[{"file_date_updated":"2022-05-23T06:47:57Z","article_number":"42","license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"This work was supported by the National Research Foundation of Korea [NRF-2019R1F1A1058473, NRF-2019R1A6A1A11053838, and NRF-2020K1A4A7A02095438].","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41427-022-00393-5","citation":{"ieee":"V. Q. Nguyen <i>et al.</i>, “Unidentified major p-type source in SnSe: Multivacancies,” <i>NPG Asia Materials</i>, vol. 14. Springer Nature, 2022.","short":"V.Q. Nguyen, T.L. Trinh, C. Chang, L.D. Zhao, T.H. Nguyen, V.T. Duong, A.T. Duong, J.H. Park, S. Park, J. Kim, S. Cho, NPG Asia Materials 14 (2022).","ama":"Nguyen VQ, Trinh TL, Chang C, et al. Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. 2022;14. doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>","apa":"Nguyen, V. Q., Trinh, T. L., Chang, C., Zhao, L. D., Nguyen, T. H., Duong, V. T., … Cho, S. (2022). Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>","ista":"Nguyen VQ, Trinh TL, Chang C, Zhao LD, Nguyen TH, Duong VT, Duong AT, Park JH, Park S, Kim J, Cho S. 2022. Unidentified major p-type source in SnSe: Multivacancies. NPG Asia Materials. 14, 42.","chicago":"Nguyen, Van Quang, Thi Ly Trinh, Cheng Chang, Li Dong Zhao, Thi Huong Nguyen, Van Thiet Duong, Anh Tuan Duong, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>.","mla":"Nguyen, Van Quang, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>, vol. 14, 42, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>."},"day":"13","isi":1,"department":[{"_id":"MaIb"}],"file":[{"success":1,"file_id":"11404","file_size":6202545,"content_type":"application/pdf","date_created":"2022-05-23T06:47:57Z","relation":"main_file","checksum":"0579997cc1d28bf66e29357e08e3e39d","access_level":"open_access","creator":"dernst","date_updated":"2022-05-23T06:47:57Z","file_name":"2022_NPGAsiaMaterials_Nguyen.pdf"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"NPG Asia Materials","ddc":["540"],"publisher":"Springer Nature","has_accepted_license":"1","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","status":"public","date_published":"2022-05-13T00:00:00Z","title":"Unidentified major p-type source in SnSe: Multivacancies","scopus_import":"1","month":"05","intvolume":"        14","_id":"11401","year":"2022","publication_identifier":{"eissn":["1884-4057"],"issn":["1884-4049"]},"date_updated":"2023-08-03T07:13:58Z","author":[{"full_name":"Nguyen, Van Quang","last_name":"Nguyen","first_name":"Van Quang"},{"full_name":"Trinh, Thi Ly","first_name":"Thi Ly","last_name":"Trinh"},{"orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","last_name":"Chang"},{"full_name":"Zhao, Li Dong","first_name":"Li Dong","last_name":"Zhao"},{"full_name":"Nguyen, Thi Huong","first_name":"Thi Huong","last_name":"Nguyen"},{"full_name":"Duong, Van Thiet","last_name":"Duong","first_name":"Van Thiet"},{"full_name":"Duong, Anh Tuan","first_name":"Anh Tuan","last_name":"Duong"},{"first_name":"Jong Ho","last_name":"Park","full_name":"Park, Jong Ho"},{"first_name":"Sudong","last_name":"Park","full_name":"Park, Sudong"},{"full_name":"Kim, Jungdae","last_name":"Kim","first_name":"Jungdae"},{"full_name":"Cho, Sunglae","first_name":"Sunglae","last_name":"Cho"}],"date_created":"2022-05-22T22:01:40Z","abstract":[{"lang":"eng","text":"Tin selenide (SnSe) is considered a robust candidate for thermoelectric applications due to its very high thermoelectric figure of merit, ZT, with values of 2.6 in p-type and 2.8 in n-type single crystals. Sn has been replaced with various lower group dopants to achieve successful p-type doping in SnSe with high ZT values. A known, facile, and powerful alternative way to introduce a hole carrier is to use a natural single Sn vacancy, VSn. Through transport and scanning tunneling microscopy studies, we discovered that VSn are dominant in high-quality (slow cooling rate) SnSe single crystals, while multiple vacancies, Vmulti, are dominant in low-quality (high cooling rate) single crystals. Surprisingly, both VSn and Vmulti help to increase the power factors of SnSe, whereas samples with dominant VSn have superior thermoelectric properties in SnSe single crystals. Additionally, the observation that Vmulti are good p-type sources observed in relatively low-quality single crystals is useful in thermoelectric applications because polycrystalline SnSe can be used due to its mechanical strength; this substance is usually fabricated at very high cooling speeds."}],"oa_version":"Published Version","external_id":{"isi":["000794880200001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":14,"oa":1},{"_id":"11402","year":"2022","intvolume":"       129","title":"Graph planning with expected finite horizon","month":"11","scopus_import":"1","date_published":"2022-11-01T00:00:00Z","ec_funded":1,"status":"public","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":129,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"oa_version":"Preprint","arxiv":1,"abstract":[{"text":"Fixed-horizon planning considers a weighted graph and asks to construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping-time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary as the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping-time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time.","lang":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"}],"date_created":"2022-05-22T22:01:40Z","project":[{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"date_updated":"2025-07-10T11:54:34Z","publication_identifier":{"eissn":["1090-2724"],"issn":["0022-0000"]},"citation":{"short":"K. Chatterjee, L. Doyen, Journal of Computer and System Sciences 129 (2022) 1–21.","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” <i>Journal of Computer and System Sciences</i>, vol. 129. Elsevier, pp. 1–21, 2022.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>, vol. 129, Elsevier, 2022, pp. 1–21, doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>.","ista":"Chatterjee K, Doyen L. 2022. Graph planning with expected finite horizon. Journal of Computer and System Sciences. 129, 1–21.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2022). Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. 