[{"contributor":[{"orcid":"0000-0001-8635-0877","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","contributor_type":"contact_person","last_name":"Siegert"}],"status":"public","corr_author":"1","_id":"11542","type":"research_data","title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","file_date_updated":"2022-07-08T10:56:52Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"id":"11995","status":"public","relation":"used_in_publication"}],"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1","relation":"contains"}]},"date_created":"2022-07-08T11:03:02Z","doi":"10.15479/AT:ISTA:11542","date_updated":"2025-04-15T07:27:21Z","year":"2022","date_published":"2022-01-01T00:00:00Z","file":[{"file_size":135784571,"success":1,"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","date_created":"2022-07-08T10:56:52Z","date_updated":"2022-07-08T10:56:52Z","creator":"rschulz","access_level":"open_access","relation":"main_file","file_name":"Source Data.xlsx","file_id":"11543","checksum":"71e8186583f3adbb6c69a88ac9e6e49b"}],"publisher":"Institute of Science and Technology Austria","oa_version":"None","citation":{"short":"R. Schulz, (2022).","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>"},"has_accepted_license":"1","author":[{"orcid":"0000-0001-5297-733X","full_name":"Schulz, Rouven","last_name":"Schulz","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"}],"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)"},"article_processing_charge":"No"},{"year":"2022","article_number":"111439","publication_identifier":{"issn":["0021-9991"]},"doi":"10.1016/j.jcp.2022.111439","acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"date_created":"2022-07-11T12:19:59Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","article_type":"original","publication_status":"published","day":"15","author":[{"last_name":"Kalinov","full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","first_name":"Aleksei","orcid":"0000-0003-2189-3904"},{"last_name":"Osinskiy","full_name":"Osinskiy, A.I.","first_name":"A.I."},{"first_name":"S.A.","full_name":"Matveev, S.A.","last_name":"Matveev"},{"first_name":"W.","full_name":"Otieno, W.","last_name":"Otieno"},{"first_name":"N.V.","full_name":"Brilliantov, N.V.","last_name":"Brilliantov"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.09481","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise."}],"date_published":"2022-10-15T00:00:00Z","external_id":{"isi":["000917225500013"],"arxiv":["2103.09481"]},"publication":"Journal of Computational Physics","date_updated":"2024-10-21T06:01:47Z","oa":1,"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"ddc":["518"],"arxiv":1,"scopus_import":"1","_id":"11556","status":"public","article_processing_charge":"No","citation":{"apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022."},"quality_controlled":"1","volume":467,"publisher":"Elsevier","intvolume":"       467","month":"10"},{"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"}],"OA_place":"publisher","month":"07","page":"248","article_processing_charge":"No","ec_funded":1,"has_accepted_license":"1","citation":{"apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022."},"degree_awarded":"PhD","ddc":["575"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2022-07-25T11:48:45Z","status":"public","corr_author":"1","_id":"11626","date_updated":"2026-06-18T19:02:05Z","oa":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8138"},{"id":"7142","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10411"},{"id":"8931","relation":"part_of_dissertation","status":"public"},{"id":"7465","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9287"},{"id":"6260","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"date_published":"2022-07-20T00:00:00Z","file":[{"content_type":"application/pdf","date_created":"2022-07-25T09:08:47Z","file_size":9730864,"creator":"mgallei","date_updated":"2022-07-25T09:08:47Z","file_id":"11645","file_name":"Thesis_Gallei.pdf","access_level":"open_access","relation":"main_file","checksum":"bd7ac35403cf5b4b2607287d2a104b3a"},{"file_name":"Thesis_Gallei_source.docx","file_id":"11646","access_level":"closed","relation":"source_file","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2022-07-25T09:09:09Z","file_size":19560720,"creator":"mgallei","date_updated":"2022-07-25T09:39:58Z"},{"file_name":"Thesis_Gallei_to_print.pdf","file_id":"11647","access_level":"closed","relation":"source_file","description":"This is the print version of the thesis including the full appendix","checksum":"3994f7f20058941b5bb8a16886b21e71","date_created":"2022-07-25T09:09:32Z","content_type":"application/pdf","file_size":24542837,"creator":"mgallei","date_updated":"2022-07-25T09:39:58Z"},{"file_size":15435966,"content_type":"application/pdf","date_created":"2022-07-25T11:48:45Z","date_updated":"2022-07-25T11:48:45Z","creator":"mgallei","relation":"main_file","access_level":"open_access","file_name":"Thesis_Gallei_Appendix.pdf","file_id":"11650","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b"}],"author":[{"orcid":"0000-0003-1286-7368","last_name":"Gallei","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"}],"day":"20","oa_version":"Published