.107916\">https://doi.org/10.1016/j.topol.2021.107916</a>.","mla":"Dikranjan, Dikran, et al. “Generalized Quasi-Metric Semilattices.” <i>Topology and Its Applications</i>, vol. 309, 107916, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.topol.2021.107916\">10.1016/j.topol.2021.107916</a>.","apa":"Dikranjan, D., Giordano Bruno, A., Künzi, H. P., Zava, N., &#38; Toller, D. (2022). Generalized quasi-metric semilattices. <i>Topology and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.topol.2021.107916\">https://doi.org/10.1016/j.topol.2021.107916</a>","ieee":"D. Dikranjan, A. Giordano Bruno, H. P. Künzi, N. Zava, and D. Toller, “Generalized quasi-metric semilattices,” <i>Topology and its Applications</i>, vol. 309. Elsevier, 2022.","ama":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. Generalized quasi-metric semilattices. <i>Topology and its Applications</i>. 2022;309. doi:<a href=\"https://doi.org/10.1016/j.topol.2021.107916\">10.1016/j.topol.2021.107916</a>"},"type":"journal_article","abstract":[{"lang":"eng","text":"Motivated by the recent introduction of the intrinsic semilattice entropy, we study generalized quasi-metric semilattices and their categories. We investigate the relationship between these objects and generalized semivaluations, extending Nakamura and Schellekens' approach. Finally, we use this correspondence to compare the intrinsic semilattice entropy and the semigroup entropy induced in particular situations, like sets, torsion abelian groups and vector spaces."}],"corr_author":"1","publisher":"Elsevier","department":[{"_id":"HeEd"}],"volume":309,"oa_version":"None","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:01:16Z","author":[{"last_name":"Dikranjan","full_name":"Dikranjan, Dikran","first_name":"Dikran"},{"first_name":"Anna","last_name":"Giordano Bruno","full_name":"Giordano Bruno, Anna"},{"full_name":"Künzi, Hans Peter","last_name":"Künzi","first_name":"Hans Peter"},{"last_name":"Zava","full_name":"Zava, Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","orcid":"0000-0001-8686-1888","first_name":"Nicolò"},{"full_name":"Toller, Daniele","last_name":"Toller","first_name":"Daniele"}],"title":"Generalized quasi-metric semilattices","acknowledgement":"Dedicated to the memory of Hans-Peter Künzi.","publication_identifier":{"issn":["0166-8641"]},"article_type":"original","year":"2022","article_number":"107916","date_published":"2022-03-15T00:00:00Z","intvolume":"       309","day":"15","doi":"10.1016/j.topol.2021.107916","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publication":"Topology and its Applications"},{"quality_controlled":"1","citation":{"short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>.","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. 2022;121(1):P44-60. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>","ieee":"T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no. 1. Elsevier, pp. P44-60, 2022."},"abstract":[{"text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n","lang":"eng"}],"pmid":1,"type":"journal_article","publisher":"Elsevier","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"volume":121,"external_id":{"isi":["000740815400007"],"pmid":["34890578"]},"date_created":"2021-12-10T09:48:19Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_status":"published","issue":"1","scopus_import":"1","month":"01","_id":"10530","year":"2022","acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","publication_identifier":{"issn":["0006-3495"]},"article_type":"original","date_published":"2022-01-04T00:00:00Z","intvolume":"       121","file":[{"access_level":"open_access","file_size":4475504,"creator":"dernst","date_created":"2022-07-29T10:17:10Z","success":1,"file_name":"2022_BiophysicalJour_Zisis.pdf","relation":"main_file","content_type":"application/pdf","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","file_id":"11697","date_updated":"2022-07-29T10:17:10Z"}],"oa":1,"day":"04","doi":"10.1016/j.bpj.2021.12.006","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"publication":"Biophysical Journal","keyword":["Biophysics"],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2022-07-29T10:17:10Z","status":"public","language":[{"iso":"eng"}],"page":"P44-60","date_updated":"2025-06-11T13:59:29Z","author":[{"first_name":"Themistoklis","last_name":"Zisis","full_name":"Zisis, Themistoklis"},{"orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","last_name":"Brückner","first_name":"David"},{"last_name":"Brandstätter","full_name":"Brandstätter, Tom","first_name":"Tom"},{"last_name":"Siow","full_name":"Siow, Wei Xiong","first_name":"Wei Xiong"},{"full_name":"d’Alessandro, Joseph","last_name":"d’Alessandro","first_name":"Joseph"},{"first_name":"Angelika M.","last_name":"Vollmar","full_name":"Vollmar, Angelika M."},{"last_name":"Broedersz","full_name":"Broedersz, Chase P.","first_name":"Chase P."},{"last_name":"Zahler","full_name":"Zahler, Stefan","first_name":"Stefan"}],"title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration"},{"date_published":"2022-05-01T00:00:00Z","intvolume":"        23","oa":1,"day":"01","doi":"10.1007/s00023-021-01136-y","acknowledgement":"NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782).","year":"2022","article_type":"original","publication_identifier":{"issn":["1424-0637"]},"ec_funded":1,"isi":1,"publication":"Annales Henri Poincaré","arxiv":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","page":"1725-1764","date_updated":"2025-04-14T07:26:53Z","author":[{"first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","full_name":"Benedikter, Niels P","last_name":"Benedikter","orcid":"0000-0002-1071-6091"},{"full_name":"Nam, Phan Thành","last_name":"Nam","first_name":"Phan Thành"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert"}],"title":"Bosonization of fermionic many-body dynamics","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” <i>Annales Henri Poincaré</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00023-021-01136-y\">https://doi.org/10.1007/s00023-021-01136-y</a>.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2022. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 23(5), 1725–1764.","mla":"Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” <i>Annales Henri Poincaré</i>, vol. 23, no. 5, Springer Nature, 2022, pp. 1725–64, doi:<a href=\"https://doi.org/10.1007/s00023-021-01136-y\">10.1007/s00023-021-01136-y</a>.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” <i>Annales Henri Poincaré</i>, vol. 23, no. 5. Springer Nature, pp. 1725–1764, 2022.