2022;129:1-21. doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>"},"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1802.03642","open_access":"1"}],"isi":1,"day":"01","acknowledgement":"This work was partially supported by Austrian Science Fund (FWF) NFN Grant No RiSE/SHiNE S11407 and by the grant ERC CoG 863818 (ForM-SMArt).","doi":"10.1016/j.jcss.2022.04.003","page":"1-21","related_material":{"record":[{"id":"7402","status":"public","relation":"earlier_version"}]},"publisher":"Elsevier","publication":"Journal of Computer and System Sciences","quality_controlled":"1","type":"journal_article","publication_status":"published","department":[{"_id":"KrCh"}]},{"intvolume":"       120","_id":"11417","year":"2022","date_published":"2022-05-12T00:00:00Z","title":"Emerging qubit systems: Guest editorial","scopus_import":"1","month":"05","status":"public","language":[{"iso":"eng"}],"article_type":"letter_note","article_processing_charge":"No","external_id":{"isi":["000796002100002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":120,"abstract":[{"text":"Over the past few years, the field of quantum information science has seen tremendous progress toward realizing large-scale quantum computers. With demonstrations of quantum computers outperforming classical computers for a select range of problems,1–3 we have finally entered the noisy, intermediate-scale quantum (NISQ) computing era. While the quantum computers of today are technological marvels, they are not yet error corrected, and it is unclear whether any system will scale beyond a few hundred logical qubits without significant changes to architecture and control schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer) systems of the 1940s, which ran on vacuum tubes. These machines were built on a solid, nominally scalable architecture and when they were developed, nobody could have predicted the development of the transistor and the impact of the resulting semiconductor industry. Simply put, the computers of today are nothing like the early computers of the 1940s. We believe that the qubits of future fault-tolerant quantum systems will look quite different from the qubits of the NISQ machines in operation today. This Special Topic issue is devoted to new and emerging quantum systems with a focus on enabling technologies that can eventually lead to the quantum analog to the transistor. We have solicited both research4–18 and perspective articles19–21 to discuss new and emerging qubit systems with a focus on novel materials, encodings, and architectures. We are proud to present a collection that touches on a wide range of technologies including superconductors,7–13,21 semiconductors,15–17,19 and individual atomic qubits.18\r\n","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Sigillito, Anthony J.","last_name":"Sigillito","first_name":"Anthony J."},{"full_name":"Covey, Jacob P.","last_name":"Covey","first_name":"Jacob P."},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Petersson","first_name":"Karl","full_name":"Petersson, Karl"},{"first_name":"Stefan","last_name":"Preble","full_name":"Preble, Stefan"}],"date_created":"2022-05-29T22:01:53Z","publication_identifier":{"issn":["0003-6951"]},"date_updated":"2023-08-03T07:16:20Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0097339"}],"citation":{"mla":"Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>, vol. 120, no. 19, 190401, American Institute of Physics, 2022, doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>.","chicago":"Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson, and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>. American Institute of Physics, 2022. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>.","ista":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit systems: Guest editorial. Applied Physics Letters. 120(19), 190401.","ama":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. 2022;120(19). doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>","apa":"Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., &#38; Preble, S. (2022). Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>","short":"A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics Letters 120 (2022).","ieee":"A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging qubit systems: Guest editorial,” <i>Applied Physics Letters</i>, vol. 120, no. 19. American Institute of Physics, 2022."},"isi":1,"day":"12","article_number":"190401","acknowledgement":"We would like to thank all of the authors who contributed to\r\nthis Special Topic. We would also like to thank the editorial team at\r\nAPL including Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen.","issue":"19","doi":"10.1063/5.0097339","publisher":"American Institute of Physics","publication":"Applied Physics Letters","type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"JoFi"}]},{"article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Normal fluctuation in quantum ergodicity for Wigner matrices","scopus_import":"1","month":"05","date_published":"2022-05-01T00:00:00Z","_id":"11418","year":"2022","intvolume":"        50","date_updated":"2023-08-03T07:16:53Z","publication_identifier":{"eissn":["2168-894X"],"issn":["0091-1798"]},"author":[{"first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-05-29T22:01:53Z","arxiv":1,"oa_version":"Preprint","abstract":[{"text":"We consider the quadratic form of a general high-rank deterministic matrix on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian fluctuation for each bulk eigenvector in the large N limit. The proof is a combination of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau (2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"oa":1,"volume":50,"external_id":{"isi":["000793963400005"],"arxiv":["2103.06730"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"984-1012","acknowledgement":"L.E. would like to thank Zhigang Bao for many illuminating discussions in an early stage of this research. The authors are also grateful to Paul Bourgade for his comments on the manuscript and the anonymous referee for several useful suggestions.","issue":"3","doi":"10.1214/21-AOP1552","main_file_link":[{"url":"https://arxiv.org/abs/2103.06730","open_access":"1"}],"citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum ergodicity for Wigner matrices,” <i>Annals of Probability</i>, vol. 50, no. 3. Institute of Mathematical Statistics, pp. 984–1012, 2022.