[{"_id":"11403","quality_controlled":"1","oa_version":"None","department":[{"_id":"GradSch"}],"scopus_import":"1","volume":3,"doi":"10.1038/s43017-022-00302-y","citation":{"short":"A. Stöllner, Nature Reviews Earth and Environment 3 (2022) 360.","chicago":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” <i>Nature Reviews Earth and Environment</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s43017-022-00302-y\">https://doi.org/10.1038/s43017-022-00302-y</a>.","ista":"Stöllner A. 2022. Measuring airborne nanoplastics using aerosol physics. Nature Reviews Earth and Environment. 3(6), 360.","apa":"Stöllner, A. (2022). Measuring airborne nanoplastics using aerosol physics. <i>Nature Reviews Earth and Environment</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43017-022-00302-y\">https://doi.org/10.1038/s43017-022-00302-y</a>","ama":"Stöllner A. Measuring airborne nanoplastics using aerosol physics. <i>Nature Reviews Earth and Environment</i>. 2022;3(6):360. doi:<a href=\"https://doi.org/10.1038/s43017-022-00302-y\">10.1038/s43017-022-00302-y</a>","ieee":"A. Stöllner, “Measuring airborne nanoplastics using aerosol physics,” <i>Nature Reviews Earth and Environment</i>, vol. 3, no. 6. Springer Nature, p. 360, 2022.","mla":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” <i>Nature Reviews Earth and Environment</i>, vol. 3, no. 6, Springer Nature, 2022, p. 360, doi:<a href=\"https://doi.org/10.1038/s43017-022-00302-y\">10.1038/s43017-022-00302-y</a>."},"author":[{"id":"4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed","full_name":"Stöllner, Andrea","first_name":"Andrea","orcid":"0000-0002-0464-8440","last_name":"Stöllner"}],"date_updated":"2024-10-09T21:02:28Z","title":"Measuring airborne nanoplastics using aerosol physics","publication_identifier":{"eissn":["2662-138X"]},"article_type":"original","day":"01","external_id":{"isi":["000791125600002"]},"issue":"6","corr_author":"1","month":"06","status":"public","publication":"Nature Reviews Earth and Environment","date_created":"2022-05-22T22:01:41Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"         3","article_processing_charge":"No","year":"2022","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-01T00:00:00Z","page":"360","isi":1,"type":"journal_article"},{"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"volume":221,"project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1093/genetics/iyac083","citation":{"apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>."},"_id":"11411","quality_controlled":"1","oa_version":"Submitted Version","day":"01","article_type":"original","related_material":{"record":[{"relation":"research_data","id":"9192","status":"public"},{"status":"public","id":"11321","relation":"research_data"},{"status":"public","id":"14651","relation":"dissertation_contains"}]},"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","file_date_updated":"2022-05-26T12:48:21Z","publication_identifier":{"eissn":["1943-2631"]},"external_id":{"isi":["000803735800001"],"pmid":["35639938"]},"author":[{"first_name":"Parvathy","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"},{"full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon","orcid":"0000-0003-1771-714X"},{"first_name":"Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","full_name":"Baskett, Carina"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","date_updated":"2026-04-07T13:28:29Z","pmid":1,"date_created":"2022-05-26T13:44:50Z","abstract":[{"lang":"eng","text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity."}],"has_accepted_license":"1","publisher":"Oxford University Press","language":[{"iso":"eng"}],"intvolume":"       221","issue":"3","publication":"Genetics","corr_author":"1","ddc":["576"],"month":"07","status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"type":"journal_article","oa":1,"publication_status":"published","year":"2022","article_processing_charge":"No","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":885374,"checksum":"cc2d56deb608bd53c5cc02f03a875107","creator":"larathoo","file_name":"Manuscript.pdf","date_created":"2022-05-26T12:48:15Z","relation":"main_file","date_updated":"2022-05-26T12:48:15Z","success":1,"file_id":"11412"},{"file_name":"SupplementalMaterial.pdf","checksum":"693742595b6c7ed809423be01460d083","creator":"larathoo","relation":"main_file","date_created":"2022-05-26T12:48:21Z","content_type":"application/pdf","access_level":"open_access","file_size":1401704,"file_id":"11413","success":1,"date_updated":"2022-05-26T12:48:21Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-07-01T00:00:00Z","article_number":"iyac083"},{"oa":1,"type":"journal_article","isi":1,"article_number":"190401","date_published":"2022-05-12T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","year":"2022","publication_status":"published","intvolume":"       120","language":[{"iso":"eng"}],"publisher":"American Institute of Physics","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"}],"date_created":"2022-05-29T22:01:53Z","publication":"Applied Physics Letters","ddc":["530"],"status":"public","month":"05","issue":"19","external_id":{"isi":["000796002100002"]},"publication_identifier":{"issn":["0003-6951"]},"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.","article_type":"letter_note","day":"12","date_updated":"2026-06-18T17:14:33Z","title":"Emerging qubit systems: Guest editorial","author":[{"first_name":"Anthony J.","last_name":"Sigillito","full_name":"Sigillito, Anthony J."},{"last_name":"Covey","first_name":"Jacob P.","full_name":"Covey, Jacob P."