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R. (2022). Bosonization of fermionic many-body dynamics. <i>Annales Henri Poincaré</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01136-y\">https://doi.org/10.1007/s00023-021-01136-y</a>","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. <i>Annales Henri Poincaré</i>. 2022;23(5):1725-1764. doi:<a href=\"https://doi.org/10.1007/s00023-021-01136-y\">10.1007/s00023-021-01136-y</a>","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré 23 (2022) 1725–1764."},"abstract":[{"lang":"eng","text":"We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations."}],"type":"journal_article","department":[{"_id":"RoSe"}],"volume":23,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08224"}],"publisher":"Springer Nature","date_created":"2021-12-12T23:01:28Z","publication_status":"published","external_id":{"arxiv":["2103.08224"],"isi":["000725405700001"]},"_id":"10537","scopus_import":"1","issue":"5","month":"05"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2023-08-02T13:37:03Z","page":"220-267","title":"Global existence analysis of energy-reaction-diffusion systems","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","first_name":"Julian L"},{"full_name":"Hopf, Katharina","last_name":"Hopf","first_name":"Katharina"},{"first_name":"Michael","last_name":"Kniely","full_name":"Kniely, Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333"},{"last_name":"Mielke","full_name":"Mielke, Alexander","first_name":"Alexander"}],"keyword":["Energy-Reaction-Diffusion Systems","Cross Diffusion","Global-In-Time Existence of Weak/Renormalised Solutions","Entropy Method","Onsager System","Soret/Dufour Effect"],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"publication":"SIAM Journal on Mathematical Analysis","isi":1,"publication_identifier":{"issn":["0036-1410"]},"article_type":"original","year":"2022","acknowledgement":"M.K. gratefully acknowledges the hospitality of WIAS Berlin, where a major part of the project was carried out. The research stay of M.K. at WIAS Berlin was funded by the Austrian Federal Ministry of Education, Science and Research through a research fellowship for graduates of a promotio sub auspiciis. The research of A.M. has been partially supported by Deutsche Forschungsgemeinschaft (DFG) through the Collaborative Research Center SFB 1114 “Scaling Cascades in Complex Systems” (Project no. 235221301), Subproject C05 “Effective models for materials and interfaces with multiple scales”. J.F. and A.M. are grateful for the hospitality of the Erwin Schrödinger Institute in Vienna, where some ideas for this work have been developed. The authors are grateful to two anonymous referees for several helpful comments, in particular for the short proof of estimate (2.7).","intvolume":"        54","date_published":"2022-01-04T00:00:00Z","day":"04","doi":"10.1137/20M1387237","oa":1,"issue":"1","scopus_import":"1","month":"01","_id":"10547","external_id":{"isi":["000762768000006"],"arxiv":["2012.03792 "]},"date_created":"2021-12-16T12:08:56Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.03792"}],"publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"JuFi"}],"volume":54,"quality_controlled":"1","type":"journal_article","abstract":[{"text":"We establish global-in-time existence results for thermodynamically consistent reaction-(cross-)diffusion systems coupled to an equation describing heat transfer. Our main interest is to model species-dependent diffusivities,\r\nwhile at the same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal case lies in the intrinsic presence of cross-diffusion type phenomena like the Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic equilibria, a nonvanishing temperature gradient may drive a concentration flux even in a situation with constant concentrations; likewise, a nonvanishing concentration gradient may drive a heat flux even in a case of spatially constant temperature. We use time discretisation and regularisation techniques and derive a priori estimates based on a suitable entropy and the associated entropy production. Renormalised solutions are used in cases where non-integrable diffusion fluxes or reaction terms appear.","lang":"eng"}],"citation":{"ieee":"J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis of energy-reaction-diffusion systems,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022.","ama":"Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(1):220-267. doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>","apa":"Fischer, J. L., Hopf, K., Kniely, M., &#38; Mielke, A. (2022). Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>","ista":"Fischer JL, Hopf K, Kniely M, Mielke A. 2022. Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 54(1), 220–267.","chicago":"Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>.","mla":"Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>.","short":"J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical Analysis 54 (2022) 220–267."}},{"publication_identifier":{"issn":["1050-5164"]},"year":"2022","acknowledgement":"The authors thank Ivan Nourdin and Felix Otto for inspiring discussions. The work of MD is financially supported by the CNRS-Momentum program. Financial support of AG is acknowledged from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2014-2019 Grant Agreement QUANTHOM 335410).","article_type":"original","intvolume":"        32","date_published":"2022-04-28T00:00:00Z","doi":"10.1214/21-AAP1705","day":"28","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Annals of applied probability","arxiv":1,"isi":1,"oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-10-09T21:01:17Z","page":"1179-1209","title":"Scaling limit of the homogenization commutator for Gaussian coefficient  fields","author":[{"first_name":"Mitia","full_name":"Duerinckx, Mitia","last_name":"Duerinckx"},{"first_name":"Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antoine","full_name":"Gloria, Antoine","last_name":"Gloria"}],"quality_controlled":"1","type":"journal_article","abstract":[{"text":"Consider a linear elliptic partial differential equation in divergence form with a random coefficient field. The solution operator displays fluctuations around its expectation. The recently developed pathwise theory of fluctuations in stochastic homogenization reduces the characterization of these fluctuations to those of the so-called standard homogenization commutator. In this contribution, we investigate the scaling limit of this key quantity: starting\r\nfrom a Gaussian-like coefficient field with possibly strong correlations, we establish the convergence of the rescaled commutator to a fractional Gaussian field, depending on the decay of correlations of the coefficient field, and we\r\ninvestigate the (non)degeneracy of the limit. This extends to general dimension $d\\ge1$ previous results so far limited to dimension $d=1$, and to the continuum setting with strong correlations recent results in the discrete iid case.","lang":"eng"}],"citation":{"ieee":"M. Duerinckx, J. L. Fischer, and A. Gloria, “Scaling limit of the homogenization commutator for Gaussian coefficient  fields,” <i>Annals of applied probability</i>, vol. 32, no. 2. Institute of Mathematical Statistics, pp. 1179–1209, 2022.","ama":"Duerinckx M, Fischer JL, Gloria A. Scaling limit of the homogenization commutator for Gaussian coefficient  fields. <i>Annals of applied probability</i>. 