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.","mla":"Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>, vol. 50, no. 3, Institute of Mathematical Statistics, 2022, pp. 984–1012, doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>","ama":"Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. 2022;50(3):984-1012. doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 984–1012.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>."},"day":"01","isi":1,"department":[{"_id":"LaEr"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"Annals of Probability","publisher":"Institute of Mathematical Statistics"},{"intvolume":"        11","year":"2022","_id":"11419","date_published":"2022-05-05T00:00:00Z","month":"05","scopus_import":"1","title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["35471147 "],"isi":["000876231600001"]},"volume":11,"oa":1,"abstract":[{"text":"Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission.","lang":"eng"}],"oa_version":"Published Version","date_created":"2022-05-29T22:01:54Z","author":[{"first_name":"Tetsuya","last_name":"Hori","full_name":"Hori, Tetsuya"},{"id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","last_name":"Eguchi","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku"},{"last_name":"Wang","first_name":"Han Ying","full_name":"Wang, Han Ying"},{"full_name":"Miyasaka, Tomohiro","last_name":"Miyasaka","first_name":"Tomohiro"},{"full_name":"Guillaud, Laurent","first_name":"Laurent","last_name":"Guillaud"},{"last_name":"Taoufiq","first_name":"Zacharie","full_name":"Taoufiq, Zacharie"},{"last_name":"Mahapatra","first_name":"Satyajit","full_name":"Mahapatra, Satyajit"},{"last_name":"Yamada","first_name":"Hiroshi","full_name":"Yamada, Hiroshi"},{"first_name":"Kohji","last_name":"Takei","full_name":"Takei, Kohji"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"publication_identifier":{"eissn":["2050-084X"]},"date_updated":"2023-08-03T07:15:49Z","isi":1,"day":"05","citation":{"short":"T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra, H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).","ieee":"T. Hori <i>et al.</i>, “Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ista":"Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. eLife. 11, e73542.","chicago":"Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>.","ama":"Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>","apa":"Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z., … Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>","mla":"Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>, vol. 11, e73542, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>."},"article_number":"e73542","doi":"10.7554/eLife.73542","acknowledgement":"We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda for technical assistant with in vitro analysis of tau. This research was supported by funding from Okinawa Institute of Science and Technology and from Technology (OIST) and Core Research for the Evolutional Science and Technology of Japan Science and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas to TM (Brain Protein Aging and Dementia Control 26117004).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-05-30T08:09:16Z","publisher":"eLife Sciences Publications","has_accepted_license":"1","publication":"eLife","ddc":["616"],"publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"RySh"}],"file":[{"file_id":"11421","success":1,"content_type":"application/pdf","file_size":2466296,"relation":"main_file","date_created":"2022-05-30T08:09:16Z","date_updated":"2022-05-30T08:09:16Z","file_name":"elife-73542-v2.pdf","access_level":"open_access","checksum":"ccddbd167e00ff8375f12998af497152","creator":"cchlebak"}]},{"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"scopus_import":"1","month":"06","title":"A cautionary tale: Burning the medial axis is unstable","date_published":"2022-06-01T00:00:00Z","year":"2022","_id":"11428","intvolume":"       224","date_updated":"2025-04-14T07:43:57Z","publication_identifier":{"isbn":["978-3-95977-227-3"],"issn":["1868-8969"]},"date_created":"2022-06-01T14:18:04Z","author":[{"full_name":"Chambers, Erin","last_name":"Chambers","first_name":"Erin"},{"full_name":"Fillmore, Christopher D","first_name":"Christopher D","last_name":"Fillmore","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425"},{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"},{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"editor":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"}],"oa_version":"Published Version","abstract":[{"text":"The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible.","lang":"eng"}],"oa":1,"volume":224,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-06-07T07:58:30Z","page":"66:1-66:9","conference":{"start_date":"2022-06-07","location":"Berlin, Germany","name":"SoCG: Symposium on Computational Geometry","end_date":"2022-06-10"},"doi":"10.4230/LIPIcs.SoCG.2022.66","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"Partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics” and the European Research Council (ERC), grant no. 788183, “Alpha Shape Theory Extended”. Erin Chambers: Supported in part by the National Science Foundation through grants DBI-1759807, CCF-1907612, and CCF-2106672. Mathijs Wintraecken: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073 Acknowledgements We thank André Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early discussions on this work. We also thank Lu Liu, Yajie Yan and Tao Ju for sharing code to generate the examples.","day":"01","citation":{"ieee":"E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “A cautionary tale: Burning the medial axis is unstable,” in <i>38th International Symposium on Computational Geometry</i>, Berlin, Germany, 2022, vol. 224, p. 66:1-66:9.","short":"E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, X. Goaoc, M. Kerber (Eds.), 38th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9.","ama":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. A cautionary tale: Burning the medial axis is unstable. In: Goaoc X, Kerber M, eds. <i>38th International Symposium on Computational Geometry</i>. Vol 224. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022:66:1-66:9. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>","apa":"Chambers, E., Fillmore, C. D., Stephenson, E. R., &#38; Wintraecken, M. (2022). A cautionary tale: Burning the medial axis is unstable. In X. Goaoc &#38; M. Kerber (Eds.), <i>38th International Symposium on Computational Geometry</i> (Vol. 224, p. 66:1-66:9). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>","chicago":"Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” In <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, 224:66:1-66:9. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>.","ista":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. 2022. A cautionary tale: Burning the medial axis is unstable. 38th International Symposium on Computational Geometry. SoCG: Symposium on Computational GeometryLIPIcs vol. 224, 66:1-66:9.","mla":"Chambers, Erin, et al. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, vol. 224, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>."},"file":[{"date_created":"2022-06-07T07:58:30Z","relation":"main_file","access_level":"open_access","checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","creator":"dernst","file_name":"2022_LIPICs_Chambers.pdf","date_updated":"2022-06-07T07:58:30Z","file_id":"11437","success":1,"file_size":17580705,"content_type":"application/pdf"}],"corr_author":"1","department":[{"_id":"HeEd"}],"series_title":"LIPIcs","quality_controlled":"1","publication_status":"published","type":"conference","ddc":["510"],"publication":"38th International Symposium on Computational Geometry","has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"date_published":"2022-05-01T00:00:00Z","doi":"10.1007/978-3-031-06245-2","month":"05","title":"Web and Wireless Geographical Information Systems","intvolume":"     13238","day":"01","_id":"11429","place":"Cham","year":"2022","citation":{"ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","short":"F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information Systems, 1st ed., Springer Nature, Cham, 2022.","mla":"Karimipour, Farid, and Sabine Storandt, editors. <i>Web and Wireless Geographical Information Systems</i>. 1st ed., vol. 13238, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>.","ama":"Karimipour F, Storandt S, eds. <i>Web and Wireless Geographical Information Systems</i>. Vol 13238. 1st ed. Cham: Springer Nature; 2022. doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>","apa":"Karimipour, F., &#38; Storandt, S. (Eds.). (2022). <i>Web and Wireless Geographical Information Systems</i> (1st ed., Vol. 13238). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>","chicago":"Karimipour, Farid, and Sabine Storandt, eds. <i>Web and Wireless Geographical Information Systems</i>. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>.","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p."},"language":[{"iso":"eng"}],"edition":"1","article_processing_charge":"No","page":"153","status":"public","abstract":[{"lang":"eng","text":"This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022.\r\nThe 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions.  The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks."}],"oa_version":"None","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":13238,"publication_identifier":{"isbn":["9783031062445"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783031062452"]},"department":[{"_id":"HeEd"}],"alternative_title":["LNCS"],"corr_author":"1","date_updated":"2024-10-09T21:02:30Z","editor":[{"orcid":"0000-0001-6746-4174","full_name":"Karimipour, Farid","first_name":"Farid","last_name":"Karimipour","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425"},{"last_name":"Storandt","first_name":"Sabine","full_name":"Storandt, Sabine"}],"publication_status":"published","type":"book_editor","date_created":"2022-06-02T05:40:53Z","quality_controlled":"1"},{"doi":"10.1111/cgf.14478","issue":"2","acknowledged_ssus":[{"_id":"ScienComp"}],"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria and MFX Team at INRIA for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","day":"01","isi":1,"citation":{"mla":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 343–53, doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>.","apa":"Schreck, C., &#38; Wojtan, C. (2022). Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>","ama":"Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. 2022;41(2):343-353. doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>","chicago":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>.","ista":"Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. Computer Graphics Forum. 41(2), 343–353.","ieee":"C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 343–353, 2022.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353."},"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03641349/","open_access":"1"}],"page":"343-353","publication":"Computer Graphics Forum","publisher":"Wiley","corr_author":"1","department":[{"_id":"ChWo"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","scopus_import":"1","month":"05","title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","date_published":"2022-05-01T00:00:00Z","year":"2022","_id":"11432","intvolume":"        41","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics."}],"volume":41,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000802723900027"]},"date_updated":"2024-10-22T09:58:19Z","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"date_created":"2022-06-05T22:01:49Z","author":[{"first_name":"Camille","last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille"},{"last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}]},{"date_published":"2022-04-11T00:00:00Z","scopus_import":"1","month":"04","title":"A quantitative Helly-type theorem: Containment in a homothet","intvolume":"        36","year":"2022","_id":"11435","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","status":"public","abstract":[{"text":"We introduce a new variant of quantitative Helly-type theorems: the minimal homothetic distance of the intersection of a family of convex sets to the intersection of a subfamily of a fixed size. As an application, we establish the following quantitative Helly-type result for the diameter. If $K$ is the intersection of finitely many convex bodies in $\\mathbb{R}^d$, then one can select $2d$ of these bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25], is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$ conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982), pp. 109--114] cannot be improved. The bounds above follow from our key result that concerns sparse approximation of a convex polytope by the convex hull of a well-chosen subset of its vertices: Assume that $Q \\subset {\\mathbb R}^d$ is a polytope whose centroid is the origin. Then there exist at most 2d vertices of $Q$ whose convex hull $Q^{\\prime \\prime}$ satisfies $Q \\subset - 8d^3 Q^{\\prime \\prime}.$","lang":"eng"}],"arxiv":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000793158200002"],"arxiv":["2103.04122"]},"oa":1,"volume":36,"publication_identifier":{"issn":["0895-4801"]},"date_updated":"2023-10-18T06:58:03Z","date_created":"2022-06-05T22:01:50Z","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","last_name":"Ivanov","full_name":"Ivanov, Grigory"},{"full_name":"Naszodi, Marton","first_name":"Marton","last_name":"Naszodi"}],"issue":"2","doi":"10.1137/21M1403308","acknowledgement":"G.I. acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and\r\nKKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI.","day":"11","isi":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2103.04122"}],"citation":{"mla":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2, Society for Industrial and Applied Mathematics, 2022, pp. 951–57, doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>.","ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","chicago":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>.","apa":"Ivanov, G., &#38; Naszodi, M. (2022). A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>","ama":"Ivanov G, Naszodi M. A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. 2022;36(2):951-957. doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957.","ieee":"G. Ivanov and M. Naszodi, “A quantitative Helly-type theorem: Containment in a homothet,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2. Society for Industrial and Applied Mathematics, pp. 951–957, 2022."},"page":"951-957","publication":"SIAM Journal on Discrete Mathematics","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"UlWa"}],"publication_status":"published","type":"journal_article","quality_controlled":"1"},{"acknowledgement":"The author thanks the whole community of researchers consciously or unconsciously working on questions related to auxin, whose hard work and enthusiasm contributed to development of this exciting story. Particular thanks go to many\r\nbrilliant present and past members of the Friml group and our numerous excellent collaborators, without whom my own personal journey would not be possible. The way of the cross with its 14 stations is a popular devotion among Roman Catholics and inspires them to make a spiritual pilgrimage through contemplation of Christ on his last day. Its aspects of gradual progress, struggle, passion, and revelation served as an inspiration for the formal depiction of our journey to understanding auxin as described in this review. It is in no way intended to reflect the personal beliefs of the author and readers. I am grateful to Nick Barton, Eva Benková, Lenka Caisová, Matyáš Fendrych, Lukáš Fiedler, Monika Frátriková, Jarmila Frimlová, Michelle Gallei, Jakub Hajný, Lukas Hoermayer, Alexandra Mally, Ondrˇej Novák, Jan Petrášek, Aleš Pěnčík, Steffen Vanneste, Tongda Xu, and Zhenbiao Yang for their valuable comments. Special thanks go to Michelle Gallei for her invaluable assistance with the figures.","doi":"10.1101/cshperspect.a039859","issue":"5","article_number":"a039859","citation":{"ieee":"J. Friml, “Fourteen stations of auxin,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, 2022.","short":"J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).","mla":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5, a039859, Cold Spring Harbor Laboratory Press, 2022, doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859\">10.1101/cshperspect.a039859</a>.","apa":"Friml, J. (2022). Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a039859\">https://doi.org/10.1101/cshperspect.a039859</a>","ama":"Friml J. Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. 2022;14(5). doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859\">10.1101/cshperspect.a039859</a>","chicago":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2022. <a href=\"https://doi.org/10.1101/cshperspect.a039859\">https://doi.org/10.1101/cshperspect.a039859</a>.","ista":"Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), a039859."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039859 "}],"isi":1,"day":"27","corr_author":"1","department":[{"_id":"JiFr"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"Cold Spring Harbor Perspectives in Biology","publisher":"Cold Spring Harbor Laboratory Press","article_type":"review","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Fourteen stations of auxin","month":"05","scopus_import":"1","date_published":"2022-05-27T00:00:00Z","year":"2022","_id":"10016","intvolume":"        14","date_updated":"2025-05-14T11:22:36Z","publication_identifier":{"issn":["1943-0264"]},"author":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"date_created":"2021-09-14T11:36:53Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research. "}],"volume":14,"oa":1,"external_id":{"isi":["000806563000003"],"pmid":["34400554"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1},{"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","intvolume":"        30","_id":"10181","year":"2022","date_published":"2022-06-01T00:00:00Z","month":"06","scopus_import":"1","title":"Rectifiable curves in proximally smooth sets","date_created":"2021-10-24T22:01:35Z","author":[{"full_name":"Ivanov, Grigory","first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"first_name":"Mariana S.","last_name":"Lopushanski","full_name":"Lopushanski, Mariana S."