[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","external_id":{"isi":["000911392100055"],"pmid":["35849565"]},"related_material":{"record":[{"id":"11711","status":"public","relation":"research_data"}]},"file":[{"file_size":1421256,"relation":"main_file","checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","date_updated":"2022-08-01T08:02:38Z","file_name":"2022_PLoSONE_Budanur.pdf","content_type":"application/pdf","creator":"dernst","success":1,"access_level":"open_access","date_created":"2022-08-01T08:02:38Z","file_id":"11712"}],"publication_identifier":{"eissn":["1932-6203"]},"has_accepted_license":"1","article_number":"e0269975","citation":{"ama":"Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. 2022;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>","chicago":"Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>.","apa":"Budanur, N. B., &#38; Hof, B. (2022). An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>","mla":"Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>, vol. 17, no. 7, e0269975, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>.","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975.","ieee":"N. B. Budanur and B. Hof, “An autonomous compartmental model for accelerating epidemics,” <i>PLoS ONE</i>, vol. 17, no. 7. Public Library of Science, 2022.","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022)."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2022-08-01T08:02:38Z","corr_author":"1","author":[{"full_name":"Budanur, Nazmi B","last_name":"Budanur","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}],"article_processing_charge":"No","date_updated":"2025-06-11T13:37:36Z","department":[{"_id":"BjHo"}],"isi":1,"status":"public","doi":"10.1371/journal.pone.0269975","publication_status":"published","oa_version":"Published Version","type":"journal_article","volume":17,"title":"An autonomous compartmental model for accelerating epidemics","article_type":"original","publication":"PLoS ONE","ddc":["510"],"pmid":1,"_id":"11704","day":"18","publisher":"Public Library of Science","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2022-07-18T00:00:00Z","issue":"7","year":"2022","date_created":"2022-07-31T22:01:48Z","abstract":[{"text":"In Fall 2020, several European countries reported rapid increases in COVID-19 cases along with growing estimates of the effective reproduction rates. Such an acceleration in epidemic spread is usually attributed to time-dependent effects, e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc. In this case however the acceleration occurred when counter measures such as testing and contact tracing exceeded their capacity limit. Considering Austria as an example, here we show that this dynamics can be captured by a time-independent, i.e. autonomous, compartmental model that incorporates these capacity limits. In this model, the epidemic acceleration coincides with the exhaustion of mitigation efforts, resulting in an increasing fraction of undetected cases that drive the effective reproduction rate progressively higher. We demonstrate that standard models which does not include this effect necessarily result in a systematic underestimation of the effective reproduction rate.","lang":"eng"}],"intvolume":"        17","quality_controlled":"1"},{"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","last_name":"Chang"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu"},{"last_name":"Lee","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"first_name":"Maria","full_name":"Spadaro, Maria","last_name":"Spadaro"},{"full_name":"Koskela, Kristopher M.","last_name":"Koskela","first_name":"Kristopher M."},{"first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns"},{"orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Richard L.","full_name":"Brutchey, Richard L.","last_name":"Brutchey"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"date_updated":"2025-04-14T07:44:07Z","status":"public","isi":1,"oa_version":"Published Version","type":"journal_article","doi":"10.1002/anie.202207002","publication_status":"published","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"external_id":{"isi":["000828274200001"],"pmid":["38505739"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"file":[{"success":1,"access_level":"open_access","date_created":"2023-02-02T08:01:00Z","file_id":"12476","content_type":"application/pdf","creator":"dernst","date_updated":"2023-02-02T08:01:00Z","file_name":"2022_AngewandteChemieInternat_Chang.pdf","file_size":4072650,"relation":"main_file","checksum":"ad601f2b9e26e46ab4785162be58b5ed"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","language":[{"iso":"eng"}],"article_number":"e202207002","has_accepted_license":"1","citation":{"mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35, e202207002, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>.","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002.","ieee":"C. Chang <i>et al.</i>, “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35. Wiley, 2022.","short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. 2022;61(35). doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>.","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>"},"project":[{"grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"file_date_updated":"2023-02-02T08:01:00Z","corr_author":"1","scopus_import":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"35","year":"2022","date_published":"2022-08-26T00:00:00Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe."}],"date_created":"2022-07-31T22:01:48Z","intvolume":"        61","title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","article_type":"original","ec_funded":1,"volume":61,"publication":"Angewandte Chemie - International Edition","pmid":1,"ddc":["540"],"day":"26","publisher":"Wiley","_id":"11705"},{"editor":[{"full_name":"Parter, Merav","last_name":"Parter","first_name":"Merav"}],"_id":"11707","day":"25","arxiv":1,"publisher":"Springer Nature","volume":13298,"title":"Local mending","ec_funded":1,"publication":"International Colloquium on Structural Information and Communication Complexity","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08703"}],"date_created":"2022-07-31T22:01:49Z","intvolume":"     13298","abstract":[{"lang":"eng","text":"In this work we introduce the graph-theoretic notion of mendability: for each locally checkable graph problem we can define its mending radius, which captures the idea of how far one needs to modify a partial solution in order to “patch a hole.” We explore how mendability is connected to the existence of efficient algorithms, especially in distributed, parallel, and fault-tolerant settings. It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds in the LOCAL model of distributed computing. One of the surprises is that in paths and cycles, a converse also holds in the following sense: if a problem Π can be solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently solvable but that is also O(1)-mendable. We also explore the structure of the landscape of mendability. For example, we show that in trees, the mending radius of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs the structure is much more diverse."}],"series_title":"LNCS","quality_controlled":"1","oa":1,"date_published":"2022-06-25T00:00:00Z","year":"2022","citation":{"ama":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. Local mending. In: Parter M, ed. <i>International Colloquium on Structural Information and Communication Complexity</i>. Vol 13298. LNCS. Springer Nature; 2022:1-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>","apa":"Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., &#38; Suomela, J. (2022). Local mending. In M. Parter (Ed.), <i>International Colloquium on Structural Information and Communication Complexity</i> (Vol. 13298, pp. 1–20). Paderborn, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>","chicago":"Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki, and Jukka Suomela. “Local Mending.” In <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, 13298:1–20. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>.","short":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, J. Suomela, in:, M. Parter (Ed.), International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2022, pp. 1–20.","ieee":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela, “Local mending,” in <i>International Colloquium on Structural Information and Communication Complexity</i>, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.","ista":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local mending. International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol. 13298, 1–20.","mla":"Balliu, Alkida, et al. “Local Mending.” <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, vol. 13298, Springer Nature, 2022, pp. 1–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"840605","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2022-06-27","location":"Paderborn, Germany","name":"SIROCCO: Structural Information and Communication Complexity","end_date":"2022-06-29"},"month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605. This work was supported in part by the Academy of Finland, Grants 314888 and 333837. The authors would also like to thank David Harris, Neven Villani, and the anonymous reviewers for their very helpful comments and feedback on previous versions of this work.","page":"1-20","publication_identifier":{"isbn":["9783031099922"],"eissn":["1611-3349"],"issn":["0302-9743"]},"isi":1,"status":"public","doi":"10.1007/978-3-031-09993-9_1","publication_status":"published","oa_version":"Preprint","type":"conference","author":[{"first_name":"Alkida","full_name":"Balliu, Alkida","last_name":"Balliu"},{"full_name":"Hirvonen, Juho","last_name":"Hirvonen","first_name":"Juho"},{"last_name":"Melnyk","full_name":"Melnyk, Darya","first_name":"Darya"},{"first_name":"Dennis","last_name":"Olivetti","full_name":"Olivetti, Dennis"},{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","last_name":"Rybicki","full_name":"Rybicki, Joel"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"}],"article_processing_charge":"No","date_updated":"2025-04-14T07:50:55Z","department":[{"_id":"DaAl"}]},{"year":"2022","department":[{"_id":"BjHo"}],"date_published":"2022-07-06T00:00:00Z","date_updated":"2025-06-11T13:37:36Z","oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"author":[{"full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2022-08-01T08:06:33Z","abstract":[{"text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\"","lang":"eng"}],"doi":"10.5281/ZENODO.6802720","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6802720"}],"status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11704"}]},"title":"burakbudanur/autoacc-public","month":"07","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Zenodo","license":"https://creativecommons.org/publicdomain/zero/1.0/","corr_author":"1","day":"06","_id":"11711","ddc":["000"],"citation":{"apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>","chicago":"Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>.","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>","ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","short":"N.B. Budanur, (2022).","mla":"Budanur, Nazmi B. <i>Burakbudanur/Autoacc-Public</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>."},"has_accepted_license":"1"},{"author":[{"full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","first_name":"Nela"},{"first_name":"Martina","last_name":"Sauert","full_name":"Sauert, Martina"},{"first_name":"Tanino G.","last_name":"Albanese","full_name":"Albanese, Tanino G."},{"first_name":"Isabella","last_name":"Moll","full_name":"Moll, Isabella"}],"article_processing_charge":"No","department":[{"_id":"CaGu"}],"date_updated":"2025-04-14T09:24:53Z","status":"public","oa_version":"Published Version","type":"journal_article","doi":"10.1186/s13104-022-06061-9","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publication_identifier":{"issn":["1756-0500"]},"external_id":{"pmid":["35562780"]},"related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"acknowledgement":"We acknowledge the Max Perutz Labs FACS Facility together with Thomas Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207), to IM. Open access funding provided by the Austrian Science Fund.","file":[{"file_name":"2022_BMCResearchNotes_Nikolic.pdf","date_updated":"2022-08-01T09:24:42Z","file_size":1545310,"relation":"main_file","checksum":"008156e5340e9789f0f6d82bde4d347a","access_level":"open_access","success":1,"date_created":"2022-08-01T09:24:42Z","file_id":"11714","creator":"dernst","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_number":"173","has_accepted_license":"1","citation":{"apa":"Nikolic, N., Sauert, M., Albanese, T. G., &#38; Moll, I. (2022). Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>","chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","ama":"Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. 2022;15. doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>","ieee":"N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli,” <i>BMC Research Notes</i>, vol. 15. Springer Nature, 2022.","ista":"Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. 15, 173.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>."},"project":[{"grant_number":"V00738","call_identifier":"FWF","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","_id":"26956E74-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2022-08-01T09:24:42Z","corr_author":"1","scopus_import":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2022","date_published":"2022-05-13T00:00:00Z","quality_controlled":"1","abstract":[{"text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.","lang":"eng"}],"intvolume":"        15","date_created":"2022-08-01T09:04:27Z","article_type":"letter_note","title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","volume":15,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"publication":"BMC Research Notes","pmid":1,"ddc":["570"],"day":"13","publisher":"Springer Nature","_id":"11713"},{"quality_controlled":"1","intvolume":"       408","abstract":[{"text":"We study rigidity of rational maps that come from Newton's root finding method for polynomials of arbitrary degrees. We establish dynamical rigidity of these maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit can be distinguished in combinatorial terms from all other orbits), or the orbit of this point eventually lands in the filled-in Julia set of a polynomial-like restriction of the original map. As a corollary, we show that the Julia sets of Newton maps in many non-trivial cases are locally connected; in particular, every cubic Newton map without Siegel points has locally connected Julia set.\r\nIn the parameter space of Newton maps of arbitrary degree we obtain the following rigidity result: any two combinatorially equivalent Newton maps are quasiconformally conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable, or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized renormalization concept called “complex box mappings” for which we extend a dynamical rigidity result by Kozlovski and van Strien so as to include irrationally indifferent and renormalizable situations.","lang":"eng"}],"date_created":"2022-08-01T17:08:16Z","year":"2022","issue":"Part A","date_published":"2022-10-29T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publisher":"Elsevier","day":"29","_id":"11717","ddc":["510"],"keyword":["General Mathematics"],"publication":"Advances in Mathematics","ec_funded":1,"title":"Rigidity of Newton dynamics","article_type":"original","volume":408,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1016/j.aim.2022.108591","status":"public","isi":1,"department":[{"_id":"VaKa"}],"date_updated":"2025-04-14T07:53:45Z","article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0002-9156-8616","id":"fe8209e2-906f-11eb-847d-950f8fc09115","first_name":"Kostiantyn","last_name":"Drach","full_name":"Drach, Kostiantyn"},{"full_name":"Schleicher, Dierk","last_name":"Schleicher","first_name":"Dierk"}],"corr_author":"1","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707"}],"file_date_updated":"2023-02-02T07:39:09Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"chicago":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>.","apa":"Drach, K., &#38; Schleicher, D. (2022). Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>","ama":"Drach K, Schleicher D. Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. 2022;408(Part A). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>","mla":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>.","ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022.","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022)."},"has_accepted_license":"1","article_number":"108591","publication_identifier":{"issn":["0001-8708"]},"acknowledgement":"We are grateful to a number of colleagues for helpful and inspiring discussions during the time when we worked on this project, in particular Dima Dudko, Misha Hlushchanka, John Hubbard, Misha Lyubich, Oleg Kozlovski, and Sebastian van Strien. Finally, we would like to thank our dynamics research group for numerous helpful and enjoyable discussions: Konstantin Bogdanov, Roman Chernov, Russell Lodge, Steffen Maaß, David Pfrang, Bernhard Reinke, Sergey Shemyakov, and Maik Sowinski. We gratefully acknowledge support by the Advanced Grant “HOLOGRAM” (#695 621) of the European Research Council (ERC), as well as hospitality of Cornell University in the spring of 2018 while much of this work was prepared. The first-named author also acknowledges the support of the ERC Advanced Grant “SPERIG” (#885 707).","file":[{"file_size":2164036,"relation":"main_file","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","file_name":"2022_AdvancesMathematics_Drach.pdf","date_updated":"2023-02-02T07:39:09Z","creator":"dernst","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2023-02-02T07:39:09Z","file_id":"12474"}],"external_id":{"isi":["000860924200005"]},"month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","file":[{"relation":"main_file","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","file_size":2506262,"date_updated":"2022-08-08T07:42:09Z","file_name":"2022_PNAS_Li.pdf","creator":"dernst","content_type":"application/pdf","file_id":"11747","access_level":"open_access","success":1,"date_created":"2022-08-08T07:42:09Z"}],"external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"citation":{"mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121058119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121058119.","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>"},"article_number":"e2121058119","has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2022-08-08T07:42:09Z","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"article_processing_charge":"No","author":[{"full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"last_name":"Alotaibi","full_name":"Alotaibi, Saqer S.","first_name":"Saqer S."},{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"full_name":"Adamowski, Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"}],"date_updated":"2025-05-14T11:01:00Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1073/pnas.2121058119","type":"journal_article","oa_version":"Published Version","volume":119,"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","article_type":"original","keyword":["Multidisciplinary"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","ddc":["580"],"pmid":1,"_id":"11723","publisher":"National Academy of Sciences","day":"25","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"date_published":"2022-07-25T00:00:00Z","year":"2022","issue":"31","intvolume":"       119","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"date_created":"2022-08-04T20:06:49Z","quality_controlled":"1"},{"date_published":"2022-07-29T00:00:00Z","year":"2022","issue":"31","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"intvolume":"       119","abstract":[{"lang":"eng","text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies."}],"date_created":"2022-08-07T22:01:56Z","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":119,"title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","article_type":"original","_id":"11733","publisher":"National Academy of Sciences","day":"29","ddc":["570"],"pmid":1,"date_updated":"2025-06-12T06:22:37Z","department":[{"_id":"MaRo"}],"article_processing_charge":"No","author":[{"last_name":"Orliac","full_name":"Orliac, Etienne J.","first_name":"Etienne J."},{"first_name":"Daniel","full_name":"Trejo Banos, Daniel","last_name":"Trejo Banos"},{"first_name":"Sven E.","last_name":"Ojavee","full_name":"Ojavee, Sven E."},{"last_name":"Läll","full_name":"Läll, Kristi","first_name":"Kristi"},{"full_name":"Mägi, Reedik","last_name":"Mägi","first_name":"Reedik"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"publication_status":"published","doi":"10.1073/pnas.2121279119","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","acknowledgement":"This project was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science and Technology Austria. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant PRG687. Estonian Biobank computations were performed in the High-Performance Computing Centre, University of Tartu.","related_material":{"record":[{"id":"13064","relation":"research_data","status":"public"}]},"file":[{"creator":"dernst","content_type":"application/pdf","access_level":"open_access","success":1,"date_created":"2022-08-08T07:31:19Z","file_id":"11745","file_size":1001164,"relation":"main_file","checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","date_updated":"2022-08-08T07:31:19Z","file_name":"2022_PNAS_Orliac.pdf"}],"external_id":{"pmid":["35905320"],"isi":["000881496900003"]},"publication_identifier":{"eissn":["1091-6490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","scopus_import":"1","corr_author":"1","file_date_updated":"2022-08-08T07:31:19Z","citation":{"ieee":"E. J. Orliac <i>et al.</i>, “Improving GWAS discovery and genomic prediction accuracy in biobank data,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ista":"Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank data. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121279119.","short":"E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher, M.R. Robinson, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121279119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>.","apa":"Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher, P. M., &#38; Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>","chicago":"Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>.","ama":"Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>"},"has_accepted_license":"1","article_number":"e2121279119","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"article_number":"e2122460119","has_accepted_license":"1","citation":{"mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>.","short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>.","apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>"},"project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"}],"file_date_updated":"2022-08-08T07:09:58Z","corr_author":"1","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_identifier":{"eissn":["1091-6490"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"external_id":{"pmid":["35878040"],"isi":["000881496900007"]},"file":[{"date_updated":"2022-08-08T07:09:58Z","file_name":"2022_PNAS_Abualia.pdf","checksum":"6e97dedc281247fc3fe238a209f14af0","relation":"main_file","file_size":3092330,"file_id":"11744","date_created":"2022-08-08T07:09:58Z","success":1,"access_level":"open_access","creator":"dernst","content_type":"application/pdf"}],"acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","status":"public","isi":1,"oa_version":"Published Version","type":"journal_article","doi":"10.1073/pnas.2122460119","publication_status":"published","article_processing_charge":"No","author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","first_name":"Rashed","full_name":"Abualia, Rashed","last_name":"Abualia"},{"full_name":"Ötvös, Krisztina","last_name":"Ötvös","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Eleonore","full_name":"Bouguyon, Eleonore","last_name":"Bouguyon"},{"first_name":"Kevin","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","orcid":"0000-0002-1215-4264","full_name":"Domanegg, Kevin","last_name":"Domanegg"},{"last_name":"Krapp","full_name":"Krapp, Anne","first_name":"Anne"},{"first_name":"Philip","full_name":"Nacry, Philip","last_name":"Nacry"},{"first_name":"Alain","last_name":"Gojon","full_name":"Gojon, Alain"},{"full_name":"Lacombe, Benoit","last_name":"Lacombe","first_name":"Benoit"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"}],"department":[{"_id":"EvBe"}],"date_updated":"2025-05-14T11:00:29Z","pmid":1,"ddc":["570"],"day":"25","publisher":"National