},{"orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"},{"first_name":"Karl","last_name":"Petersson","full_name":"Petersson, Karl"},{"first_name":"Stefan","last_name":"Preble","full_name":"Preble, Stefan"}],"citation":{"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>.","short":"A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics Letters 120 (2022).","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>.","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.","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>","ista":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit systems: Guest editorial. Applied Physics Letters. 120(19), 190401."},"doi":"10.1063/5.0097339","volume":120,"scopus_import":"1","department":[{"_id":"JoFi"}],"main_file_link":[{"url":"https://doi.org/10.1063/5.0097339","open_access":"1"}],"oa_version":"Published Version","quality_controlled":"1","_id":"11417"},{"language":[{"iso":"eng"}],"intvolume":"        50","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"}],"date_created":"2022-05-29T22:01:53Z","publisher":"Institute of Mathematical Statistics","month":"05","status":"public","publication":"Annals of Probability","issue":"3","isi":1,"type":"journal_article","oa":1,"page":"984-1012","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-05-01T00:00:00Z","year":"2022","article_processing_charge":"No","publication_status":"published","citation":{"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>","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>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 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>.","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.","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>."},"doi":"10.1214/21-AOP1552","department":[{"_id":"LaEr"}],"scopus_import":"1","volume":50,"_id":"11418","main_file_link":[{"url":"https://arxiv.org/abs/2103.06730","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","external_id":{"isi":["000793963400005"],"arxiv":["2103.06730"]},"publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]},"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.","article_type":"original","day":"01","arxiv":1,"date_updated":"2023-08-03T07:16:53Z","title":"Normal fluctuation in quantum ergodicity for Wigner matrices","author":[{"first_name":"Giorgio","last_name":"Cipolloni","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-2904-1856","last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}]},{"date_updated":"2023-08-03T07:15:49Z","title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","author":[{"full_name":"Hori, Tetsuya","first_name":"Tetsuya","last_name":"Hori"},{"orcid":"0000-0002-6170-2546","last_name":"Eguchi","first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku"},{"first_name":"Han Ying","last_name":"Wang","full_name":"Wang, Han Ying"},{"full_name":"Miyasaka, Tomohiro","last_name":"Miyasaka","first_name":"Tomohiro"},{"full_name":"Guillaud, Laurent","last_name":"Guillaud","first_name":"Laurent"},{"last_name":"Taoufiq","first_name":"Zacharie","full_name":"Taoufiq, Zacharie"},{"full_name":"Mahapatra, Satyajit","first_name":"Satyajit","last_name":"Mahapatra"},{"first_name":"Hiroshi","last_name":"Yamada","full_name":"Yamada, Hiroshi"},{"full_name":"Takei, Kohji","first_name":"Kohji","last_name":"Takei"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"pmid":["35471147 "],"isi":["000876231600001"]},"article_type":"original","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).","publication_identifier":{"eissn":["2050-084X"]},"file_date_updated":"2022-05-30T08:09:16Z","day":"05","_id":"11419","quality_controlled":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/eLife.73542","citation":{"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.","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>","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>","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.","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>.","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).","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>."},"scopus_import":"1","department":[{"_id":"RySh"}],"volume":11,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e73542","date_published":"2022-05-05T00:00:00Z","year":"2022","article_processing_charge":"No","publication_status":"published","file":[{"file_size":2466296,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-30T08:09:16Z","checksum":"ccddbd167e00ff8375f12998af497152","file_name":"elife-73542-v2.pdf","creator":"cchlebak","date_updated":"2022-05-30T08:09:16Z","success":1,"file_id":"11421"}],"type":"journal_article","isi":1,"oa":1,"ddc":["616"],"publication":"eLife","status":"public","month":"05","language":[{"iso":"eng"}],"intvolume":"        11","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"}],"pmid":1,"date_created":"2022-05-29T22:01:54Z","has_accepted_license":"1","publisher":"eLife Sciences Publications"},{"conference":{"end_date":"2022-06-10","start_date":"2022-06-07","location":"Berlin, Germany","name":"SoCG: Symposium on Computational Geometry"},"day":"01","publication_identifier":{"isbn":["978-3-95977-227-3"],"issn":["1868-8969"]},"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.","file_date_updated":"2022-06-07T07:58:30Z","title":"A cautionary tale: Burning the medial axis is unstable","date_updated":"2025-04-14T07:43:57Z","author":[{"first_name":"Erin","last_name":"Chambers","full_name":"Chambers, Erin"},{"id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","full_name":"Fillmore, Christopher D","first_name":"Christopher D","last_name":"Fillmore"},{"last_name":"Stephenson","orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"},{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"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>","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>.","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.","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>."