Version","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"type":"dissertation","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","language":[{"iso":"eng"}],"publication_status":"published","doi":"10.15479/at:ista:11626","year":"2022","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2022-07-20T11:21:53Z","alternative_title":["ISTA Thesis"]},{"citation":{"short":"M.N. Elkrewi, (2022).","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>"},"has_accepted_license":"1","oa_version":"Published Version","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)"},"day":"05","article_processing_charge":"No","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"}],"date_published":"2022-08-05T00:00:00Z","file":[{"creator":"melkrewi","date_updated":"2022-08-08T22:30:04Z","content_type":"application/x-zip-compressed","date_created":"2022-07-26T12:37:52Z","file_size":2209382998,"checksum":"5f1d7c6d7ab5375ed2564521432bed0c","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","title":"Supplementary Datasets","file_id":"11655","file_name":"Data.zip","access_level":"open_access","relation":"main_file","embargo":"2022-08-07"}],"month":"08","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"date_created":"2022-07-26T11:01:47Z","related_material":{"record":[{"id":"12248","status":"public","relation":"used_in_publication"}]},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","doi":"10.15479/AT:ISTA:11653","date_updated":"2025-04-15T08:34:17Z","corr_author":"1","_id":"11653","contributor":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Luca","last_name":"Sax"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"first_name":"Francisco","last_name":"Hontoria "},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"status":"public","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file_date_updated":"2022-08-08T22:30:04Z","ddc":["570"],"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","type":"research_data"},{"ddc":["510"],"file_date_updated":"2022-07-27T09:25:53Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"corr_author":"1","_id":"11658","status":"public","date_updated":"2026-04-07T12:58:48Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"15380"},{"status":"public","relation":"dissertation_contains","id":"15094"}]},"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","month":"07","ec_funded":1,"article_processing_charge":"No","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)"},"has_accepted_license":"1","citation":{"ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik."},"quality_controlled":"1","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342"},{"call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","publication_status":"draft","year":"2022","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","date_created":"2022-07-27T09:27:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements."}],"file":[{"checksum":"b2f511e8b1cae5f1892b0cdec341acac","relation":"main_file","access_level":"open_access","file_id":"11659","file_name":"D-S-E.pdf","date_updated":"2022-07-27T09:25:53Z","creator":"scultrer","file_size":639266,"content_type":"application/pdf","date_created":"2022-07-27T09:25:53Z"}],"date_published":"2022-07-27T00:00:00Z","publication":"Leibniz International Proceedings on Mathematics","day":"27","author":[{"full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890"},{"orcid":"0000-0001-6249-0832","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"oa_version":"Submitted Version"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","month":"07","article_processing_charge":"No","ec_funded":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)"},"quality_controlled":"1","has_accepted_license":"1","citation":{"ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>."},"ddc":["510"],"file_date_updated":"2022-07-27T09:30:30Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"status":"public","corr_author":"1","_id":"11660","date_updated":"2026-04-07T12:58:47Z","related_material":{"record":[{"id":"15094","relation":"dissertation_contains","status":"public"}]},"oa":1,"abstract":[{"text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. ","lang":"eng"}],"publication":"LIPIcs","file":[{"checksum":"95903f9d1649e8e437a967b6f2f64730","access_level":"open_access","relation":"main_file","file_name":"window 1.pdf","file_id":"11661","date_updated":"2022-07-27T09:30:30Z","creator":"scultrer","file_size":564836,"content_type":"application/pdf","date_created":"2022-07-27T09:30:30Z"}],"date_published":"2022-07-25T00:00:00Z","author":[{"first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","first_name":"Morteza"}],"day":"25","oa_version":"Submitted