Academy of Sciences","_id":"11734","title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","article_type":"original","volume":119,"publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","intvolume":"       119","date_created":"2022-08-07T22:01:57Z","abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"issue":"31","year":"2022","date_published":"2022-07-25T00:00:00Z"},{"date_published":"2022-07-22T00:00:00Z","year":"2022","issue":"4","oa":1,"date_created":"2022-08-07T22:01:57Z","abstract":[{"text":"Interlocking puzzles are intriguing geometric games where the puzzle pieces are held together based on their geometric arrangement, preventing the puzzle from falling apart. High-level-of-difficulty, or simply high-level, interlocking puzzles are a subclass of interlocking puzzles that require multiple moves to take out the first subassembly from the puzzle. Solving a high-level interlocking puzzle is a challenging task since one has to explore many different configurations of the puzzle pieces until reaching a configuration where the first subassembly can be taken out. Designing a high-level interlocking puzzle with a user-specified level of difficulty is even harder since the puzzle pieces have to be interlocking in all the configurations before the first subassembly is taken out.\r\n\r\nIn this paper, we present a computational approach to design high-level interlocking puzzles. The core idea is to represent all possible configurations of an interlocking puzzle as well as transitions among these configurations using a rooted, undirected graph called a disassembly graph and leverage this graph to find a disassembly plan that requires a minimal number of moves to take out the first subassembly from the puzzle. At the design stage, our algorithm iteratively constructs the geometry of each puzzle piece to expand the disassembly graph incrementally, aiming to achieve a user-specified level of difficulty. We show that our approach allows efficient generation of high-level interlocking puzzles of various shape complexities, including new solutions not attainable by state-of-the-art approaches.","lang":"eng"}],"intvolume":"        41","quality_controlled":"1","publication":"ACM Transactions on Graphics","volume":41,"ec_funded":1,"title":"Computational design of high-level interlocking puzzles","article_type":"original","_id":"11735","publisher":"Association for Computing Machinery","day":"22","ddc":["000"],"date_updated":"2025-04-14T07:28:57Z","department":[{"_id":"BeBi"}],"author":[{"full_name":"Chen, Rulin","last_name":"Chen","first_name":"Rulin"},{"first_name":"Ziqi","full_name":"Wang, Ziqi","last_name":"Wang"},{"first_name":"Peng","full_name":"Song, Peng","last_name":"Song"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel"}],"article_processing_charge":"No","publication_status":"published","doi":"10.1145/3528223.3530071","type":"journal_article","oa_version":"Submitted Version","isi":1,"status":"public","file":[{"file_id":"11992","success":1,"access_level":"open_access","date_created":"2022-08-28T07:56:19Z","content_type":"application/pdf","creator":"bbickel","file_name":"Chen-2022-High-LevelPuzzle_authorVersion.pdf","date_updated":"2022-08-28T07:56:19Z","relation":"main_file","checksum":"0b51651be45b1b33f2072bd5d2686c69","file_size":16896871}],"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/unlocking-interlocking-riddles/","relation":"press_release"}]},"acknowledgement":"We thank the reviewers for the valuable comments, David Gontier for sharing the source code of the baseline design approach, Christian Hafner for proofreading the paper, Keenan Crane for the 3D model of Cow, and Thingiverse for the 3D models of Moai and Owl. This work was supported by the SUTD Start-up Research Grant (Number: SRG ISTD 2019 148), the Swiss National Science Foundation (NCCR Digital Fabrication Agreement #51NF40-141853), and\r\nthe European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 715767 – MATERIALIZABLE).","external_id":{"isi":["000830989200018"]},"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","scopus_import":"1","file_date_updated":"2022-08-28T07:56:19Z","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767"}],"citation":{"apa":"Chen, R., Wang, Z., Song, P., &#38; Bickel, B. (2022). Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>","chicago":"Chen, Rulin, Ziqi Wang, Peng Song, and Bernd Bickel. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>.","ama":"Chen R, Wang Z, Song P, Bickel B. Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>","short":"R. Chen, Z. Wang, P. Song, B. Bickel, ACM Transactions on Graphics 41 (2022).","ieee":"R. Chen, Z. Wang, P. Song, and B. Bickel, “Computational design of high-level interlocking puzzles,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ista":"Chen R, Wang Z, Song P, Bickel B. 2022. Computational design of high-level interlocking puzzles. ACM Transactions on Graphics. 41(4), 150.","mla":"Chen, Rulin, et al. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 150, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>."},"article_number":"150","has_accepted_license":"1","language":[{"iso":"eng"}]},{"_id":"11737","day":"15","publisher":"American Physical Society","ddc":["530"],"publication":"Physical Review B","volume":106,"article_type":"original","title":"Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells","abstract":[{"lang":"eng","text":"Spin-orbit coupling in thin HgTe quantum wells results in a relativistic-like electron band structure, making it a versatile solid state platform to observe and control nontrivial electrodynamic phenomena. Here we report an observation of universal terahertz (THz) transparency determined by fine-structure constant α≈1/137 in 6.5-nm-thick HgTe layer, close to the critical thickness separating phases with topologically different electronic band structure. Using THz spectroscopy in a magnetic field we obtain direct evidence of asymmetric spin splitting of the Dirac cone. This particle-hole asymmetry facilitates optical control of edge spin currents in the quantum wells."}],"intvolume":"       106","date_created":"2022-08-07T22:01:58Z","quality_controlled":"1","date_published":"2022-07-15T00:00:00Z","issue":"4","year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"scopus_import":"1","file_date_updated":"2022-08-08T06:58:22Z","has_accepted_license":"1","article_number":"045302","citation":{"short":"U. Dziom, A. Shuvaev, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, Z. Alpichshev, A. Pimenov, Physical Review B 106 (2022).","ieee":"U. Dziom <i>et al.</i>, “Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells,” <i>Physical Review B</i>, vol. 106, no. 4. American Physical Society, 2022.","ista":"Dziom U, Shuvaev A, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon ZD, Alpichshev Z, Pimenov A. 2022. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. Physical Review B. 106(4), 045302.","mla":"Dziom, Uladzislau, et al. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>, vol. 106, no. 4, 045302, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>.","apa":"Dziom, U., Shuvaev, A., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov, N. N., … Pimenov, A. (2022). Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>","chicago":"Dziom, Uladzislau, A. Shuvaev, J. Gospodarič, E. G. Novik, A. A. Dobretsova, N. N. Mikhailov, Z. D. Kvon, Zhanybek Alpichshev, and A. Pimenov. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>.","ama":"Dziom U, Shuvaev A, Gospodarič J, et al. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. 