2022;32(2):1179-1209. doi:<a href=\"https://doi.org/10.1214/21-AAP1705\">10.1214/21-AAP1705</a>","apa":"Duerinckx, M., Fischer, J. L., &#38; Gloria, A. (2022). Scaling limit of the homogenization commutator for Gaussian coefficient  fields. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AAP1705\">https://doi.org/10.1214/21-AAP1705</a>","ista":"Duerinckx M, Fischer JL, Gloria A. 2022. Scaling limit of the homogenization commutator for Gaussian coefficient  fields. Annals of applied probability. 32(2), 1179–1209.","chicago":"Duerinckx, Mitia, Julian L Fischer, and Antoine Gloria. “Scaling Limit of the Homogenization Commutator for Gaussian Coefficient  Fields.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AAP1705\">https://doi.org/10.1214/21-AAP1705</a>.","mla":"Duerinckx, Mitia, et al. “Scaling Limit of the Homogenization Commutator for Gaussian Coefficient  Fields.” <i>Annals of Applied Probability</i>, vol. 32, no. 2, Institute of Mathematical Statistics, 2022, pp. 1179–209, doi:<a href=\"https://doi.org/10.1214/21-AAP1705\">10.1214/21-AAP1705</a>.","short":"M. Duerinckx, J.L. Fischer, A. Gloria, Annals of Applied Probability 32 (2022) 1179–1209."},"main_file_link":[{"url":"https://arxiv.org/abs/1910.04088","open_access":"1"}],"corr_author":"1","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JuFi"}],"volume":32,"external_id":{"arxiv":["1910.04088"],"isi":["000791003700011"]},"date_created":"2021-12-16T12:10:16Z","publication_status":"published","scopus_import":"1","issue":"2","month":"04","_id":"10548"},{"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"year":"2022","article_number":"jcs259715","date_published":"2022-01-19T00:00:00Z","intvolume":"       135","oa":1,"doi":"10.1242/jcs.259715","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"Journal of Cell Science","oa_version":"Published Version","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-06-04T09:51:20Z","title":"Cell scientist to watch – Martin Loose","author":[{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"quality_controlled":"1","citation":{"short":"M. Loose, Cell Scientist to Watch – Martin Loose, The Company of Biologists, 2022.","chicago":"Loose, Martin. <i>Cell Scientist to Watch – Martin Loose</i>. <i>Journal of Cell Science</i>. Vol. 135. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.259715\">https://doi.org/10.1242/jcs.259715</a>.","ista":"Loose M. 2022. Cell scientist to watch – Martin Loose, The Company of Biologists,p.","mla":"Loose, Martin. “Cell Scientist to Watch – Martin Loose.” <i>Journal of Cell Science</i>, vol. 135, no. 2, jcs259715, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.259715\">10.1242/jcs.259715</a>.","apa":"Loose, M. (2022). <i>Cell scientist to watch – Martin Loose</i>. <i>Journal of Cell Science</i> (Vol. 135). The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.259715\">https://doi.org/10.1242/jcs.259715</a>","ieee":"M. Loose, <i>Cell scientist to watch – Martin Loose</i>, vol. 135, no. 2. The Company of Biologists, 2022.","ama":"Loose M. <i>Cell Scientist to Watch – Martin Loose</i>. Vol 135. The Company of Biologists; 2022. doi:<a href=\"https://doi.org/10.1242/jcs.259715\">10.1242/jcs.259715</a>"},"type":"other_academic_publication","abstract":[{"lang":"eng","text":"Martin Loose studied chemistry at the University of Heidelberg, Germany. He then joined Petra Schwille's group at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, where he obtained his PhD degree in 2010 for work on self-organization and pattern formation in the bacterial Min protein system. He then moved to Tim Mitchison's lab at Harvard Medical School, Boston, USA for his postdoc, funded by Human Frontier Science Program (HSFP) and European Molecular Biology Organization (EMBO) long-term fellowships; there, he discovered that the bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Martin established his independent research group at the Institute of Science and Technology (IST) Austria in 2015, supported by an European Research Council (ERC) starting grant and HFSP Young Investigator Grant. His lab studies the self-organization of bacterial cell division and small GTPase networks."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.259715"}],"publisher":"The Company of Biologists","department":[{"_id":"MaLo"}],"volume":135,"external_id":{"isi":["000762665200015"]},"date_created":"2024-05-28T13:28:30Z","publication_status":"published","issue":"2","month":"01","_id":"17057"},{"day":"22","doi":"10.4064/aa210430-1-7","oa":1,"intvolume":"       204","date_published":"2022-08-22T00:00:00Z","article_type":"original","publication_identifier":{"issn":["0065-1036"],"eissn":["1730-6264"]},"year":"2022","arxiv":1,"publication":"Acta Arithmetica","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","title":"On the leading constant in the Manin-type conjecture for Campana points","author":[{"full_name":"Shute, Alec L","last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1812-2810","first_name":"Alec L"}],"date_updated":"2025-09-10T09:57:03Z","related_material":{"record":[{"status":"public","id":"12077","relation":"earlier_version"}]},"page":"317-346","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","type":"journal_article","abstract":[{"lang":"eng","text":"We compare the Manin-type conjecture for Campana points recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado with an alternative prediction of Browning and Van Valckenborgh in the special case of the orbifold (P1,D), where D=1/2[0]+1/2[1]+1/2[∞]. We find that the two predicted leading constants do not agree, and we discuss whether thin sets could explain this discrepancy. Motivated by this, we provide a counterexample to the Manin-type conjecture for Campana points, by considering orbifolds corresponding to squareful values of binary quadratic forms."