Version","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"submitted","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. ","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"date_created":"2022-07-27T09:31:15Z"},{"publisher":"National Academy of Sciences","intvolume":"       119","month":"07","article_processing_charge":"No","tmp":{"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","short":"CC BY-NC-ND (4.0)"},"has_accepted_license":"1","citation":{"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>.","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>","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.","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>.","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>","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.","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)."},"volume":119,"quality_controlled":"1","ddc":["580"],"file_date_updated":"2022-08-08T07:42:09Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"scopus_import":"1","_id":"11723","corr_author":"1","status":"public","date_updated":"2025-05-14T11:01:00Z","oa":1,"abstract":[{"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.","lang":"eng"}],"date_published":"2022-07-25T00:00:00Z","file":[{"checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","file_id":"11747","file_name":"2022_PNAS_Li.pdf","relation":"main_file","access_level":"open_access","creator":"dernst","date_updated":"2022-08-08T07:42:09Z","content_type":"application/pdf","date_created":"2022-08-08T07:42:09Z","success":1,"file_size":2506262}],"external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"25","author":[{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"},{"first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen"},{"first_name":"Saqer S.","full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"issue":"31","oa_version":"Published Version","pmid":1,"isi":1,"language":[{"iso":"eng"}],"project":[{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","type":"journal_article","article_type":"original","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2022","article_number":"e2121058119","keyword":["Multidisciplinary"],"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).”","doi":"10.1073/pnas.2121058119","date_created":"2022-08-04T20:06:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"call_identifier":"H2020","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"type":"journal_article","title":"The BCS energy gap at high density","isi":1,"language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"acknowledgement":"We are grateful to Robert Seiringer for helpful discussions and many valuable comments\r\non an earlier version of the manuscript. J.H. acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond’ No. 101020331. Open access funding provided by Institute of Science and Technology (IST Austria)","doi":"10.1007/s10955-022-02965-9","year":"2022","publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"article_number":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2022-08-05T11:36:56Z","abstract":[{"text":"We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic formula, which strongly depends on the strength of the interaction potential V on the Fermi surface. In combination with the recent result by one of us (Math. Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities, we prove the universality of the ratio of the energy gap and the critical temperature.","lang":"eng"}],"publication":"Journal of Statistical Physics","external_id":{"isi":["000833007200002"]},"file":[{"checksum":"b398c4dbf65f71d417981d6e366427e9","access_level":"open_access","relation":"main_file","file_name":"2022_JourStatisticalPhysics_Henheik.pdf","file_id":"11746","date_updated":"2022-08-08T07:36:34Z","creator":"dernst","file_size":419563,"success":1,"content_type":"application/pdf","date_created":"2022-08-08T07:36:34Z"}],"date_published":"2022-07-29T00:00:00Z","author":[{"orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","last_name":"Henheik","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288"}],"day":"29","oa_version":"Published Version","scopus_import":"1","ddc":["530"],"file_date_updated":"2022-08-08T07:36:34Z","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"status":"public","corr_author":"1","_id":"11732","date_updated":"2026-04-07T13:01:40Z","oa":1,"related_material":{"record":[{"id":"19540","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"18135"}]},"intvolume":"       189","publisher":"Springer Nature","month":"07","article_processing_charge":"Yes (via OA deal)","ec_funded":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)"},"volume":189,"quality_controlled":"1","has_accepted_license":"1","citation":{"chicago":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>.","ama":"Henheik SJ, Lauritsen AB. The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. 