}],"publication_identifier":{"eissn":["1877-0541"],"issn":["0927-6947"]},"date_updated":"2024-05-22T09:23:37Z","external_id":{"isi":["000705774800001"],"arxiv":["2012.10691"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":30,"abstract":[{"lang":"eng","text":"In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space."}],"arxiv":1,"oa_version":"Published Version","page":"657-675","day":"01","isi":1,"citation":{"mla":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>, vol. 30, no. 2, Springer Nature, 2022, pp. 657–75, doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>.","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. 2022;30(2):657-675. doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>","apa":"Ivanov, G., &#38; Lopushanski, M. S. (2022). Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>","chicago":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>.","ista":"Ivanov G, Lopushanski MS. 2022. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 30(2), 657–675.","ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” <i>Set-Valued and Variational Analysis</i>, vol. 30, no. 2. Springer Nature, pp. 657–675, 2022.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis 30 (2022) 657–675."},"main_file_link":[{"url":"https://arxiv.org/abs/2012.10691","open_access":"1"}],"issue":"2","doi":"10.1007/s11228-021-00612-1","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication":"Set-Valued and Variational Analysis"},{"page":"141–161","doi":"10.1038/s41580-021-00415-0","citation":{"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.","short":"I. Vercellino, L.A. Sazanov, Nature Reviews Molecular Cell Biology 23 (2022) 141–161.","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>","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>","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>.","ista":"Vercellino I, Sazanov LA. 2022. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 23, 141–161.","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>."},"isi":1,"day":"01","corr_author":"1","department":[{"_id":"LeSa"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"Nature Reviews Molecular Cell Biology","publisher":"Springer Nature","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"The assembly, regulation and function of the mitochondrial respiratory chain","month":"02","scopus_import":"1","date_published":"2022-02-01T00:00:00Z","year":"2022","_id":"10182","intvolume":"        23","date_updated":"2024-10-09T21:01:03Z","publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"author":[{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino","first_name":"Irene","full_name":"Vercellino, Irene","orcid":" 0000-0001-5618-3449"},{"last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"date_created":"2021-10-24T22:01:35Z","oa_version":"None","abstract":[{"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.","lang":"eng"}],"volume":23,"external_id":{"isi":["000705697100001"],"pmid":["34621061"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1},{"citation":{"short":"M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics 22 (2022) 1513–1566.","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.","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>.","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>.","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.","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>","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>"},"isi":1,"day":"01","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.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s10208-021-09531-x","issue":"5","page":"1513-1566","file_date_updated":"2021-12-13T15:47:54Z","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computational Mathematics","Analysis"],"publisher":"Springer","has_accepted_license":"1","publication":"Foundations of Computational Mathematics","ddc":["510"],"type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"MaMo"}],"file":[{"access_level":"open_access","checksum":"9ea12dd8045a0678000a3a59295221cb","creator":"alisjak","file_name":"2021_Springer_Mondelli.pdf","date_updated":"2021-12-13T15:47:54Z","date_created":"2021-12-13T15:47:54Z","relation":"main_file","content_type":"application/pdf","file_size":2305731,"success":1,"file_id":"10542"}],"intvolume":"        22","_id":"10211","year":"2022","date_published":"2022-10-01T00:00:00Z","title":"Optimal combination of linear and spectral estimators for generalized linear models","scopus_import":"1","month":"10","status":"public","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000685721000001"],"arxiv":["2008.03326"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":22,"oa":1,"abstract":[{"lang":"eng","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."}],"arxiv":1,"oa_version":"Published Version","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"full_name":"Thrampoulidis, Christos","last_name":"Thrampoulidis","first_name":"Christos"},{"first_name":"Ramji","last_name":"Venkataramanan","full_name":"Venkataramanan, Ramji"}],"date_created":"2021-11-03T10:59:08Z","publication_identifier":{"issn":["1615-3375"],"eissn":["1615-3383"]},"date_updated":"2025-04-15T06:53:08Z"},{"_id":"10282","year":"2022","intvolume":"       233","scopus_import":"1","month":"01","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","date_published":"2022-01-01T00:00:00Z","status":"public","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"volume":233,"oa":1,"external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"date_created":"2021-11-14T23:01:24Z","author":[{"full_name":"Kashkan, Ivan","first_name":"Ivan","last_name":"Kashkan"},{"full_name":"Hrtyan, Mónika","first_name":"Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"full_name":"Humpolíčková, Jana","first_name":"Jana","last_name":"Humpolíčková"},{"first_name":"Aswathy","last_name":"Jayasree","full_name":"Jayasree, Aswathy"},{"first_name":"Roberta","last_name":"Filepová","full_name":"Filepová, Roberta"},{"full_name":"Vondráková, Zuzana","first_name":"Zuzana","last_name":"Vondráková"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741"},{"first_name":"Debbie","last_name":"Rombaut","full_name":"Rombaut, Debbie"},{"last_name":"Jacobs","first_name":"Thomas B.","full_name":"Jacobs, Thomas B."