}],"citation":{"apa":"Shute, A. L. (2022). On the leading constant in the Manin-type conjecture for Campana points. <i>Acta Arithmetica</i>. Institute of Mathematics. <a href=\"https://doi.org/10.4064/aa210430-1-7\">https://doi.org/10.4064/aa210430-1-7</a>","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>Acta Arithmetica</i>, vol. 204, no. 4. Institute of Mathematics, pp. 317–346, 2022.","ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>Acta Arithmetica</i>. 2022;204(4):317-346. doi:<a href=\"https://doi.org/10.4064/aa210430-1-7\">10.4064/aa210430-1-7</a>","mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>Acta Arithmetica</i>, vol. 204, no. 4, Institute of Mathematics, 2022, pp. 317–46, doi:<a href=\"https://doi.org/10.4064/aa210430-1-7\">10.4064/aa210430-1-7</a>.","ista":"Shute AL. 2022. On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. 204(4), 317–346.","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>Acta Arithmetica</i>. Institute of Mathematics, 2022. <a href=\"https://doi.org/10.4064/aa210430-1-7\">https://doi.org/10.4064/aa210430-1-7</a>.","short":"A.L. Shute, Acta Arithmetica 204 (2022) 317–346."},"quality_controlled":"1","volume":204,"department":[{"_id":"TiBr"}],"publisher":"Institute of Mathematics","corr_author":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2104.14946","open_access":"1"}],"publication_status":"published","date_created":"2024-05-28T13:39:26Z","external_id":{"isi":["000844789100001"],"arxiv":["2104.14946"]},"_id":"17058","month":"08","scopus_import":"1","issue":"4"},{"publication":"39th International Conference on Machine Learning","isi":1,"ddc":["000"],"project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       162","date_published":"2022-07-20T00:00:00Z","day":"20","file":[{"content_type":"application/pdf","checksum":"5179a1e4dfc0fbfab6674907299e414a","relation":"main_file","date_updated":"2024-08-19T06:54:41Z","file_id":"17440","access_level":"open_access","date_created":"2024-08-19T06:54:41Z","success":1,"file_name":"2022_PMLR_Frantar.pdf","creator":"dernst","file_size":615916}],"oa":1,"ec_funded":1,"acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No 805223 ScaleML),\r\nas well as computational support from AWS EC2. We thank Eldar Kurtic for code and hyper-parameters for BERT pruning, and the Neural Magic Team, notably Michael Goin and\r\nMark Kurtz, for support with their software.","year":"2022","page":"6726-6743","date_updated":"2025-04-14T07:49:14Z","title":"SPDY: Accurate pruning with speedup guarantees","author":[{"first_name":"Elias","last_name":"Frantar","full_name":"Frantar, Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"file_date_updated":"2024-08-19T06:54:41Z","has_accepted_license":"1","article_processing_charge":"Yes","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","department":[{"_id":"DaAl"}],"volume":162,"corr_author":"1","publisher":"ML Research Press","quality_controlled":"1","type":"conference","abstract":[{"text":"The recent focus on the efficiency of deep neural networks (DNNs) has led to significant work on model compression approaches, of which weight pruning is one of the most popular. At the same time, there is rapidly-growing computational support for efficiently executing the unstructured-sparse models obtained via pruning. Yet, most existing pruning methods minimize just the number of remaining weights, i.e. the size of the model, rather than optimizing for inference time. We address this gap by introducing SPDY, a new compression method which automatically determines layer-wise sparsity targets achieving a desired inference speedup on a given system, while minimizing accuracy loss. SPDY is the composition of two new techniques. The first is an efficient and general dynamic programming algorithm for solving constrained layer-wise compression problems, given a set of layer-wise error scores. The second technique is a local search procedure for automatically determining such scores in an accurate and robust manner. Experiments across popular vision and language models show that SPDY guarantees speedups while recovering higher accuracy relative to existing strategies, both for one-shot and gradual pruning scenarios, and is compatible with most existing pruning approaches. We also extend our approach to the recently-proposed task of pruning with very little data, where we achieve the best known accuracy recovery when pruning to the GPU-supported 2:4 sparsity pattern.","lang":"eng"}],"citation":{"short":"E. Frantar, D.-A. Alistarh, in:, 39th International Conference on Machine Learning, ML Research Press, 2022, pp. 6726–6743.","chicago":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” In <i>39th International Conference on Machine Learning</i>, 162:6726–43. ML Research Press, 2022.","ista":"Frantar E, Alistarh D-A. 2022. SPDY: Accurate pruning with speedup guarantees. 39th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 162, 6726–6743.","mla":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” <i>39th International Conference on Machine Learning</i>, vol. 162, ML Research Press, 2022, pp. 6726–43.","ama":"Frantar E, Alistarh D-A. SPDY: Accurate pruning with speedup guarantees. In: <i>39th International Conference on Machine Learning</i>. Vol 162. ML Research Press; 2022:6726-6743.","ieee":"E. Frantar and D.-A. Alistarh, “SPDY: Accurate pruning with speedup guarantees,” in <i>39th International Conference on Machine Learning</i>, Baltimore, MD, United States, 2022, vol. 162, pp. 6726–6743.","apa":"Frantar, E., &#38; Alistarh, D.-A. (2022). SPDY: Accurate pruning with speedup guarantees. In <i>39th International Conference on Machine Learning</i> (Vol. 162, pp. 6726–6743). Baltimore, MD, United States: ML Research Press."},"_id":"17059","scopus_import":"1","month":"07","date_created":"2024-05-28T13:45:20Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000922378801029"]},"alternative_title":["PMLR"],"conference":{"location":"Baltimore, MD, United States","name":"ICML: International Conference on Machine Learning","start_date":"2022-07-17","end_date":"2022-07-23"}},{"file":[{"checksum":"54a7d405f8e57dba24728599ca63818c","content_type":"application/pdf","relation":"main_file","date_updated":"2024-08-19T06:45:21Z","file_id":"17439","access_level":"open_access","creator":"dernst","file_size":574728,"success":1,"file_name":"2022_AFT_Tiwari.pdf","date_created":"2024-08-19T06:45:21Z"}],"oa":1,"doi":"10.1145/3558535.3559775","day":"19","date_published":"2022-09-19T00:00:00Z","publication_identifier":{"isbn":["9781450398619"]},"acknowledgement":"This work was supported partially by ERC Starting Grant QIP–805241, by the Vienna business agency (Wirtschaftsagentur) through the Vienna Cybersecurity and Privacy Research Center\r\n(ViSP) and by the Austrian Science Fund (FWF) project I 4800-N (ADVISE).