2022;189. doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>","ieee":"S. J. Henheik and A. B. Lauritsen, “The BCS energy gap at high density,” <i>Journal of Statistical Physics</i>, vol. 189. Springer Nature, 2022.","apa":"Henheik, S. J., &#38; Lauritsen, A. B. (2022). The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>","mla":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>, vol. 189, 5, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>.","ista":"Henheik SJ, Lauritsen AB. 2022. The BCS energy gap at high density. Journal of Statistical Physics. 189, 5.","short":"S.J. Henheik, A.B. Lauritsen, Journal of Statistical Physics 189 (2022)."}},{"oa":1,"related_material":{"record":[{"id":"20147","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-04-07T12:02:56Z","_id":"11775","corr_author":"1","status":"public","ddc":["000"],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2023-01-20T07:34:50Z","scopus_import":"1","has_accepted_license":"1","citation":{"ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative specifications. 22nd International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 13498, 200–220.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference on Runtime Verification, Springer Nature, 2022, pp. 200–220.","mla":"Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.” <i>22nd International Conference on Runtime Verification</i>, vol. 13498, Springer Nature, 2022, pp. 200–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2022). Abstract monitors for quantitative specifications. In <i>22nd International Conference on Runtime Verification</i> (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for quantitative specifications,” in <i>22nd International Conference on Runtime Verification</i>, Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract Monitors for Quantitative Specifications.” In <i>22nd International Conference on Runtime Verification</i>, 13498:200–220. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications. In: <i>22nd International Conference on Runtime Verification</i>. Vol 13498. Springer Nature; 2022:200-220. doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>"},"volume":13498,"quality_controlled":"1","ec_funded":1,"article_processing_charge":"Yes","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)"},"page":"200-220","month":"09","publisher":"Springer Nature","intvolume":"     13498","alternative_title":["LNCS"],"date_created":"2022-08-08T17:09:09Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","conference":{"end_date":"2022-09-30","name":"RV: Runtime Verification","start_date":"2022-09-28","location":"Tbilisi, Georgia"},"publication_identifier":{"issn":["0302-9743"]},"year":"2022","doi":"10.1007/978-3-031-17196-3_11","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"type":"conference","title":"Abstract monitors for quantitative specifications","oa_version":"Published Version","day":"23","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"},{"full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"external_id":{"isi":["000866539700011"]},"file":[{"file_size":477110,"date_created":"2023-01-20T07:34:50Z","content_type":"application/pdf","success":1,"date_updated":"2023-01-20T07:34:50Z","creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"12317","file_name":"2022_LNCS_RV_Henzinger.pdf","checksum":"05c7dcfbb9053a98f46441fb2eccb213"}],"date_published":"2022-09-23T00:00:00Z","publication":"22nd International Conference on Runtime Verification","abstract":[{"lang":"eng","text":"Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time. "}]},{"abstract":[{"text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.","lang":"eng"}],"file":[{"description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","relation":"supplementary_material","access_level":"open_access","file_name":"flags.py","file_id":"11780","date_updated":"2022-08-10T15:34:04Z","creator":"pwild","file_size":16828,"date_created":"2022-08-10T15:34:04Z","content_type":"text/x-python"},{"checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","description":"Code for proof of Lemma 8.20 in Thesis","relation":"supplementary_material","access_level":"open_access","file_id":"11781","file_name":"lowerbound.cpp","date_updated":"2022-08-10T15:34:10Z","creator":"pwild","file_size":12226,"date_created":"2022-08-10T15:34:10Z","content_type":"text/x-c++src"},{"date_created":"2022-08-10T15:34:17Z","content_type":"text/x-python","file_size":3240,"creator":"pwild","date_updated":"2022-08-10T15:34:17Z","file_id":"11782","file_name":"upperbound.py","relation":"supplementary_material","access_level":"open_access","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","description":"Code for proof of Proposition 7.9 in