},"doi":"10.4230/LIPIcs.SoCG.2022.66","department":[{"_id":"HeEd"}],"scopus_import":"1","volume":224,"_id":"11428","oa_version":"Published Version","quality_controlled":"1","type":"conference","ec_funded":1,"oa":1,"editor":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"}],"page":"66:1-66:9","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-01T00:00:00Z","publication_status":"published","year":"2022","article_processing_charge":"No","series_title":"LIPIcs","file":[{"creator":"dernst","checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","file_name":"2022_LIPICs_Chambers.pdf","date_created":"2022-06-07T07:58:30Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":17580705,"file_id":"11437","success":1,"date_updated":"2022-06-07T07:58:30Z"}],"language":[{"iso":"eng"}],"intvolume":"       224","has_accepted_license":"1","abstract":[{"lang":"eng","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."}],"date_created":"2022-06-01T14:18:04Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","corr_author":"1","status":"public","ddc":["510"],"month":"06","publication":"38th International Symposium on Computational Geometry"},{"date_updated":"2024-10-09T21:02:30Z","date_published":"2022-05-01T00:00:00Z","title":"Web and Wireless Geographical Information Systems","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Cham","year":"2022","article_processing_charge":"No","publication_status":"published","type":"book_editor","page":"153","editor":[{"id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","full_name":"Karimipour, Farid","orcid":"0000-0001-6746-4174","last_name":"Karimipour","first_name":"Farid"},{"full_name":"Storandt, Sabine","first_name":"Sabine","last_name":"Storandt"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031062445"],"eisbn":["9783031062452"],"issn":["0302-9743"]},"day":"01","month":"05","oa_version":"None","corr_author":"1","quality_controlled":"1","status":"public","_id":"11429","citation":{"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>","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p.","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>.","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.","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>."},"doi":"10.1007/978-3-031-06245-2","intvolume":"     13238","language":[{"iso":"eng"}],"volume":13238,"publisher":"Springer Nature","edition":"1","alternative_title":["LNCS"],"date_created":"2022-06-02T05:40:53Z","department":[{"_id":"HeEd"}],"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."}]},{"date_updated":"2024-10-22T09:58:19Z","title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","author":[{"full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"external_id":{"isi":["000802723900027"]},"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"article_type":"original","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","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03641349/","open_access":"1"}],"quality_controlled":"1","oa_version":"Submitted Version","_id":"11432","citation":{"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>","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.","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>","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>.","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.","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>."},"doi":"10.1111/cgf.14478","project":[{"grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"volume":41,"scopus_import":"1","department":[{"_id":"ChWo"}],"date_published":"2022-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","year":"2022","publication_status":"published","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"page":"343-353","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","publication":"Computer Graphics Forum","month":"05","status":"public","issue":"2","intvolume":"        41","language":[{"iso":"eng"}],"publisher":"Wiley","date_created":"2022-06-05T22:01:49Z","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."}]},{"year":"2022","article_processing_charge":"No","publication_status":"published","date_published":"2022-04-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"951-957","oa":1,"isi":1,"type":"journal_article","issue":"2","status":"public","month":"04","publication":"SIAM Journal on Discrete Mathematics","publisher":"Society for Industrial and Applied Mathematics","date_created":"2022-06-05T22:01:50Z","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"}],"intvolume":"        36","language":[{"iso":"eng"}],"author":[{"last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory"},{"first_name":"Marton","last_name":"Naszodi","full_name":"Naszodi, Marton"}],"date_updated":"2023-10-18T06:58:03Z","title":"A quantitative Helly-type theorem: Containment in a homothet","arxiv":1,"publication_identifier":{"issn":["0895-4801"]},"article_type":"original","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","external_id":{"isi":["000793158200002"],"arxiv":["2103.04122"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2103.04122"}],"quality_controlled":"1","oa_version":"Preprint","_id":"11435","volume":36,"scopus_import":"1","department":[{"_id":"UlWa"}],"citation":{"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.","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>.","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>","ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","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>","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>.","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957."