\r\nThe first author would like to thank Daniel Dadush for suggesting the use of discrepancy techniques to solve the transaction aggregation problem.","year":"2022","isi":1,"publication":"Proceedings of the 4th ACM Conference on Advances in Financial Technologies","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"oa_version":"Published Version","author":[{"last_name":"Tiwari","full_name":"Tiwari, Samarth","first_name":"Samarth"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo","full_name":"Yeo, Michelle X","orcid":"0009-0001-3676-4809","first_name":"Michelle X"},{"first_name":"Zeta","full_name":"Avarikioti, Zeta","last_name":"Avarikioti"},{"last_name":"Salem","full_name":"Salem, Iosif","first_name":"Iosif"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"title":"Wiser: Increasing throughput in payment channel networks with transaction aggregation","date_updated":"2025-09-10T09:57:48Z","page":"217-231","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2024-08-19T06:45:21Z","citation":{"short":"S. Tiwari, M.X. Yeo, Z. Avarikioti, I. Salem, K.Z. Pietrzak, S. Schmid, in:, Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Association for Computing Machinery, 2022, pp. 217–231.","apa":"Tiwari, S., Yeo, M. X., Avarikioti, Z., Salem, I., Pietrzak, K. Z., &#38; Schmid, S. (2022). Wiser: Increasing throughput in payment channel networks with transaction aggregation. In <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i> (pp. 217–231). Cambridge, MA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558535.3559775\">https://doi.org/10.1145/3558535.3559775</a>","ama":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. Wiser: Increasing throughput in payment channel networks with transaction aggregation. In: <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>. Association for Computing Machinery; 2022:217-231. doi:<a href=\"https://doi.org/10.1145/3558535.3559775\">10.1145/3558535.3559775</a>","ieee":"S. Tiwari, M. X. Yeo, Z. Avarikioti, I. Salem, K. Z. Pietrzak, and S. Schmid, “Wiser: Increasing throughput in payment channel networks with transaction aggregation,” in <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>, Cambridge, MA, United States, 2022, pp. 217–231.","chicago":"Tiwari, Samarth, Michelle X Yeo, Zeta Avarikioti, Iosif Salem, Krzysztof Z Pietrzak, and Stefan Schmid. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” In <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>, 217–31. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3558535.3559775\">https://doi.org/10.1145/3558535.3559775</a>.","ista":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. 2022. Wiser: Increasing throughput in payment channel networks with transaction aggregation. Proceedings of the 4th ACM Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, 217–231.","mla":"Tiwari, Samarth, et al. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>, Association for Computing Machinery, 2022, pp. 217–31, doi:<a href=\"https://doi.org/10.1145/3558535.3559775\">10.1145/3558535.3559775</a>."},"type":"conference","abstract":[{"lang":"eng","text":"Payment channel networks (PCNs) are one of the most prominent solutions to the limited transaction throughput of blockchains. Nevertheless, PCNs suffer themselves from a throughput limitation due to the capital constraints of their channels. A similar dependence on high capital is also found in inter-bank payment settlements, where the so-called netting technique is used to mitigate liquidity demands.\r\nIn this work, we alleviate this limitation by introducing the notion of transaction aggregation: instead of executing transactions sequentially through a PCN, we enable senders to aggregate multiple transactions and execute them simultaneously to benefit from several amounts that may \"cancel out\". Two direct advantages of our proposal is the decrease in intermediary fees paid by senders as well as the obfuscation of the transaction data from the intermediaries.\r\nWe formulate the transaction aggregation as a computational problem, a generalization of the Bank Clearing Problem. We present a generic framework for the transaction aggregation execution, and thereafter we propose Wiser as an implementation of this framework in a specific hub-based setting. To overcome the NP-hardness of the transaction aggregation problem, in Wiser we propose a fixed-parameter linear algorithm for a special case of transaction aggregation as well as the Bank Clearing Problem. Wiser can also be seen as a modern variant of the Hawala money transfer system, as well as a decentralized implementation of the overseas remittance service of Wise."}],"quality_controlled":"1","department":[{"_id":"KrPi"}],"publisher":"Association for Computing Machinery","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2024-05-28T13:58:35Z","conference":{"start_date":"2022-09-19","location":"Cambridge, MA, United States","name":"AFT: Conference on Advances in Financial Technologies","end_date":"2022-09-21"},"external_id":{"isi":["001041852800015"],"arxiv":["2205.11597"]},"_id":"17060","month":"09","scopus_import":"1"},{"oa":1,"file":[{"date_updated":"2024-08-06T07:33:30Z","file_id":"17400","checksum":"79a8e3e4be7e8a2b407b4efddd65f3f3","content_type":"application/pdf","relation":"main_file","file_name":"2022_PNASNexus_McAvoy.pdf","success":1,"date_created":"2024-08-06T07:33:30Z","creator":"dernst","file_size":2410962,"access_level":"open_access"}],"day":"01","doi":"10.1093/pnasnexus/pgac141","date_published":"2022-09-01T00:00:00Z","intvolume":"         1","article_number":"pgac141","publication_identifier":{"issn":["2752-6542"]},"acknowledgement":"The authors are grateful to Jörg Oechssler for many helpful comments. A.M. was supported by a Simons Postdoctoral Fellowship (Math+X) at the University of Pennsylvania; K.C. was supported by the European Research Council Consolidator Grant 863818 (ForM-SMArt); and C.H. was supported by the European Research Council Starting Grant 850529 (E-DIRECT).","article_type":"original","year":"2022","ec_funded":1,"publication":"PNAS Nexus","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"ddc":["000"],"oa_version":"Published Version","title":"Evolutionary instability of selfish learning in repeated