Thesis"},{"file_size":5086282,"date_created":"2022-08-11T16:08:33Z","content_type":"application/pdf","date_updated":"2022-08-11T16:08:33Z","creator":"pwild","access_level":"open_access","relation":"main_file","file_id":"11809","file_name":"finalthesisPascalWildPDFA.pdf","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","checksum":"4e96575b10cbe4e0d0db2045b2847774"},{"file_name":"ThesisSubmission.zip","file_id":"11810","relation":"source_file","access_level":"closed","checksum":"92d94842a1fb6dca5808448137573b2e","date_created":"2022-08-11T16:09:19Z","content_type":"application/zip","file_size":18150068,"creator":"pwild","date_updated":"2022-08-11T16:09:19Z"}],"date_published":"2022-08-11T00:00:00Z","day":"11","author":[{"full_name":"Wild, Pascal","last_name":"Wild","first_name":"Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"title":"High-dimensional expansion and crossing numbers of simplicial complexes","type":"dissertation","publication_status":"published","year":"2022","publication_identifier":{"isbn":["978-3-99078-021-3"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:11777","alternative_title":["ISTA Thesis"],"date_created":"2022-08-10T15:51:19Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"OA_place":"publisher","month":"08","article_processing_charge":"No","ec_funded":1,"page":"170","has_accepted_license":"1","citation":{"apa":"Wild, P. (2022). <i>High-dimensional expansion and crossing numbers of simplicial complexes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>","mla":"Wild, Pascal. <i>High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>.","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology Austria, 2022.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology Austria.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>.","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology Austria, 2022."},"ddc":["500","516","514"],"file_date_updated":"2022-08-11T16:09:19Z","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"degree_awarded":"PhD","corr_author":"1","_id":"11777","status":"public","date_updated":"2026-04-07T14:18:26Z","oa":1},{"external_id":{"isi":["000904104000021"],"arxiv":["2208.03160"]},"date_published":"2022-10-23T00:00:00Z","publication":"Computer Vision – ECCV 2022","abstract":[{"text":"It is a highly desirable property for deep networks to be robust against\r\nsmall input changes. One popular way to achieve this property is by designing\r\nnetworks with a small Lipschitz constant. In this work, we propose a new\r\ntechnique for constructing such Lipschitz networks that has a number of\r\ndesirable properties: it can be applied to any linear network layer\r\n(fully-connected or convolutional), it provides formal guarantees on the\r\nLipschitz constant, it is easy to implement and efficient to run, and it can be\r\ncombined with any training objective and optimization method. In fact, our\r\ntechnique is the first one in the literature that achieves all of these\r\nproperties simultaneously. Our main contribution is a rescaling-based weight\r\nmatrix parametrization that guarantees each network layer to have a Lipschitz\r\nconstant of at most 1 and results in the learned weight matrices to be close to\r\northogonal. Hence we call such layers almost-orthogonal Lipschitz (AOL).\r\nExperiments and ablation studies in the context of image classification with\r\ncertified robust accuracy confirm that AOL layers achieve results that are on\r\npar with most existing methods. Yet, they are simpler to implement and more\r\nbroadly applicable, because they do not require computationally expensive\r\nmatrix orthogonalization or inversion steps as part of the network\r\narchitecture. We provide code at https://github.com/berndprach/AOL.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2208.03160"}],"oa_version":"Preprint","day":"23","author":[{"first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd","last_name":"Prach"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"publication_status":"published","isi":1,"language":[{"iso":"eng"}],"title":"Almost-orthogonal layers for efficient general-purpose Lipschitz networks","type":"conference","date_created":"2022-08-12T15:09:47Z","alternative_title":["LNCS"],"conference":{"end_date":"2022-10-27","location":"Tel Aviv, Israel","start_date":"2022-10-23","name":"ECCV: European Conference on Computer Vision"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2022","publication_identifier":{"isbn":["9783031198021"],"eisbn":["9783031198038"]},"doi":"10.1007/978-3-031-19803-8_21","month":"10","publisher":"Springer Nature","intvolume":"     13681","citation":{"ieee":"B. Prach and C. Lampert, “Almost-orthogonal layers for efficient general-purpose Lipschitz networks,” in <i>Computer Vision – ECCV 2022</i>, Tel Aviv, Israel, 2022, vol. 13681, pp. 350–365.","chicago":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” In <i>Computer Vision – ECCV 2022</i>, 13681:350–65. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>.","ama":"Prach B, Lampert C. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In: <i>Computer Vision – ECCV 2022</i>. Vol 13681. Springer Nature; 2022:350-365. doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>","ista":"Prach B, Lampert C. 2022. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. Computer Vision – ECCV 2022. ECCV: European Conference on Computer Vision, LNCS, vol. 13681, 350–365.","short":"B. Prach, C. Lampert, in:, Computer Vision – ECCV 2022, Springer Nature, 2022, pp. 350–365.","mla":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” <i>Computer Vision – ECCV 2022</i>, vol. 13681, Springer Nature, 2022, pp. 350–65, doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>.","apa":"Prach, B., &#38; Lampert, C. (2022). Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In <i>Computer Vision – ECCV 2022</i> (Vol. 13681, pp. 350–365). Tel Aviv, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>"},"quality_controlled":"1","volume":13681,"article_processing_charge":"No","page":"350-365","corr_author":"1","_id":"11839","status":"public","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"scopus_import":"1","arxiv":1,"related_material":{"record":[{"id":"19759","status":"public","relation":"dissertation_contains"}]},"oa":1,"date_updated":"2026-04-07T11:49:51Z"},{"keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"doi":"10.15479/at:ista:11879","acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","year":"2022","publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"date_created":"2022-08-17T07:58:53Z","project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","type":"dissertation","language":[{"iso":"eng"}],"publication_status":"published","author":[{"last_name":"Artner","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina"}],"day":"17","oa_version":"Published Version","abstract":[{"text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT.","lang":"eng"}],"file":[{"file_id":"11907","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","access_level":"open_access","embargo":"2023-09-08","relation":"main_file","checksum":"a2c2fdc28002538840490bfa6a08b2cb","content_type":"application/pdf","date_created":"2022-08-17T12:08:49Z","file_size":11113608,"creator":"cartner","date_updated":"2023-09-09T22:30:03Z"},{"file_size":19097730,"date_created":"2022-08-17T12:08:59Z","content_type":"application/octet-stream","date_updated":"2023-09-09T22:30:03Z","creator":"cartner","access_level":"closed","relation":"source_file","file_id":"11908","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","checksum":"66b461c074b815fbe63481b3f46a9f43","embargo_to":"open_access"}],"date_published":"2022-08-17T00:00:00Z","date_updated":"2026-04-07T14:30:39Z","oa":1,"degree_awarded":"PhD","ddc":["580"],"file_date_updated":"2023-09-09T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"status":"public","_id":"11879","corr_author":"1","page":"128","article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"has_accepted_license":"1","citation":{"short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","apa":"Artner, C. (2022). <i>Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>","mla":"Artner, Christina. <i>Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>.","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>.","ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>"},"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","month":"08"},{"month":"08","OA_place":"publisher","supervisor":[{"last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"}],"publisher":"Institute of Science and Technology Austria","citation":{"short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>.","apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>."},"has_accepted_license":"1","ec_funded":1,"article_processing_charge":"No","page":"136","corr_author":"1","_id":"11932","status":"public","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"file_date_updated":"2023-06-20T22:30:04Z","ddc":["573"],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6194"},{"status":"public","relation":"part_of_dissertation","id":"10077"}]},"oa":1,"date_updated":"2026-04-07T14:22:58Z","date_published":"2022-08-19T00:00:00Z","file":[{"access_level":"closed","relation":"source_file","file_id":"11935","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","embargo_to":"open_access","file_size":13515457,"content_type":"application/zip","date_created":"2022-08-19T16:31:34Z","date_updated":"2023-06-20T22:30:04Z","creator":"mnardin"},{"file_size":9906458,"content_type":"application/pdf","date_created":"2022-08-22T09:43:50Z","date_updated":"2023-06-20T22:30:04Z","creator":"mnardin","access_level":"open_access","embargo":"2023-06-19","relation":"main_file","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","file_id":"11941","checksum":"0ec94035ea35a47a9f589ed168e60b48"}],"abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"oa_version":"Published