},{"last_name":"Frilander","first_name":"Mikko J.","full_name":"Frilander, Mikko J."},{"full_name":"Hejátko, Jan","first_name":"Jan","last_name":"Hejátko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Růžička","first_name":"Kamil","full_name":"Růžička, Kamil"}],"date_updated":"2024-05-22T11:33:15Z","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"day":"01","isi":1,"citation":{"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.","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>.","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>","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.","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>."},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2","open_access":"1"}],"issue":"1","doi":"10.1111/nph.17792","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.","page":"329-343","publisher":"Wiley","publication":"New Phytologist","quality_controlled":"1","publication_status":"published","type":"journal_article","department":[{"_id":"JiFr"}]},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"status":"public","date_published":"2022-01-01T00:00:00Z","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","month":"01","scopus_import":"1","intvolume":"        25","year":"2022","_id":"10284","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"date_updated":"2025-04-14T13:55:31Z","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E"},{"first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher"},{"full_name":"Naiser, Filip","first_name":"Filip","last_name":"Naiser"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"full_name":"Matas, Jiri","first_name":"Jiri","last_name":"Matas"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"date_created":"2021-11-14T23:01:25Z","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","external_id":{"isi":["000713396100001"],"pmid":["34725912"]},"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":25,"oa":1,"file_date_updated":"2022-02-03T13:37:11Z","page":"89-100","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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.","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1111/ele.13907","issue":"1","citation":{"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.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, Ecology Letters 25 (2022) 89–100.","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>","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>","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.","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>.","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>."},"isi":1,"day":"01","department":[{"_id":"SyCr"}],"file":[{"date_updated":"2022-02-03T13:37:11Z","file_name":"2021_EcologyLetters_CasillasPerez.pdf","checksum":"0bd4210400e9876609b7c538ab4f9a3c","creator":"cchlebak","access_level":"open_access","relation":"main_file","date_created":"2022-02-03T13:37:11Z","file_size":700087,"content_type":"application/pdf","file_id":"10721","success":1}],"corr_author":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"Ecology Letters","ddc":["573"],"publisher":"Wiley","related_material":{"record":[{"relation":"research_data","status":"public","id":"13061"}]},"has_accepted_license":"1"},{"publisher":"Springer Nature","publication":"Combinatorica","ddc":["514","516"],"publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"UlWa"}],"corr_author":"1","isi":1,"day":"01","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1907.05055"}],"citation":{"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.","short":"V. Kaluza, M. Tancer, Combinatorica 42 (2022) 1317–1345.","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>","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>","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>."},"doi":"10.1007/s00493-021-4443-7","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.","page":"1317-1345","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000798210100003"],"arxiv":["1907.05055"]},"oa":1,"volume":42,"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","arxiv":1,"date_created":"2021-11-25T13:49:16Z","author":[{"orcid":"0000-0002-2512-8698","full_name":"Kaluza, Vojtech","first_name":"Vojtech","last_name":"Kaluza","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"}],"publication_identifier":{"issn":["0209-9683"]},"date_updated":"2024-10-09T20:53:51Z","intvolume":"        42","_id":"10335","year":"2022","date_published":"2022-12-01T00:00:00Z","month":"12","scopus_import":"1","title":"Even maps, the Colin de Verdière number and representations of graphs","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","status":"public","date_published":"2022-06-01T00:00:00Z","month":"06","scopus_import":"1","title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","intvolume":"        21","year":"2022","_id":"10364","publication_identifier":{"issn":["1536-1276"],"eissn":["1558-2248"]},"date_updated":"2025-04-15T07:50:11Z","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"date_created":"2021-11-28T23:01:29Z","author":[{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"last_name":"Fazeli","first_name":"Arman","full_name":"Fazeli, Arman"},{"first_name":"Alexander","last_name":"Vardy","full_name":"Vardy, Alexander"},{"first_name":"John","last_name":"Cioffi","full_name":"Cioffi, John"},{"last_name":"Goldsmith","first_name":"Andrea","full_name":"Goldsmith, Andrea"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","arxiv":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2012.13378"],"isi":["000809406400028"]},"oa":1,"volume":21,"page":"3909-3920","doi":"10.1109/TWC.2021.3125626","issue":"6","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.","isi":1,"day":"01","citation":{"short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 21 (2022) 3909–3920.","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.","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>.","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>.","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>"},"main_file_link":[{"url":"https://arxiv.org/abs/2012.13378","open_access":"1"}],"department":[{"_id":"MaMo"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","publication":"IEEE