2022;106(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>"},"language":[{"iso":"eng"}],"external_id":{"isi":["000834349200010"]},"file":[{"file_name":"2022_PhysRevB_Dziom.pdf","date_updated":"2022-08-08T06:58:22Z","file_size":774455,"checksum":"115aff9e0cde2f806cb26953d7262791","relation":"main_file","date_created":"2022-08-08T06:58:22Z","success":1,"access_level":"open_access","file_id":"11743","content_type":"application/pdf","creator":"dernst"}],"acknowledgement":"This work was supported by the Austrian Science Funds (W 1243, I 3456-N27, I 5539-N).","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/PhysRevB.106.045302","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","date_updated":"2023-08-03T12:38:57Z","department":[{"_id":"ZhAl"}],"author":[{"first_name":"Uladzislau","id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","orcid":"0000-0002-1648-0999","full_name":"Dziom, Uladzislau","last_name":"Dziom"},{"full_name":"Shuvaev, A.","last_name":"Shuvaev","first_name":"A."},{"full_name":"Gospodarič, J.","last_name":"Gospodarič","first_name":"J."},{"first_name":"E. G.","full_name":"Novik, E. G.","last_name":"Novik"},{"last_name":"Dobretsova","full_name":"Dobretsova, A. A.","first_name":"A. A."},{"last_name":"Mikhailov","full_name":"Mikhailov, N. N.","first_name":"N. N."},{"last_name":"Kvon","full_name":"Kvon, Z. D.","first_name":"Z. D."},{"first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek"},{"last_name":"Pimenov","full_name":"Pimenov, A.","first_name":"A."}],"article_processing_charge":"No"},{"status":"public","isi":1,"oa_version":"Preprint","type":"journal_article","doi":"10.1137/21M1410968","publication_status":"published","article_processing_charge":"No","author":[{"full_name":"Forkert, Dominik L","last_name":"Forkert","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maas, Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"department":[{"_id":"JaMa"}],"date_updated":"2025-04-15T08:31:31Z","language":[{"iso":"eng"}],"citation":{"ama":"Forkert DL, Maas J, Portinale L. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(4):4297-4333. doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>","apa":"Forkert, D. L., Maas, J., &#38; Portinale, L. (2022). Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>.","ista":"Forkert DL, Maas J, Portinale L. 2022. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. SIAM Journal on Mathematical Analysis. 54(4), 4297–4333.","short":"D.L. Forkert, J. Maas, L. Portinale, SIAM Journal on Mathematical Analysis 54 (2022) 4297–4333.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4. Society for Industrial and Applied Mathematics, pp. 4297–4333, 2022.","mla":"Forkert, Dominik L., et al. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4, Society for Industrial and Applied Mathematics, 2022, pp. 4297–333, doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>."},"project":[{"grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"W1245","name":"Dissipation and dispersion in nonlinear partial differential equations","_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"corr_author":"1","scopus_import":"1","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"external_id":{"arxiv":["2008.10962"],"isi":["000889274600001"]},"related_material":{"record":[{"id":"10022","relation":"earlier_version","status":"public"}]},"page":"4297-4333","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme grant 716117 and by the AustrianScience Fund (FWF) through grants F65 and W1245.","quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2008.10962"}],"date_created":"2022-08-07T22:01:59Z","intvolume":"        54","abstract":[{"lang":"eng","text":"We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality."}],"oa":1,"issue":"4","year":"2022","date_published":"2022-07-18T00:00:00Z","day":"18","arxiv":1,"publisher":"Society for Industrial and Applied Mathematics","_id":"11739","article_type":"original","title":"Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","ec_funded":1,"volume":54,"publication":"SIAM Journal on Mathematical Analysis","keyword":["Fokker--Planck equation","gradient flow","evolutionary $\\Gamma$-convergence"]},{"date_updated":"2024-10-09T21:03:03Z","department":[{"_id":"MaKw"}],"article_processing_charge":"No","author":[{"last_name":"Cooley","full_name":"Cooley, Oliver","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","first_name":"Oliver"},{"first_name":"Nicola","last_name":"Del Giudice","full_name":"Del Giudice, Nicola"},{"first_name":"Mihyun","full_name":"Kang, Mihyun","last_name":"Kang"},{"first_name":"Philipp","last_name":"Sprüssel","full_name":"Sprüssel, Philipp"}],"doi":"10.37236/10607","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","external_id":{"arxiv":["2005.07103"],"isi":["000836200300001"]},"file":[{"file_name":"2022_ElecJournCombinatorics_Cooley.pdf","date_updated":"2022-08-08T06:28:52Z","file_size":1768663,"checksum":"057c676dcee70236aa234d4ce6138c69","relation":"main_file","date_created":"2022-08-08T06:28:52Z","success":1,"access_level":"open_access","file_id":"11742","content_type":"application/pdf","creator":"dernst"}],"acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","publication_identifier":{"eissn":["1077-8926"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","scopus_import":"1","file_date_updated":"2022-08-08T06:28:52Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","corr_author":"1","article_number":"P3.27","has_accepted_license":"1","citation":{"short":"O. Cooley, N. Del Giudice, M. Kang, P. Sprüssel, Electronic Journal of Combinatorics 29 (2022).","ieee":"O. Cooley, N. Del Giudice, M. Kang, and P. Sprüssel, “Phase transition in cohomology groups of non-uniform random simplicial complexes,” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3. Electronic Journal of Combinatorics, 2022.","ista":"Cooley O, Del Giudice N, Kang M, Sprüssel P. 2022. Phase transition in cohomology groups of non-uniform random simplicial complexes. Electronic Journal of Combinatorics. 29(3), P3.27.","mla":"Cooley, Oliver, et al. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3, P3.27, Electronic Journal of Combinatorics, 2022, doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>.","apa":"Cooley, O., Del Giudice, N., Kang, M., &#38; Sprüssel, P. (2022). Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>","chicago":"Cooley, Oliver, Nicola Del Giudice, Mihyun Kang, and Philipp Sprüssel. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2022. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>.","ama":"Cooley O, Del Giudice N, Kang M, Sprüssel P. Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. 2022;29(3). doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>"},"language":[{"iso":"eng"}],"date_published":"2022-07-29T00:00:00Z","issue":"3","year":"2022","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"oa":1,"intvolume":"        29","abstract":[{"text":"We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].\r\nWe consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition.","lang":"eng"}],"date_created":"2022-08-07T22:01:59Z","quality_controlled":"1","publication":"Electronic Journal of Combinatorics","volume":29,"title":"Phase transition in cohomology groups of non-uniform random simplicial complexes","article_type":"original","_id":"11740","day":"29","publisher":"Electronic Journal of Combinatorics","arxiv":1,"ddc":["510"]},{"publication":"Journal of Mathematical Physics","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"volume":63,"ec_funded":1,"article_type":"original","title":"Low-energy spectrum and dynamics of the weakly interacting Bose gas","_id":"11783","publisher":"AIP Publishing","arxiv":1,"day":"10","ddc":["530"],"date_published":"2022-06-10T00:00:00Z","year":"2022","issue":"6","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"abstract":[{"text":"We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix.","lang":"eng"}],"intvolume":"        63","date_created":"2022-08-11T06:37:52Z","quality_controlled":"1","acknowledgement":"The author thanks Nataˇsa Pavlovic, Sören Petrat, Peter Pickl, Robert Seiringer, and Avy Soffer for the collaboration on Refs. 1, 2 and 21. Funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skℓodowska-Curie Grant Agreement\r\nNo. 754411 is gratefully acknowledged.","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"11784","success":1,"access_level":"open_access","date_created":"2022-08-11T07:03:02Z","relation":"main_file","checksum":"d0d32c338c1896680174be88c70968fa","file_size":5957888,"file_name":"2022_JourMathPhysics_Bossmann.pdf","date_updated":"2022-08-11T07:03:02Z"}],"external_id":{"isi":["000809648100002"],"arxiv":["2203.00730"]},"publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","scopus_import":"1","corr_author":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"file_date_updated":"2022-08-11T07:03:02Z","citation":{"short":"L. Bossmann, Journal of Mathematical Physics 63 (2022).","ista":"Bossmann L. 2022. Low-energy spectrum and dynamics of the weakly interacting Bose gas. Journal of Mathematical Physics. 