},"doi":"10.1137/21M1403308"},{"external_id":{"arxiv":["2102.11397"]},"arxiv":1,"day":"27","publication_identifier":{"eisbn":["9783030955199"],"isbn":["9783030955182"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18667"}]},"acknowledgement":"This project started during the Women in Computational Topology workshop held in Canberra in July of 2019. All authors are very grateful for its organisation and the financial support for the workshop from the Mathematical Sciences Institute at ANU, the US National Science Foundation through the award CCF-1841455, the Australian Mathematical Sciences Institute and the Association for Women in Mathematics. AG is supported by the Swiss National Science Foundation grant CRSII5_177237. TH is supported by the European Research Council (ERC) Horizon 2020 project “Alpha Shape Theory Extended” No. 788183. KM is supported by the ERC Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 859860. VR was supported by Australian Research Council Future Fellowship FT140100604 during the early stages of this project.","title":"The persistent homology of dual digital image constructions","date_updated":"2026-04-07T12:54:09Z","author":[{"full_name":"Bleile, Bea","first_name":"Bea","last_name":"Bleile"},{"full_name":"Garin, Adélie","first_name":"Adélie","last_name":"Garin"},{"full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","last_name":"Heiss","orcid":"0000-0002-1780-2689"},{"full_name":"Maggs, Kelly","last_name":"Maggs","first_name":"Kelly"},{"last_name":"Robins","first_name":"Vanessa","full_name":"Robins, Vanessa"}],"doi":"10.1007/978-3-030-95519-9_1","citation":{"ieee":"B. Bleile, A. Garin, T. Heiss, K. Maggs, and V. Robins, “The persistent homology of dual digital image constructions,” in <i>Research in Computational Topology 2</i>, 1st ed., vol. 30, E. Gasparovic, V. Robins, and K. Turner, Eds. Cham: Springer Nature, 2022, pp. 1–26.","mla":"Bleile, Bea, et al. “The Persistent Homology of Dual Digital Image Constructions.” <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic et al., 1st ed., vol. 30, Springer Nature, 2022, pp. 1–26, doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>.","ista":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. 2022.The persistent homology of dual digital image constructions. In: Research in Computational Topology 2. Association for Women in Mathematics Series, vol. 30, 1–26.","apa":"Bleile, B., Garin, A., Heiss, T., Maggs, K., &#38; Robins, V. (2022). The persistent homology of dual digital image constructions. In E. Gasparovic, V. Robins, &#38; K. Turner (Eds.), <i>Research in Computational Topology 2</i> (1st ed., Vol. 30, pp. 1–26). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>","ama":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. The persistent homology of dual digital image constructions. In: Gasparovic E, Robins V, Turner K, eds. <i>Research in Computational Topology 2</i>. Vol 30. 1st ed. AWMS. Cham: Springer Nature; 2022:1-26. doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>","chicago":"Bleile, Bea, Adélie Garin, Teresa Heiss, Kelly Maggs, and Vanessa Robins. “The Persistent Homology of Dual Digital Image Constructions.” In <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic, Vanessa Robins, and Katharine Turner, 1st ed., 30:1–26. AWMS. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>.","short":"B. Bleile, A. Garin, T. Heiss, K. Maggs, V. Robins, in:, E. Gasparovic, V. Robins, K. Turner (Eds.), Research in Computational Topology 2, 1st ed., Springer Nature, Cham, 2022, pp. 1–26."},"project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"}],"edition":"1","volume":30,"scopus_import":"1","department":[{"_id":"HeEd"}],"oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2102.11397"}],"_id":"11440","oa":1,"type":"book_chapter","ec_funded":1,"editor":[{"full_name":"Gasparovic, Ellen","last_name":"Gasparovic","first_name":"Ellen"},{"full_name":"Robins, Vanessa","last_name":"Robins","first_name":"Vanessa"},{"full_name":"Turner, Katharine","first_name":"Katharine","last_name":"Turner"}],"page":"1-26","date_published":"2022-01-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Cham","series_title":"AWMS","publication_status":"published","article_processing_charge":"No","year":"2022","intvolume":"        30","language":[{"iso":"eng"}],"publisher":"Springer Nature","abstract":[{"text":"To compute the persistent homology of a grayscale digital image one needs to build a simplicial or cubical complex from it. For cubical complexes, the two commonly used constructions (corresponding to direct and indirect digital adjacencies) can give different results for the same image. The two constructions are almost dual to each other, and we use this relationship to extend and modify the cubical complexes to become dual filtered cell complexes. We derive a general relationship between the persistent homology of two dual filtered cell complexes, and also establish how various modifications to a filtered complex change the persistence diagram. Applying these results to images, we derive a method to transform the persistence diagram computed using one type of cubical complex into a persistence diagram for the other construction. This means software for computing persistent homology from images can now be easily adapted to produce results for either of the two cubical complex constructions without additional low-level code implementation.","lang":"eng"}],"date_created":"2022-06-07T08:21:11Z","alternative_title":["Association for Women in Mathematics Series"],"status":"public","publication":"Research in Computational Topology 