games","author":[{"full_name":"McAvoy, Alex","last_name":"McAvoy","first_name":"Alex"},{"full_name":"Kates-Harbeck, Julian","last_name":"Kates-Harbeck","first_name":"Julian"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe"}],"date_updated":"2025-06-11T13:54:20Z","related_material":{"link":[{"relation":"software","url":"https://github.com/alexmcavoy/fmtl/"}]},"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-08-06T07:33:30Z","citation":{"short":"A. McAvoy, J. Kates-Harbeck, K. Chatterjee, C. Hilbe, PNAS Nexus 1 (2022).","mla":"McAvoy, Alex, et al. “Evolutionary Instability of Selfish Learning in Repeated Games.” <i>PNAS Nexus</i>, vol. 1, no. 4, pgac141, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">10.1093/pnasnexus/pgac141</a>.","chicago":"McAvoy, Alex, Julian Kates-Harbeck, Krishnendu Chatterjee, and Christian Hilbe. “Evolutionary Instability of Selfish Learning in Repeated Games.” <i>PNAS Nexus</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">https://doi.org/10.1093/pnasnexus/pgac141</a>.","ista":"McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. 2022. Evolutionary instability of selfish learning in repeated games. PNAS Nexus. 1(4), pgac141.","ieee":"A. McAvoy, J. Kates-Harbeck, K. Chatterjee, and C. Hilbe, “Evolutionary instability of selfish learning in repeated games,” <i>PNAS Nexus</i>, vol. 1, no. 4. Oxford University Press, 2022.","apa":"McAvoy, A., Kates-Harbeck, J., Chatterjee, K., &#38; Hilbe, C. (2022). Evolutionary instability of selfish learning in repeated games. <i>PNAS Nexus</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">https://doi.org/10.1093/pnasnexus/pgac141</a>","ama":"McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. Evolutionary instability of selfish learning in repeated games. <i>PNAS Nexus</i>. 2022;1(4). doi:<a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">10.1093/pnasnexus/pgac141</a>"},"abstract":[{"text":"Across many domains of interaction, both natural and artificial, individuals use past experience to shape future behaviors. The results of such learning processes depend on what individuals wish to maximize. A natural objective is one’s own success. However, when two such “selfish” learners interact with each other, the outcome can be detrimental to both, especially when there are conflicts of interest. Here, we explore how a learner can align incentives with a selfish opponent. Moreover, we consider the dynamics that arise when learning rules themselves are subject to evolutionary pressure. By combining extensive simulations and analytical techniques, we demonstrate that selfish learning is unstable in most classical two-player repeated games. If evolution operates on the level of long-run payoffs, selection instead favors learning rules that incorporate social (other-regarding) preferences. To further corroborate these results, we analyze data from a repeated prisoner’s dilemma experiment. We find that selfish learning is insufficient to explain human behavior when there is a trade-off between payoff maximization and fairness.","lang":"eng"}],"type":"journal_article","pmid":1,"quality_controlled":"1","volume":1,"department":[{"_id":"KrCh"}],"publisher":"Oxford University Press","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2024-05-28T14:23:12Z","external_id":{"pmid":["36714856"],"arxiv":["2105.06199"]},"_id":"17061","month":"09","scopus_import":"1","issue":"4"},{"conference":{"end_date":"2022-03-11","start_date":"2022-03-07","location":"Spain/Virtual","name":"SNI: Semiconductor Nanocrystals"},"publication_status":"published","oa_version":"Published Version","date_created":"2024-05-29T05:38:47Z","language":[{"iso":"eng"}],"status":"public","month":"02","article_processing_charge":"No","author":[{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","first_name":"Yu"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","full_name":"Calcabrini, Mariano","last_name":"Calcabrini","orcid":"0000-0003-4566-5877","first_name":"Mariano"}],"title":"The importance of surface adsorbates in solution-processed thermoelectric materials","related_material":{"record":[{"status":"public","id":"10123","relation":"earlier_version"}]},"_id":"17062","date_updated":"2025-04-15T06:54:34Z","article_number":"159","year":"2022","acknowledgement":"Werner Siemens Foundation\r\nEuropean Union's Horizon 2020\r\nFWF “Lise Meitner Fellowship”","oa":1,"citation":{"mla":"Ibáñez, Maria, et al. “The Importance of Surface Adsorbates in Solution-Processed Thermoelectric Materials.” <i>Proceedings of the NanoGe Spring Meeting 2022</i>, 159, Fundació Scito, 2022, doi:<a href=\"https://doi.org/10.29363/nanoge.nsm.2022.159\">10.29363/nanoge.nsm.2022.159</a>.","ista":"Ibáñez M, Liu Y, Calcabrini M. 2022. The importance of surface adsorbates in solution-processed thermoelectric materials. Proceedings of the nanoGe Spring Meeting 2022. SNI: Semiconductor Nanocrystals, 159.","chicago":"Ibáñez, Maria, Yu Liu, and Mariano Calcabrini. “The Importance of Surface Adsorbates in Solution-Processed Thermoelectric Materials.” In <i>Proceedings of the NanoGe Spring Meeting 2022</i>. Fundació Scito, 2022. <a href=\"https://doi.org/10.29363/nanoge.nsm.2022.159\">https://doi.org/10.29363/nanoge.nsm.2022.159</a>.","ieee":"M. Ibáñez, Y. Liu, and M. Calcabrini, “The importance of surface adsorbates in solution-processed thermoelectric materials,” in <i>Proceedings of the nanoGe Spring Meeting 2022</i>, Spain/Virtual, 2022.","ama":"Ibáñez M, Liu Y, Calcabrini M. The importance of surface adsorbates in solution-processed thermoelectric materials. In: <i>Proceedings of the NanoGe Spring Meeting 2022</i>. Fundació Scito; 2022. doi:<a href=\"https://doi.org/10.29363/nanoge.nsm.2022.159\">10.29363/nanoge.nsm.2022.159</a>","apa":"Ibáñez, M., Liu, Y., &#38; Calcabrini, M. (2022). The importance of surface adsorbates in solution-processed thermoelectric materials. In <i>Proceedings of the nanoGe Spring Meeting 2022</i>. Spain/Virtual: Fundació Scito. <a href=\"https://doi.org/10.29363/nanoge.nsm.2022.159\">https://doi.org/10.29363/nanoge.nsm.2022.159</a>","short":"M. Ibáñez, Y. Liu, M. Calcabrini, in:, Proceedings of the NanoGe Spring Meeting 2022, Fundació Scito, 2022."