Version","day":"19","author":[{"full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570"}],"publication_status":"published","language":[{"iso":"eng"}],"title":"On the encoding, transfer, and consolidation of spatial memories","type":"dissertation","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"alternative_title":["ISTA Thesis"],"date_created":"2022-08-19T08:52:30Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"year":"2022","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","doi":"10.15479/at:ista:11932"},{"date_updated":"2026-04-07T14:17:59Z","related_material":{"record":[{"id":"11995","status":"public","relation":"dissertation_contains"}]},"oa":1,"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"file_date_updated":"2022-08-25T09:33:31Z","degree_awarded":"PhD","corr_author":"1","_id":"11945","status":"public","article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"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)"},"page":"133","has_accepted_license":"1","citation":{"ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11945\">10.15479/at:ista:11945</a>","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11945\">https://doi.org/10.15479/at:ista:11945</a>.","short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria.","mla":"Schulz, Rouven. <i>Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11945\">10.15479/at:ista:11945</a>.","apa":"Schulz, R. (2022). <i>Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11945\">https://doi.org/10.15479/at:ista:11945</a>"},"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Siegert","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877"}],"OA_place":"publisher","month":"08","year":"2022","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:11945","alternative_title":["ISTA Thesis"],"date_created":"2022-08-23T11:33:11Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"project":[{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"type":"dissertation","title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","publication_status":"published","day":"23","author":[{"full_name":"Schulz, Rouven","last_name":"Schulz","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level."}],"date_published":"2022-08-23T00:00:00Z","file":[{"checksum":"61b1b666a210ff7cdd0e95ea75207a13","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","file_id":"11970","access_level":"open_access","relation":"main_file","creator":"rschulz","date_updated":"2022-08-25T08:59:57Z","success":1,"date_created":"2022-08-25T08:59:57Z","content_type":"application/pdf","file_size":28079331},{"creator":"rschulz","date_updated":"2022-08-25T09:33:31Z","date_created":"2022-08-25T09:00:11Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":27226963,"checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","file_id":"11971","file_name":"Thesis_Rouven_Schulz_2022_final.docx","access_level":"closed","relation":"source_file"}]},{"citation":{"ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12072\">https://doi.org/10.15479/at:ista:12072</a>.","ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12072\">10.15479/at:ista:12072</a>","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","mla":"Shute, Alec L. <i>Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12072\">10.15479/at:ista:12072</a>.","apa":"Shute, A. L. (2022). <i>Existence and density problems in Diophantine geometry: From norm forms to Campana points</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12072\">https://doi.org/10.15479/at:ista:12072</a>"},"has_accepted_license":"1","page":"208","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"article_processing_charge":"No","ec_funded":1,"month":"09","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning"}],"related_material":{"record":[{"id":"12076","relation":"part_of_dissertation","status":"public"},{"id":"12077","status":"public","relation":"part_of_dissertation"}]},"oa":1,"date_updated":"2026-04-07T14:13:35Z","status":"public","corr_author":"1","_id":"12072","degree_awarded":"PhD","file_date_updated":"2022-09-12T11:24:21Z","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"ddc":["512"],"oa_version":"Published Version","author":[{"orcid":"0000-0002-1812-2810","first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","full_name":"Shute, Alec