2","month":"01"},{"external_id":{"isi":["000830989200091"],"arxiv":["2201.11819"]},"OA_place":"publisher","arxiv":1,"day":"01","file_date_updated":"2022-06-28T08:32:58Z","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/","relation":"press_release","description":"News on ISTA website"}]},"article_type":"original","acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","title":"Closed-loop control of direct ink writing via reinforcement learning","date_updated":"2025-09-10T09:36:45Z","author":[{"first_name":"Michael","orcid":"0000-0002-5062-4474","last_name":"Piovarci","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael"},{"full_name":"Foshey, Michael","first_name":"Michael","last_name":"Foshey"},{"full_name":"Xu, Jie","last_name":"Xu","first_name":"Jie"},{"full_name":"Erps, Timothy","last_name":"Erps","first_name":"Timothy"},{"full_name":"Babaei, Vahid","first_name":"Vahid","last_name":"Babaei"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"full_name":"Rusinkiewicz, Szymon","first_name":"Szymon","last_name":"Rusinkiewicz"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"}],"citation":{"short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>.","ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>","apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>","ieee":"M. Piovarci <i>et al.</i>, “Closed-loop control of direct ink writing via reinforcement learning,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1145/3528223.3530144","project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication","grant_number":"M03319"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"volume":41,"department":[{"_id":"BeBi"}],"scopus_import":"1","quality_controlled":"1","oa_version":"Submitted Version","_id":"11442","oa":1,"type":"journal_article","isi":1,"ec_funded":1,"article_number":"112","date_published":"2022-06-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"date_created":"2022-06-28T08:32:58Z","relation":"main_file","checksum":"27f6fe41c6ff84d50445cc9b0176d45b","file_name":"2022_ACM_acceptedversion_Piovarci.pdf","creator":"dernst","file_size":33994829,"access_level":"open_access","content_type":"application/pdf","file_id":"11467","success":1,"date_updated":"2022-06-28T08:32:58Z"}],"publication_status":"published","year":"2022","article_processing_charge":"No","intvolume":"        41","PlanS_conform":"1","language":[{"iso":"eng"}],"OA_type":"hybrid","publisher":"Association for Computing Machinery","has_accepted_license":"1","abstract":[{"text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. ","lang":"eng"}],"date_created":"2022-06-10T06:41:47Z","status":"public","publication":"ACM Transactions on Graphics","corr_author":"1","ddc":["000"],"month":"06","issue":"4"},{"_id":"11443","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2006.08836","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","department":[{"_id":"MaKw"}],"scopus_import":"1","volume":375,"citation":{"short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250.","chicago":"Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2022. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>.","ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.","ama":"Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. 2022;375(6):4209-4250. doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>","apa":"Kwan, M. A., Sauermann, L., &#38; Zhao, Y. (2022). Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>","ieee":"M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional polytopes,” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6. American Mathematical Society, pp. 4209–4250, 2022.","mla":"Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6, American Mathematical Society, 2022, pp. 4209–50, doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>."},"doi":"10.1090/tran/8614","author":[{"orcid":"0000-0002-4003-7567","last_name":"Kwan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"first_name":"Lisa","last_name":"Sauermann","full_name":"Sauermann, Lisa"},{"last_name":"Zhao","first_name":"Yufei","full_name":"Zhao, Yufei"}],"date_updated":"2024-10-09T21:02:31Z","title":"Extension complexity of low-dimensional polytopes","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"article_type":"original","acknowledgement":"The research of the first author was supported by SNSF Project 178493 and NSF Award DMS-1953990. The research of the second author supported by NSF Award DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176, NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum Fund. ","day":"01","arxiv":1,"external_id":{"arxiv":["2006.08836"],"isi":["000798461500001"]},"issue":"6","status":"public","corr_author":"1","month":"06","publication":"Transactions of the American Mathematical Society","abstract":[{"text":"Sometimes, it is possible to represent a complicated polytope as a projection of a much simpler polytope. To quantify this phenomenon, the extension complexity of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional) polytope from which P can be obtained as a (linear) projection. This notion is motivated by its relevance to combinatorial optimisation, and has been studied intensively for various specific polytopes associated with important optimisation problems. In this paper we study extension complexity as a parameter of general polytopes, more specifically considering various families of low-dimensional polytopes. First, we prove that for a fixed dimension d, the extension complexity of a random d-dimensional polytope (obtained as the convex hull of random points in a ball or on a sphere) is typically on the order of the square root of its number of vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie on a circle) has extension complexity at most 24√n. This bound is tight up to the constant factor 24. Finally, we show that there exists an no(1)-dimensional polytope with at most n vertices and extension complexity n1−o(1). Our theorems are proved with a range of different techniques, which we hope will be of further interest.","lang":"eng"}],"date_created":"2022-06-12T22:01:45Z","publisher":"American Mathematical Society","language":[{"iso":"eng"}],"intvolume":"       375","article_processing_charge":"No","year":"2022","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-01T00:00:00Z","page":"4209-4250","isi":1,"type":"journal_article","oa":1},{"citation":{"ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","apa":"Chlebak, C. A., &#38; Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. Edinburgh University Press. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. 2022;38(1):23-41. doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” <i>Library and Information History</i>, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>.","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>. Edinburgh University Press, 2022. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>."},"doi":"10.3366/lih.2022.0097","volume":38,"department":[{"_id":"E-Lib"}],"scopus_import":"1","oa_version":"Submitted Version","quality_controlled":"1","main_file_link":[{"url":"https://rgu-repository.worktribe.com/output/1635939","open_access":"1"}],"_id":"11444","day":"01","publication_identifier":{"issn":["1758-3489"],"eissn":["1758-3497"]},"article_type":"original","title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","date_updated":"2024-10-09T21:02:31Z","author":[{"orcid":"0000-0002-3385-3865","last_name":"Chlebak","first_name":"Clara A","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","full_name":"Chlebak, Clara A"},{"full_name":"Reid, Peter H.","last_name":"Reid","first_name":"Peter H."}],"intvolume":"        38","language":[{"iso":"eng"}],"publisher":"Edinburgh University Press","abstract":[{"lang":"eng","text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride."}],"date_created":"2022-06-12T22:01:45Z","month":"04","corr_author":"1","publication":"Library and Information History","status":"public","issue":"1","oa":1,"type":"journal_article","page":"23-41","date_published":"2022-04-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","article_processing_charge":"No","year":"2022"},{"oa":1,"ec_funded":1,"isi":1,"type":"journal_article","date_published":"2022-06-17T00:00:00Z","article_number":"74","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","checksum":"05a1fe7d10914a00c2bca9b447993a65","file_name":"2022_BulletinMathBiology_Saona.pdf","relation":"main_file","date_created":"2022-06-20T07:51:32Z","content_type":"application/pdf","access_level":"open_access","file_size":463025,"file_id":"11455","success":1,"date_updated":"2022-06-20T07:51:32Z"}],"publication_status":"published","year":"2022","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"article_processing_charge":"Yes (via OA deal)","intvolume":"        84","language":[{"iso":"eng"}],"publisher":"Springer Nature","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"has_accepted_license":"1","date_created":"2022-06-17T16:16:15Z","pmid":1,"ddc":["510","570"],"status":"public","corr_author":"1","publication":"Bulletin of Mathematical Biology","month":"06","issue":"8","external_id":{"isi":["000812509800001"],"pmid":["35713756"]},"day":"17","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"article_type":"original","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}],"record":[{"id":"21918","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2022-06-20T07:51:32Z","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","date_updated":"2026-06-12T12:43:34Z","author":[{"last_name":"Saona Urmeneta","orcid":"0000-0001-5103-038X","first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor"},{"last_name":"Khudiakova","orcid":"0000-0002-6246-1465","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"}],"citation":{"chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s11538-022-01029-z","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"},{"name":"Evolutionary analysis of gene regulation","grant_number":"I05127","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181"}],"volume":84,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"oa_version":"Published Version","quality_controlled":"1","_id":"11447"},{"_id":"11448","oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.7554/elife.75842","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>","ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>."},"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"volume":11,"date_updated":"2026-04-07T13:25:01Z","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","author":[{"full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","first_name":"Louisa"},{"full_name":"Fleiss, Aubin","first_name":"Aubin","last_name":"Fleiss"},{"full_name":"Mishin, Alexander S","first_name":"Alexander S","last_name":"Mishin"},{"first_name":"Nina G","last_name":"Bozhanova","full_name":"Bozhanova, Nina G"},{"full_name":"Igolkina, Anna A","first_name":"Anna A","last_name":"Igolkina"},{"last_name":"Meiler","first_name":"Jens","full_name":"Meiler, Jens"},{"full_name":"Alaball Pujol, Maria-Elisenda","last_name":"Alaball Pujol","first_name":"Maria-Elisenda"},{"full_name":"Putintseva, Ekaterina V","last_name":"Putintseva","first_name":"Ekaterina V"},{"full_name":"Sarkisyan, Karen S","first_name":"Karen