},"doi":"10.29363/nanoge.nsm.2022.159","day":"07","type":"conference_abstract","date_published":"2022-02-07T00:00:00Z","quality_controlled":"1","corr_author":"1","publisher":"Fundació Scito","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"main_file_link":[{"url":"https://doi.org/10.29363/nanoge.nsm.2022.159","open_access":"1"}],"department":[{"_id":"MaIb"}],"publication":"Proceedings of the nanoGe Spring Meeting 2022"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Oberwolfach Reports","publication_identifier":{"eissn":["1660-8941"],"issn":["1660-8933"]},"article_type":"original","year":"2022","doi":"10.4171/owr/2021/33","day":"26","oa":1,"intvolume":"        18","date_published":"2022-11-26T00:00:00Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Dynamische Systeme","author":[{"last_name":"Arnaud","full_name":"Arnaud, Marie-Claude","first_name":"Marie-Claude"},{"full_name":"Hofer, Helmut W.","last_name":"Hofer","first_name":"Helmut W."},{"first_name":"Michael","last_name":"Hutchings","full_name":"Hutchings, Michael"},{"first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"page":"1735-1803","date_updated":"2024-08-06T07:28:50Z","oa_version":"Published Version","publisher":"European Mathematical Society","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.4171/OWR/2021/33"}],"volume":18,"department":[{"_id":"VaKa"}],"abstract":[{"text":"This workshop continued a biannual series of workshops at Oberwolfach on dynamical systems that started with a meeting organized by Moser and Zehnder in 1981. Workshops in this series focus on new results and developments in dynamical systems and related areas of mathematics, with symplectic geometry playing an important role in recent years in connection with Hamiltonian dynamics. In this year special emphasis was placed on various kinds of spectra (in contact geometry, in Riemannian geometry, in dynamical systems and in symplectic topology) and their applications to dynamics.","lang":"eng"}],"type":"journal_article","citation":{"ieee":"M.-C. Arnaud, H. W. Hofer, M. Hutchings, and V. Kaloshin, “Dynamische Systeme,” <i>Oberwolfach Reports</i>, vol. 18, no. 3. European Mathematical Society, pp. 1735–1803, 2022.","apa":"Arnaud, M.-C., Hofer, H. W., Hutchings, M., &#38; Kaloshin, V. (2022). Dynamische Systeme. <i>Oberwolfach Reports</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/owr/2021/33\">https://doi.org/10.4171/owr/2021/33</a>","ama":"Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. Dynamische Systeme. <i>Oberwolfach Reports</i>. 2022;18(3):1735-1803. doi:<a href=\"https://doi.org/10.4171/owr/2021/33\">10.4171/owr/2021/33</a>","mla":"Arnaud, Marie-Claude, et al. “Dynamische Systeme.” <i>Oberwolfach Reports</i>, vol. 18, no. 3, European Mathematical Society, 2022, pp. 1735–803, doi:<a href=\"https://doi.org/10.4171/owr/2021/33\">10.4171/owr/2021/33</a>.","chicago":"Arnaud, Marie-Claude, Helmut W. Hofer, Michael Hutchings, and Vadim Kaloshin. “Dynamische Systeme.” <i>Oberwolfach Reports</i>. European Mathematical Society, 2022. <a href=\"https://doi.org/10.4171/owr/2021/33\">https://doi.org/10.4171/owr/2021/33</a>.","ista":"Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. 2022. Dynamische Systeme. Oberwolfach Reports. 18(3), 1735–1803.","short":"M.-C. Arnaud, H.W. Hofer, M. Hutchings, V. Kaloshin, Oberwolfach Reports 18 (2022) 1735–1803."},"quality_controlled":"1","month":"11","scopus_import":"1","issue":"3","_id":"17063","publication_status":"published","date_created":"2024-05-29T06:01:19Z"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12265","open_access":"1"}],"publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"volume":41,"quality_controlled":"1","citation":{"ieee":"H. Zhao <i>et al.</i>, “Co-optimization of design and fabrication plans for carpentry,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 3. Association for Computing Machinery, 2022.","ama":"Zhao H, Willsey M, Zhu A, et al. Co-optimization of design and fabrication plans for carpentry. <i>ACM Transactions on Graphics</i>. 2022;41(3). doi:<a href=\"https://doi.org/10.1145/3508499\">10.1145/3508499</a>","apa":"Zhao, H., Willsey, M., Zhu, A., Nandi, C., Tatlock, Z., Solomon, J., &#38; Schulz, A. (2022). Co-optimization of design and fabrication plans for carpentry. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3508499\">https://doi.org/10.1145/3508499</a>","mla":"Zhao, Haisen, et al. “Co-Optimization of Design and Fabrication Plans for Carpentry.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 3, 32, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3508499\">10.1145/3508499</a>.","ista":"Zhao H, Willsey M, Zhu A, Nandi C, Tatlock Z, Solomon J, Schulz A. 2022. Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. 41(3), 32.","chicago":"Zhao, Haisen, Max Willsey, Amy Zhu, Chandrakana Nandi, Zachary Tatlock, Justin Solomon, and Adriana Schulz. “Co-Optimization of Design and Fabrication Plans for Carpentry.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3508499\">https://doi.org/10.1145/3508499</a>.","short":"H. Zhao, M. Willsey, A. Zhu, C. Nandi, Z. Tatlock, J. Solomon, A. Schulz, ACM Transactions on Graphics 41 (2022)."},"type":"journal_article","abstract":[{"text":"Past work on optimizing fabrication plans given a carpentry design can provide Pareto-optimal plans trading off between material waste, fabrication time, precision, and other considerations. However, when developing fabrication plans, experts rarely restrict to a single design, instead considering families of design variations, sometimes adjusting designs to simplify fabrication. Jointly exploring the design and fabrication plan spaces for each design is intractable using current techniques. We present a new approach to jointly optimize design and fabrication plans for carpentered objects. To make this bi-level optimization tractable, we adapt recent work from program synthesis based on equality graphs (e-graphs), which encode sets of equivalent programs. Our insight is that subproblems within our bi-level problem share significant substructures. By representing both designs and fabrication plans in a new bag of parts (BOP) e-graph, we amortize the cost of optimizing design components shared among multiple candidates. Even using BOP e-graphs, the optimization space grows quickly in practice. Hence, we also show how a feedback-guided search strategy dubbed Iterative Contraction and Expansion on E-graphs (ICEE) can keep the size of the e-graph manageable and direct the search towards promising candidates. We illustrate the advantages of our pipeline through examples from the carpentry domain.","lang":"eng"}],"issue":"3","scopus_import":"1","month":"03","_id":"17065","external_id":{"arxiv":["2107.12265"]},"date_created":"2024-05-29T06:09:23Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication":"ACM Transactions on Graphics","year":"2022","article_type":"original","acknowledgement":"The authors would like to thank anonymous reviewers for their helpful feedback; Haomiao