63(6), 061102.","ieee":"L. Bossmann, “Low-energy spectrum and dynamics of the weakly interacting Bose gas,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6. AIP Publishing, 2022.","mla":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6, 061102, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>.","ama":"Bossmann L. Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. 2022;63(6). doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>","apa":"Bossmann, L. (2022). Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>","chicago":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>."},"has_accepted_license":"1","article_number":"061102","language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:43:58Z","department":[{"_id":"RoSe"}],"author":[{"full_name":"Bossmann, Lea","last_name":"Bossmann","first_name":"Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","orcid":"0000-0002-6854-1343"}],"article_processing_charge":"Yes (via OA deal)","publication_status":"published","doi":"10.1063/5.0089983","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public"},{"date_published":"2022-04-29T00:00:00Z","year":"2022","alternative_title":["LIPIcs"],"oa":1,"abstract":[{"text":"In recent years, significant advances have been made in the design and analysis of fully dynamic algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. Here, we present a quick reference guide to recent engineering and theory results in the area of fully dynamic graph algorithms.","lang":"eng"}],"date_created":"2022-08-11T14:35:52Z","intvolume":"       221","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.SAND.2022.1","open_access":"1"}],"quality_controlled":"1","publication":"1st Symposium on Algorithmic Foundations of Dynamic Networks","volume":221,"title":"Recent advances in fully dynamic graph algorithms","_id":"11808","arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"29","date_updated":"2024-11-06T08:23:49Z","author":[{"full_name":"Hanauer, Kathrin","last_name":"Hanauer","first_name":"Kathrin"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Christian","full_name":"Schulz, Christian","last_name":"Schulz"}],"article_processing_charge":"No","publication_status":"published","doi":"10.4230/LIPIcs.SAND.2022.1","type":"conference","oa_version":"Published Version","status":"public","external_id":{"arxiv":["2102.11169"]},"publication_identifier":{"isbn":["9783959772242"],"eissn":["1868-8969"]},"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2022-03-30","name":"SAND: Symposium on Algorithmic Foundations of Dynamic Networks","start_date":"2022-03-28","location":"Virtual"},"extern":"1","scopus_import":"1","citation":{"ieee":"K. Hanauer, M. Henzinger, and C. Schulz, “Recent advances in fully dynamic graph algorithms,” in <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Virtual, 2022, vol. 221.","ista":"Hanauer K, Henzinger M, Schulz C. 2022. Recent advances in fully dynamic graph algorithms. 1st Symposium on Algorithmic Foundations of Dynamic Networks. SAND: Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 221, 1.","short":"K. Hanauer, M. Henzinger, C. Schulz, in:, 1st Symposium on Algorithmic Foundations of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","mla":"Hanauer, Kathrin, et al. “Recent Advances in Fully Dynamic Graph Algorithms.” <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, vol. 221, 1, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">10.4230/LIPIcs.SAND.2022.1</a>.","apa":"Hanauer, K., Henzinger, M., &#38; Schulz, C. (2022). Recent advances in fully dynamic graph algorithms. In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i> (Vol. 221). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">https://doi.org/10.4230/LIPIcs.SAND.2022.1</a>","chicago":"Hanauer, Kathrin, Monika Henzinger, and Christian Schulz. “Recent Advances in Fully Dynamic Graph Algorithms.” In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Vol. 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">https://doi.org/10.4230/LIPIcs.SAND.2022.1</a>.","ama":"Hanauer K, Henzinger M, Schulz C. Recent advances in fully dynamic graph algorithms. In: <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>. Vol 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">10.4230/LIPIcs.SAND.2022.1</a>"},"article_number":"1","language":[{"iso":"eng"}]},{"date_published":"2022-04-29T00:00:00Z","year":"2022","alternative_title":["LIPIcs"],"oa":1,"abstract":[{"text":"This paper presents a comprehensive study of algorithms for maintaining the number of all connected four-vertex subgraphs in a dynamic graph. Specifically, our algorithms maintain the number of paths of length three in deterministic amortized O(m^{1/2}) update time, and any other connected four-vertex subgraph which is not a clique in deterministic amortized update time O(m^{2/3}). Queries can be answered in constant time. We also study the query times for subgraphs containing an arbitrary edge that is supplied only with the query as well as the case where only subgraphs containing a vertex s that is fixed beforehand are considered. For length-3 paths, paws, 4-cycles, and diamonds our bounds match or are not far from (conditional) lower bounds: Based on the OMv conjecture we show that any dynamic algorithm that detects the existence of paws, diamonds, or 4-cycles or that counts length-3 paths takes update time Ω(m^{1/2-δ}).\r\nAdditionally, for 4-cliques and all connected induced subgraphs, we show a lower bound of Ω(m^{1-δ}) for any small constant δ > 0 for the amortized update time, assuming the static combinatorial 4-clique conjecture holds. This shows that the O(m) algorithm by Eppstein et al. [David Eppstein et al., 2012] for these subgraphs cannot be improved by a polynomial factor.","lang":"eng"}],"intvolume":"       221","date_created":"2022-08-12T06:57:55Z","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.SAND.2022.18","open_access":"1"}],"quality_controlled":"1","publication":"1st Symposium on Algorithmic Foundations of Dynamic Networks","volume":221,"title":"Fully dynamic four-vertex subgraph counting","_id":"11812","arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"29","date_updated":"2024-11-06T08:22:47Z","author":[{"full_name":"Hanauer, Kathrin","last_name":"Hanauer","first_name":"Kathrin"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"last_name":"Hua","full_name":"Hua, Qi Cheng","first_name":"Qi Cheng"}],"article_processing_charge":"No","publication_status":"published","doi":"10.4230/LIPIcs.SAND.2022.18","type":"conference","oa_version":"Published Version","status":"public","external_id":{"arxiv":["2106.15524"]},"publication_identifier":{"isbn":["9783959772242"],"issn":["1868-8969"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","conference":{"end_date":"2022-04-30","name":"SAND: Symposium on Algorithmic Foundations of Dynamic Networks","start_date":"2022-04-28","location":"Virtual"},"extern":"1","scopus_import":"1","citation":{"apa":"Hanauer, K., Henzinger, M., &#38; Hua, Q. C. (2022). Fully dynamic four-vertex subgraph counting. In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i> (Vol. 221). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">https://doi.org/10.4230/LIPIcs.SAND.2022.18</a>","chicago":"Hanauer, Kathrin, Monika Henzinger, and Qi Cheng Hua. “Fully Dynamic Four-Vertex Subgraph Counting.” In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Vol. 