Transactions on Wireless Communications","publisher":"Institute of Electrical and Electronics Engineers","related_material":{"record":[{"relation":"earlier_version","id":"10053","status":"public"}]}},{"publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"HeEd"}],"corr_author":"1","publisher":"Elsevier","publication":"Topology and its Applications","isi":1,"day":"15","citation":{"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.","short":"D. Dikranjan, A. Giordano Bruno, H.P. Künzi, N. Zava, D. Toller, Topology and Its Applications 309 (2022).","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>.","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>","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>","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>.","ista":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. 2022. Generalized quasi-metric semilattices. Topology and its Applications. 309, 107916."},"article_number":"107916","doi":"10.1016/j.topol.2021.107916","acknowledgement":"Dedicated to the memory of Hans-Peter Künzi.","date_created":"2021-12-05T23:01:44Z","author":[{"full_name":"Dikranjan, Dikran","last_name":"Dikranjan","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"},{"id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","last_name":"Zava","first_name":"Nicolò","full_name":"Zava, Nicolò","orcid":"0000-0001-8686-1888"},{"full_name":"Toller, Daniele","first_name":"Daniele","last_name":"Toller"}],"publication_identifier":{"issn":["0166-8641"]},"date_updated":"2024-10-09T21:01:16Z","external_id":{"isi":["000791838800012"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":309,"abstract":[{"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.","lang":"eng"}],"oa_version":"None","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","intvolume":"       309","year":"2022","_id":"10413","date_published":"2022-03-15T00:00:00Z","scopus_import":"1","month":"03","title":"Generalized quasi-metric semilattices"},{"month":"01","scopus_import":"1","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","date_published":"2022-01-04T00:00:00Z","_id":"10530","year":"2022","intvolume":"       121","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","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"}],"oa":1,"volume":121,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["34890578"],"isi":["000740815400007"]},"date_updated":"2025-06-11T13:59:29Z","publication_identifier":{"issn":["0006-3495"]},"date_created":"2021-12-10T09:48:19Z","author":[{"full_name":"Zisis, Themistoklis","first_name":"Themistoklis","last_name":"Zisis"},{"last_name":"Brückner","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"first_name":"Tom","last_name":"Brandstätter","full_name":"Brandstätter, Tom"},{"full_name":"Siow, Wei Xiong","first_name":"Wei Xiong","last_name":"Siow"},{"full_name":"d’Alessandro, Joseph","first_name":"Joseph","last_name":"d’Alessandro"},{"full_name":"Vollmar, Angelika M.","first_name":"Angelika M.","last_name":"Vollmar"},{"first_name":"Chase P.","last_name":"Broedersz","full_name":"Broedersz, Chase P."},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"doi":"10.1016/j.bpj.2021.12.006","issue":"1","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.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"04","isi":1,"citation":{"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.","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.","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>","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>.","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.","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>."},"keyword":["Biophysics"],"file_date_updated":"2022-07-29T10:17:10Z","page":"P44-60","publication":"Biophysical Journal","ddc":["570"],"has_accepted_license":"1","publisher":"Elsevier","file":[{"date_created":"2022-07-29T10:17:10Z","relation":"main_file","access_level":"open_access","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","creator":"dernst","file_name":"2022_BiophysicalJour_Zisis.pdf","date_updated":"2022-07-29T10:17:10Z","success":1,"file_id":"11697","file_size":4475504,"content_type":"application/pdf"}],"department":[{"_id":"EdHa"},{"_id":"GaTk"}],"quality_controlled":"1","publication_status":"published","type":"journal_article"},{"date_published":"2022-05-01T00:00:00Z","title":"Bosonization of fermionic many-body dynamics","month":"05","scopus_import":"1","intvolume":"        23","_id":"10537","year":"2022","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","ec_funded":1,"status":"public","abstract":[{"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.","lang":"eng"}],"arxiv":1,"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000725405700001"],"arxiv":["2103.08224"]},"oa":1,"volume":23,"publication_identifier":{"issn":["1424-0637"]},"date_updated":"2025-04-14T07:26:53Z","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"author":[{"full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091","last_name":"Benedikter","first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Phan Thành","last_name":"Nam","full_name":"Nam, Phan Thành"},{"full_name":"Porta, Marcello","first_name":"Marcello","last_name":"Porta"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"date_created":"2021-12-12T23:01:28Z","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).","issue":"5","doi":"10.1007/s00023-021-01136-y","citation":{"short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré 23 (2022) 1725–1764.","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.","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.","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>","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>."},"main_file_link":[{"url":"https://arxiv.org/abs/2103.08224","open_access":"1"}],"day":"01","isi":1,"page":"1725-1764","publication":"Annales Henri Poincaré","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"type":"journal_article","publication_status":"published","quality_controlled":"1"}]