Wu for her contribution to the algorithm development in the early stage of the project; Elias Baldwin, David Tsay, Alexander Lefort, and Qiyang Tan for helping the experiments.","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"article_number":"32","date_published":"2022-03-09T00:00:00Z","intvolume":"        41","oa":1,"doi":"10.1145/3508499","day":"09","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2024-08-06T07:03:14Z","title":"Co-optimization of design and fabrication plans for carpentry","author":[{"first_name":"Haisen","orcid":"0000-0002-6389-1045","full_name":"Zhao, Haisen","last_name":"Zhao","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4"},{"first_name":"Max","last_name":"Willsey","full_name":"Willsey, Max"},{"full_name":"Zhu, Amy","last_name":"Zhu","first_name":"Amy"},{"last_name":"Nandi","full_name":"Nandi, Chandrakana","first_name":"Chandrakana"},{"full_name":"Tatlock, Zachary","last_name":"Tatlock","first_name":"Zachary"},{"first_name":"Justin","full_name":"Solomon, Justin","last_name":"Solomon"},{"first_name":"Adriana","last_name":"Schulz","full_name":"Schulz, Adriana"}],"oa_version":"Preprint"},{"article_type":"original","year":"2022","acknowledgement":"We thank members of the Conradt, Lambie, and Hajnal labs for discussions and comments on the manuscript. We thank M. Bauer, L. Jocham, N. Lebedeva, and L. McGuinness for excellent technical support; A. Hajnal and T. Kohlbrenner (University of Zurich, Switzerland) for allele zh135; and H.R. Horvitz (Massachusetts of Technology, USA) for plasmid pET-CED-3.\r\nSome strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (https://orip.nih.gov/) (P40 OD010440). This work was supported by UCL (Capital Equipment Fund, CEF2), a predoctoral fellowship from the China Scholarship Council (https://www.csc.edu.cn/) to HW, a predoctoral fellowship from the Studienstiftung des Deutschen Volkes (https://www.studienstiftung.de/) to NM, a Wolfson Fellowship from the Royal Society (https://royalsociety.org/) to BC (RSWF\\R1\\180008), the Deutsche Forschungsgemeinschaft (https://www.dfg.de/en/index.jsp) (ZA619/3-1 and ZA619/3-2 to EZ; C0204/10-1 and EXC114 to BC), and the Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1 to BC). ","publication_identifier":{"issn":["1545-7885"]},"article_number":"e3001786","date_published":"2022-10-06T00:00:00Z","intvolume":"        20","oa":1,"file":[{"checksum":"a7b46460b7819c196028481cc18a7c85","content_type":"application/pdf","relation":"main_file","date_updated":"2024-08-06T07:07:52Z","file_id":"17399","access_level":"open_access","file_name":"2022_PlosBio_Sethi.pdf","date_created":"2024-08-06T07:07:52Z","success":1,"creator":"dernst","file_size":2515388}],"day":"06","doi":"10.1371/journal.pbio.3001786","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"PLOS Biology","oa_version":"Published Version","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-08-06T07:07:52Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-08-06T07:08:54Z","title":"A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans","author":[{"first_name":"Aditya","full_name":"Sethi, Aditya","last_name":"Sethi"},{"last_name":"Wei","full_name":"Wei, Hai","first_name":"Hai"},{"orcid":"0000-0002-6425-5788","last_name":"Mishra","full_name":"Mishra, Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","first_name":"Nikhil"},{"last_name":"Segos","full_name":"Segos, Ioannis","first_name":"Ioannis"},{"full_name":"Lambie, Eric J.","last_name":"Lambie","first_name":"Eric J."},{"first_name":"Esther","full_name":"Zanin, Esther","last_name":"Zanin"},{"first_name":"Barbara","full_name":"Conradt, Barbara","last_name":"Conradt"}],"quality_controlled":"1","citation":{"chicago":"Sethi, Aditya, Hai Wei, Nikhil Mishra, Ioannis Segos, Eric J. Lambie, Esther Zanin, and Barbara Conradt. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” <i>PLOS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001786\">https://doi.org/10.1371/journal.pbio.3001786</a>.","ista":"Sethi A, Wei H, Mishra N, Segos I, Lambie EJ, Zanin E, Conradt B. 2022. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. 20(10), e3001786.","mla":"Sethi, Aditya, et al. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” <i>PLOS Biology</i>, vol. 20, no. 10, e3001786, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001786\">10.1371/journal.pbio.3001786</a>.","apa":"Sethi, A., Wei, H., Mishra, N., Segos, I., Lambie, E. J., Zanin, E., &#38; Conradt, B. (2022). A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. <i>PLOS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001786\">https://doi.org/10.1371/journal.pbio.3001786</a>","ama":"Sethi A, Wei H, Mishra N, et al. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. <i>PLOS Biology</i>. 2022;20(10). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001786\">10.1371/journal.pbio.3001786</a>","ieee":"A. Sethi <i>et al.</i>, “A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans,” <i>PLOS Biology</i>, vol. 20, no. 10. Public Library of Science, 2022.","short":"A. Sethi, H. Wei, N. Mishra, I. Segos, E.J. Lambie, E. Zanin, B. Conradt, PLOS Biology 20 (2022)."},"abstract":[{"text":"A cell’s size affects the likelihood that it will die. But how is cell size controlled in this context and how does cell size impact commitment to the cell death fate? We present evidence that the caspase CED-3 interacts with the RhoGEF ECT-2 in Caenorhabditis elegans neuroblasts that generate “unwanted” cells. We propose that this interaction promotes polar actomyosin contractility, which leads to unequal neuroblast division and the generation of a daughter cell that is below the critical “lethal” size threshold. Furthermore, we find that hyperactivation of ECT-2 RhoGEF reduces the sizes of unwanted cells. Importantly, this suppresses the “cell death abnormal” phenotype caused by the partial loss of ced-3 caspase and therefore increases the likelihood that unwanted cells die. A putative null mutation of ced-3 caspase, however, is not suppressed, which indicates that cell size affects CED-3 caspase activation and/or activity. Therefore, we have uncovered novel sequential and reciprocal interactions between the apoptosis pathway and cell size that impact a cell’s commitment to the cell death fate.","lang":"eng"}],"type":"journal_article","pmid":1,"publisher":"Public Library of Science","department":[{"_id":"CaHe"}],"volume":20,"external_id":{"pmid":["36201522"]},"date_created":"2024-05-29T06:09:34Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","issue":"10","scopus_import":"1","month":"10","_id":"17066"}]