S","last_name":"Sarkisyan"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000799197200001"],"pmid":["35510622"]},"publication_identifier":{"issn":["2050-084X"]},"file_date_updated":"2022-06-20T07:44:19Z","article_type":"original","acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","related_material":{"link":[{"url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks","relation":"software"}],"record":[{"status":"public","relation":"dissertation_contains","id":"17850"}]},"day":"05","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"ddc":["570"],"publication":"eLife","status":"public","month":"05","corr_author":"1","language":[{"iso":"eng"}],"intvolume":"        11","date_created":"2022-06-18T09:06:59Z","abstract":[{"text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.","lang":"eng"}],"pmid":1,"has_accepted_license":"1","publisher":"eLife Sciences Publications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-05-05T00:00:00Z","article_number":"75842","article_processing_charge":"No","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"year":"2022","publication_status":"published","file":[{"file_id":"11454","success":1,"date_updated":"2022-06-20T07:44:19Z","date_created":"2022-06-20T07:44:19Z","relation":"main_file","file_name":"2022_eLife_Somermeyer.pdf","checksum":"7573c28f44028ab0cc81faef30039e44","creator":"dernst","file_size":5297213,"access_level":"open_access","content_type":"application/pdf"}],"isi":1,"ec_funded":1,"type":"journal_article","oa":1},{"publisher":"Elsevier","date_created":"2022-06-19T22:01:57Z","pmid":1,"abstract":[{"lang":"eng","text":"Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans."}],"intvolume":"        13","language":[{"iso":"eng"}],"issue":"6","month":"06","ddc":["570"],"status":"public","publication":"Cell Systems","page":"438-453.e5","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","publication_status":"published","article_processing_charge":"No","year":"2022","date_published":"2022-06-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":13,"scopus_import":"1","department":[{"_id":"SiHi"}],"doi":"10.1016/j.cels.2022.03.006","citation":{"mla":"Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>, vol. 13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>.","ieee":"D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development,” <i>Cell Systems</i>, vol. 13, no. 6. Elsevier, p. 438–453.e5, 2022.","apa":"Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>","ista":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. 13(6), 438–453.e5.","ama":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. 2022;13(6):438-453.e5. doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>","chicago":"Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>.","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5."},"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cels.2022.03.006"}],"_id":"11449","day":"15","article_type":"original","acknowledgement":"D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program 725780 LinPro to S.H.","publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"author":[{"last_name":"Anderson","first_name":"Donovan J.","full_name":"Anderson, Donovan J."},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian"},{"full_name":"Mckenna, Aaron","first_name":"Aaron","last_name":"Mckenna"},{"full_name":"Shendure, Jay","first_name":"Jay","last_name":"Shendure"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","date_updated":"2026-06-18T17:15:22Z"},{"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","date_updated":"2025-04-14T07:43:58Z","author":[{"id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","orcid":"0000-0001-8945-6992","last_name":"Artan","first_name":"Murat"},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443"}],"day":"04","acknowledgement":"We thank de Bono lab members for the helpful comments on the manuscript. The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J. Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly sent by Dr. Dominique Glauser (University of Fribourg). This work was supported by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","publication_identifier":{"eissn":["1940-6045"],"issn":["0893-2336"],"eisbn":["9781071623213"],"isbn":["9781071623206"]},"_id":"11456","oa_version":"None","quality_controlled":"1","project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"citation":{"apa":"Artan, M., &#38; de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), <i>Behavioral Neurogenetics</i> (Vol. 181, pp. 277–294). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>","ama":"Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Yamamoto D, ed. <i>Behavioral Neurogenetics</i>. Vol 181. NM. New York: Springer Nature; 2022:277-294. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>","ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","ieee":"M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling,” in <i>Behavioral Neurogenetics</i>, vol. 181, D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>.","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294.","chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>."},"doi":"10.1007/978-1-0716-2321-3_15","scopus_import":"1","department":[{"_id":"MaDe"}],"volume":181,"place":"New York","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-04T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2022","series_title":"NM","ec_funded":1,"type":"book_chapter","editor":[{"full_name":"Yamamoto, Daisuke","first_name":"Daisuke","last_name":"Yamamoto"}],"page":"277-294","month":"06","publication":"Behavioral Neurogenetics","corr_author":"1","status":"public","language":[{"iso":"eng"}],"intvolume":"       181","abstract":[{"lang":"eng","text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal."}],"date_created":"2022-06-20T08:10:34Z","alternative_title":["Neuromethods"],"publisher":"Springer Nature"},{"date_published":"2022-06-09T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","date_created":"2022-06-27T07:38:21Z","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","creator":"dernst","file_name":"2022_PLDI_Zikelic.pdf","file_size":318697,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"11466","date_updated":"2022-06-27T07:38:21Z"}],"publication_status":"published","article_processing_charge":"No","year":"2022","oa":1,"ec_funded":1,"isi":1,"type":"conference","page":"442-457","status":"public","ddc":["000"],"corr_author":"1","month":"06","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","has_accepted_license":"1","date_created":"2022-06-21T09:26:15Z","abstract":[{"lang":"eng","text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples."}],"title":"Differential cost analysis with simultaneous potentials and anti-potentials","date_updated":"2025-04-14T07:52:47Z","author":[{"first_name":"Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"},{"last_name":"Chang","first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan"},{"full_name":"Bolignano, Pauline","first_name":"Pauline","last_name":"Bolignano"},{"full_name":"Raimondi, Franco","last_name":"Raimondi","first_name":"Franco"}],"external_id":{"isi":["000850435600030"],"arxiv":["2204.00870"]},"conference":{"end_date":"2022-06-17","name":"PLDI: Programming Language Design and Implementation","location":"San Diego, CA, United States","start_date":"2022-06-13"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","arxiv":1,"day":"09","acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt).","file_date_updated":"2022-06-27T07:38:21Z","publication_identifier":{"isbn":["9781450392655"]},"oa_version":"Published Version","quality_controlled":"1","_id":"11459","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1145/3519939.3523435","citation":{"ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>","ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>.","ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457.","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>."},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"KrCh"}]},{"keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"year":"2022","article_processing_charge":"No","publication_status":"published","file":[{"date_updated":"2022-06-24T08:22:59Z","file_id":"11461","success":1,"content_type":"application/pdf","access_level":"open_access","file_size":7552298,"creator":"dernst","file_name":"2022_MolecularAutism_Schaaf.pdf","checksum":"525d2618e855139089bbfc3e3d49d1b2","relation":"main_file","date_created":"2022-06-24T08:22:59Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"27","date_published":"2022-06-22T00:00:00Z","isi":1,"type":"journal_article","oa":1,"publication":"Molecular Autism","month":"06","ddc":["570"],"status":"public","abstract":[{"text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life.","lang":"eng"}],"pmid":1,"date_created":"2022-06-23T14:28:55Z","has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"        13","author":[{"full_name":"Schaaf, Zachary A.","first_name":"Zachary A.","last_name":"Schaaf"},{"full_name":"Tat, Lyvin","last_name":"Tat","first_name":"Lyvin"},{"last_name":"Cannizzaro","first_name":"Noemi","full_name":"Cannizzaro, Noemi"},{"last_name":"Green","first_name":"Ralph","full_name":"Green, Ralph"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Zarbalis, Konstantinos S.","first_name":"Konstantinos S.","last_name":"Zarbalis"}],"date_updated":"2025-06-11T13:34:57Z","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"article_type":"original","publication_identifier":{"issn":["2040-2392"]},"file_date_updated":"2022-06-24T08:22:59Z","acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","day":"22","external_id":{"isi":["000814641400001"],"pmid":["35733184"]},"_id":"11460","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","department":[{"_id":"SiHi"}],"volume":13,"citation":{"ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1186/s13229-022-00508-3"},{"date_updated":"2023-10-10T07:15:02Z","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","author":[{"full_name":"Dormeshkin, Dmitri","first_name":"Dmitri","last_name":"Dormeshkin"},{"full_name":"Shapira, Michail","first_name":"Michail","last_name":"Shapira"},{"last_name":"Karputs","first_name":"Alena","full_name":"Karputs, Alena"},{"full_name":"Kavaleuski, Anton","id":"62304f89-eb97-11eb-a6c2-8903dd183976","first_name":"Anton","last_name":"Kavaleuski","orcid":"0000-0003-2091-526X"},{"first_name":"Ivan","last_name":"Kuzminski","full_name":"Kuzminski, Ivan"},{"full_name":"Stepanova, Elena","first_name":"Elena","last_name":"Stepanova"},{"full_name":"Gilep, Andrei","first_name":"Andrei","last_name":"Gilep"}],"external_id":{"isi":["000813677500001"],"pmid":["35723693"]},"article_type":"original","publication_identifier":{"issn":["0175-7598"],"eissn":["1432-0614"]},"acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","day":"01","quality_controlled":"1","oa_version":"None","_id":"11462","citation":{"short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022."},"doi":"10.1007/s00253-022-12022-w","volume":106,"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"scopus_import":"1","date_published":"2022-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","article_processing_charge":"No","publication_status":"published","isi":1,"type":"journal_article","page":"5093-5103","publication":"Applied Microbiology and Biotechnology","month":"08","status":"public","intvolume":"       106","language":[{"iso":"eng"}],"publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens."}],"pmid":1,"date_created":"2022-06-26T22:01:34Z"}]