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">https://doi.org/10.4230/LIPIcs.SAND.2022.18</a>.","ama":"Hanauer K, Henzinger M, Hua QC. Fully dynamic four-vertex subgraph counting. In: <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>. Vol 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">10.4230/LIPIcs.SAND.2022.18</a>","ieee":"K. Hanauer, M. Henzinger, and Q. C. Hua, “Fully dynamic four-vertex subgraph counting,” in <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Virtual, 2022, vol. 221.","short":"K. Hanauer, M. Henzinger, Q.C. Hua, in:, 1st Symposium on Algorithmic Foundations of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ista":"Hanauer K, Henzinger M, Hua QC. 2022. Fully dynamic four-vertex subgraph counting. 1st Symposium on Algorithmic Foundations of Dynamic Networks. SAND: Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 221, 18.","mla":"Hanauer, Kathrin, et al. “Fully Dynamic Four-Vertex Subgraph Counting.” <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, vol. 221, 18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">10.4230/LIPIcs.SAND.2022.18</a>."},"article_number":"18","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"citation":{"chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>.","apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2109718119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>.","ieee":"Z. Toprakcioglu <i>et al.</i>, “Adsorption free energy predicts amyloid protein nucleation rates,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A, Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2109718119."},"article_number":"e2109718119","has_accepted_license":"1","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960"}],"file_date_updated":"2023-10-04T09:05:44Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"14386","access_level":"open_access","success":1,"date_created":"2023-10-04T09:05:44Z","relation":"main_file","checksum":"0fe3878896cbeb6c44e29222ec2f336a","file_size":2476021,"file_name":"2022_PNAS_Toprakcioglu.pdf","date_updated":"2023-10-04T09:05:44Z"}],"acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969). We are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.), the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for Misfolding Diseases (CMD).","external_id":{"isi":["000903753500002"],"pmid":["35901206"]},"status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1073/pnas.2109718119","article_processing_charge":"No","author":[{"first_name":"Zenon","last_name":"Toprakcioglu","full_name":"Toprakcioglu, Zenon"},{"full_name":"Kamada, Ayaka","last_name":"Kamada","first_name":"Ayaka"},{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"first_name":"Mengqi","last_name":"Xie","full_name":"Xie, Mengqi"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"last_name":"Wei","full_name":"Wei, Jiapeng","first_name":"Jiapeng"},{"full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"department":[{"_id":"AnSa"}],"date_updated":"2025-06-12T06:21:34Z","pmid":1,"ddc":["570"],"publisher":"National Academy of Sciences","day":"28","_id":"11841","ec_funded":1,"title":"Adsorption free energy predicts amyloid protein nucleation rates","article_type":"original","volume":119,"publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","abstract":[{"lang":"eng","text":"Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process."}],"intvolume":"       119","date_created":"2022-08-14T22:01:45Z","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"year":"2022","issue":"31","date_published":"2022-07-28T00:00:00Z"},{"related_material":{"record":[{"id":"10316","status":"public","relation":"earlier_version"}]},"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strains CFT073, UTI89, and 536, Frank Assen, Vlad Gavra, Maximilian Götz, Bor Kavčič, Jonna Alanko, and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp, and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to IG, the European Research Council (CoG 724373), and the Austrian Science Fund (FWF P29911) to MS.","file":[{"date_created":"2022-08-16T08:57:37Z","success":1,"access_level":"open_access","file_id":"11861","content_type":"application/pdf","creator":"cchlebak","file_name":"2022_eLife_Tomasek.pdf","date_updated":"2022-08-16T08:57:37Z","file_size":2057577,"checksum":"002a3c7c7ea5caa9af9cfbea308f6ea4","relation":"main_file"}],"external_id":{"isi":["000838410200001"],"pmid":["35881547"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["2050-084X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","scopus_import":"1","corr_author":"1","file_date_updated":"2022-08-16T08:57:37Z","project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373"},{"call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911"}],"citation":{"ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, ELife 11 (2022).","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. 2022. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. eLife. 11, e78995.","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>ELife</i>, vol. 11, e78995, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.78995\">10.7554/eLife.78995</a>.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.78995\">10.7554/eLife.78995</a>","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (2022). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.78995\">https://doi.org/10.7554/eLife.78995</a>","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.78995\">https://doi.org/10.7554/eLife.78995</a>."},"article_number":"e78995","has_accepted_license":"1","language":[{"iso":"eng"}],"date_updated":"2025-04-15T07:17:32Z","department":[{"_id":"MiSi"},{"_id":"CaGu"}],"author":[{"full_name":"Tomasek, Kathrin","last_name":"Tomasek","first_name":"Kathrin","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner"},{"last_name":"Glatzová","full_name":"Glatzová, Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","first_name":"Ivana"},{"last_name":"Lukesch","full_name":"Lukesch, Michael S.","first_name":"Michael S."},{"last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"article_processing_charge":"Yes","publication_status":"published","doi":"10.7554/eLife.78995","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","publication":"eLife","volume":11,"ec_funded":1,"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","article_type":"original","_id":"11843","publisher":"eLife Sciences Publications","day":"26","ddc":["570"],"pmid":1,"date_published":"2022-07-26T00:00:00Z","year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"abstract":[{"lang":"eng","text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease."}],"intvolume":"        11","date_created":"2022-08-14T22:01:46Z","quality_controlled":"1"},{"status":"public","isi":1,"oa_version":"Published Version","type":"conference","doi":"10.1145/3519270.3538435","publication_status":"published","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sasha","last_name":"Voitovych","full_name":"Voitovych, Sasha"}],"department":[{"_id":"DaAl"}],"date_updated":"2025-12-30T09:04:17Z","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"ista":"Alistarh D-A, Rybicki J, Voitovych S. 2022. Near-optimal leader election in population protocols on graphs. Proceedings of the Annual ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 246–256.","ieee":"D.-A. Alistarh, J. Rybicki, and S. Voitovych, “Near-optimal leader election in population protocols on graphs,” in <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>, Salerno, Italy, 2022, pp. 246–256.","short":"D.-A. Alistarh, J. Rybicki, S. Voitovych, in:, Proceedings of the Annual ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2022, pp. 246–256.","mla":"Alistarh, Dan-Adrian, et al. “Near-Optimal Leader Election in Population Protocols on Graphs.” <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2022, pp. 246–56, doi:<a href=\"https://doi.org/10.1145/3519270.3538435\">10.1145/3519270.3538435</a>.","apa":"Alistarh, D.-A., Rybicki, J., &#38; Voitovych, S. (2022). Near-optimal leader election in population protocols on graphs. In <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i> (pp. 246–256). Salerno, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519270.3538435\">https://doi.org/10.1145/3519270.3538435</a>","chicago":"Alistarh, Dan-Adrian, Joel Rybicki, and Sasha Voitovych. “Near-Optimal Leader Election in Population Protocols on Graphs.” In <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>, 246–56. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519270.3538435\">https://doi.org/10.1145/3519270.3538435</a>.","ama":"Alistarh D-A, Rybicki J, Voitovych S. Near-optimal leader election in population protocols on graphs. In: <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2022:246-256. doi:<a href=\"https://doi.org/10.1145/3519270.3538435\">10.1145/3519270.3538435</a>"},"file_date_updated":"2022-08-16T08:05:15Z","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"corr_author":"1","scopus_import":"1","conference":{"end_date":"2022-07-29","name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2022-07-25","location":"Salerno, Italy"},"month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"isbn":["9781450392624"]},"external_id":{"isi":["001031439100030"],"arxiv":["2205.12597"]},"page":"246-256","file":[{"access_level":"open_access","success":1,"date_created":"2022-08-16T08:05:15Z","file_id":"11854","creator":"cchlebak","content_type":"application/pdf","date_updated":"2022-08-16T08:05:15Z","file_name":"2022_PODC_Alistarh.pdf","file_size":1593474,"relation":"main_file","checksum":"4c6b29172b8e355b4fbc364a2e0827b2"}],"acknowledgement":"We thank the anonymous reviewers for their helpful comments. We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","related_material":{"record":[{"id":"19969","relation":"later_version","status":"public"}]},"quality_controlled":"1","date_created":"2022-08-14T22:01:46Z","abstract":[{"text":"In the stochastic population protocol model, we are given a connected graph with n nodes, and in every time step, a scheduler samples an edge of the graph uniformly at random and the nodes connected by this edge interact. A fundamental task in this model is stable leader election, in which all nodes start in an identical state and the aim is to reach a configuration in which (1) exactly one node is elected as leader and (2) this node remains as the unique leader no matter what sequence of interactions follows. On cliques, the complexity of this problem has recently been settled: time-optimal protocols stabilize in Θ(n log n) expected steps using Θ(log log n) states, whereas protocols that use O(1) states require Θ(n2) expected steps.\r\n\r\nIn this work, we investigate the complexity of stable leader election on general graphs. We provide the first non-trivial time lower bounds for leader election on general graphs, showing that, when moving beyond cliques, the complexity landscape of leader election becomes very diverse: the time required to elect a leader can range from O(1) to Θ(n3) expected steps. On the upper bound side, we first observe that there exists a protocol that is time-optimal on many graph families, but uses polynomially-many states. In contrast, we give a near-time-optimal protocol that uses only O(log2n) states that is at most a factor log n slower. Finally, we show that the constant-state protocol of Beauquier et al. [OPODIS 2013] is at most a factor n log n slower than the fast polynomial-state protocol. Moreover, among constant-state protocols, this protocol has near-optimal average case complexity on dense random graphs.","lang":"eng"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2022","date_published":"2022-07-21T00:00:00Z","ddc":["000"],"day":"21","arxiv":1,"publisher":"Association for Computing Machinery","_id":"11844","title":"Near-optimal leader election in population protocols on graphs","ec_funded":1,"publication":"Proceedings of the Annual ACM Symposium on Principles of Distributed Computing"},{"ddc":["510"],"_id":"11858","day":"01","publisher":"Springer Nature","volume":22,"article_type":"original","title":"Nonlinear parabolic stochastic evolution equations in critical spaces part II","publication":"Journal of Evolution Equations","keyword":["Mathematics (miscellaneous)"],"abstract":[{"text":"This paper is a continuation of Part I of this project, where we developed a new local well-posedness theory for nonlinear stochastic PDEs with Gaussian noise. In the current Part II we consider blow-up criteria and regularization phenomena. As in Part I we can allow nonlinearities with polynomial growth and rough initial values from critical spaces. In the first main result we obtain several new blow-up criteria for quasi- and semilinear stochastic evolution equations. In particular, for semilinear equations we obtain a Serrin type blow-up criterium, which extends a recent result of Prüss–Simonett–Wilke (J Differ Equ 264(3):2028–2074, 2018) to the stochastic setting. Blow-up criteria can be used to prove global well-posedness for SPDEs. As in Part I, maximal regularity techniques and weights in time play a central role in the proofs. Our second contribution is a new method to bootstrap Sobolev and Hölder regularity in time and space, which does not require smoothness of the initial data. The blow-up criteria are at the basis of these new methods. Moreover, in applications the bootstrap results can be combined with our blow-up criteria, to obtain efficient ways to prove global existence. This gives new results even in classical 𝐿2-settings, which we illustrate for a concrete SPDE. In future works in preparation we apply the results of the current paper to obtain global well-posedness results and regularity for several concrete SPDEs. These include stochastic Navier–Stokes equations, reaction– diffusion equations and the Allen–Cahn equation. Our setting allows to put these SPDEs into a more flexible framework, where less restrictions on the nonlinearities are needed, and we are able to treat rough initial values from critical spaces. Moreover, we will obtain higher-order regularity results.","lang":"eng"}],"date_created":"2022-08-16T08:39:43Z","intvolume":"        22","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2022-06-01T00:00:00Z","issue":"2","year":"2022","article_number":"56","has_accepted_license":"1","citation":{"ieee":"A. Agresti and M. Veraar, “Nonlinear parabolic stochastic evolution equations in critical spaces part II,” <i>Journal of Evolution Equations</i>, vol. 22, no. 2. Springer Nature, 2022.","short":"A. Agresti, M. Veraar, Journal of Evolution Equations 22 (2022).","ista":"Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations in critical spaces part II. Journal of Evolution Equations. 22(2), 56.","mla":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part II.” <i>Journal of Evolution Equations</i>, vol. 22, no. 2, 56, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s00028-022-00786-7\">10.1007/s00028-022-00786-7</a>.","apa":"Agresti, A., &#38; Veraar, M. (2022). Nonlinear parabolic stochastic evolution equations in critical spaces part II. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00786-7\">https://doi.org/10.1007/s00028-022-00786-7</a>","chicago":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part II.” <i>Journal of Evolution Equations</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00028-022-00786-7\">https://doi.org/10.1007/s00028-022-00786-7</a>.","ama":"Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in critical spaces part II. <i>Journal of Evolution Equations</i>. 2022;22(2). doi:<a href=\"https://doi.org/10.1007/s00028-022-00786-7\">10.1007/s00028-022-00786-7</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2022-08-16T08:52:46Z","corr_author":"1","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000809108500001"]},"acknowledgement":"The authors thank Emiel Lorist for helpful comments. The authors thank the anonymous referees for their helpful remarks to improve the presentation.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","file":[{"date_updated":"2022-08-16T08:52:46Z","file_name":"2022_Journal of Evolution Equations_Agresti.pdf","file_size":1758371,"relation":"main_file","checksum":"59b99d1b48b6bd40983e7ce298524a21","access_level":"open_access","success":1,"date_created":"2022-08-16T08:52:46Z","file_id":"11862","creator":"kschuh","content_type":"application/pdf"}],"publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"isi":1,"status":"public","doi":"10.1007/s00028-022-00786-7","publication_status":"published","oa_version":"Published Version","type":"journal_article","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"date_updated":"2024-10-09T21:03:06Z","department":[{"_id":"JuFi"}]}]