L","last_name":"Shute"}],"day":"08","file":[{"date_updated":"2022-09-08T21:50:34Z","creator":"ashute","file_size":1907386,"date_created":"2022-09-08T21:50:34Z","content_type":"application/pdf","success":1,"checksum":"bf073344320e05d92c224786cec2e92d","access_level":"open_access","relation":"main_file","file_id":"12073","file_name":"Thesis_final_draft.pdf"},{"access_level":"closed","relation":"source_file","file_id":"12074","file_name":"athesis.tex","checksum":"b054ac6baa09f70e8235403a4abbed80","file_size":495393,"date_created":"2022-09-08T21:50:42Z","content_type":"application/octet-stream","date_updated":"2022-09-12T11:24:21Z","creator":"ashute"},{"creator":"ashute","date_updated":"2022-09-12T11:24:21Z","date_created":"2022-09-09T12:05:00Z","content_type":"application/x-zip-compressed","file_size":944534,"checksum":"0a31e905f1cff5eb8110978cc90e1e79","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","file_id":"12078","access_level":"closed","relation":"source_file"}],"date_published":"2022-09-08T00:00:00Z","abstract":[{"lang":"eng","text":"In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. "}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"date_created":"2022-09-08T21:53:03Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","acknowledgement":"I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385.","doi":"10.15479/at:ista:12072","year":"2022","publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"publication_status":"published","type":"dissertation","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}]},{"oa":1,"date_updated":"2025-07-10T11:50:23Z","corr_author":"1","_id":"12102","status":"public","file_date_updated":"2023-01-20T10:39:44Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"ddc":["000"],"scopus_import":"1","citation":{"ista":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. 2022. Algorithms and hardness results for computing cores of Markov chains. 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer Science vol. 250, 29.","short":"A. Ahmadi, K. Chatterjee, A.K. Goharshady, T. Meggendorfer, R. Safavi Hemami, D. Zikelic, in:, 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","apa":"Ahmadi, A., Chatterjee, K., Goharshady, A. K., Meggendorfer, T., Safavi Hemami, R., &#38; Zikelic, D. (2022). Algorithms and hardness results for computing cores of Markov chains. In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 250). Madras, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29</a>","mla":"Ahmadi, Ali, et al. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 250, 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">10.4230/LIPIcs.FSTTCS.2022.29</a>.","ieee":"A. Ahmadi, K. Chatterjee, A. K. Goharshady, T. Meggendorfer, R. Safavi Hemami, and D. Zikelic, “Algorithms and hardness results for computing cores of Markov chains,” in <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Madras, India, 2022, vol. 250.","chicago":"Ahmadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Tobias Meggendorfer, Roodabeh Safavi Hemami, and Dorde Zikelic. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29</a>.","ama":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. Algorithms and hardness results for computing cores of Markov chains. In: <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">10.4230/LIPIcs.FSTTCS.2022.29</a>"},"has_accepted_license":"1","volume":250,"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)"},"ec_funded":1,"article_processing_charge":"No","month":"12","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       250","date_created":"2023-01-01T23:00:50Z","conference":{"end_date":"2022-12-20","location":"Madras, India","start_date":"2022-12-18","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","article_number":"29","publication_identifier":{"isbn":["9783959772617"],"issn":["1868-8969"]},"acknowledgement":"The research was partially supported by the Hong Kong Research Grants Council ECS\r\nProject No. 26208122, ERC CoG 863818 (FoRM-SMArt), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, HKUST– Kaisa Joint Research Institute Project Grant HKJRI3A-055 and HKUST Startup Grant R9272. Ali Ahmadi and Roodabeh Safavi were interns at HKUST.","doi":"10.4230/LIPIcs.FSTTCS.2022.29","publication_status":"published","language":[{"iso":"eng"}],"title":"Algorithms and hardness results for computing cores of Markov chains","type":"conference","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","day":"14","author":[{"last_name":"Ahmadi","full_name":"Ahmadi, Ali","first_name":"Ali"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165"},{"id":"72ed2640-8972-11ed-ae7b-f9c81ec75154","first_name":"Roodabeh","last_name":"Safavi Hemami","full_name":"Safavi Hemami, Roodabeh"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699"}],"file":[{"creator":"dernst","date_updated":"2023-01-20T10:39:44Z","content_type":"application/pdf","date_created":"2023-01-20T10:39:44Z","success":1,"file_size":872534,"checksum":"6660c802489013f034c9e8bd57f4d46e","file_id":"12324","file_name":"2022_LIPICs_Ahmadi.pdf","access_level":"open_access","relation":"main_file"}],"date_published":"2022-12-14T00:00:00Z","publication":"42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","abstract":[{"text":"Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset.","lang":"eng"}]},{"issue":"4","pmid":1,"oa_version":"Published Version","day":"16","author":[{"last_name":"Hübschmann","full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","first_name":"Medina","last_name":"Korkut","full_name":"Korkut, Medina"},{"orcid":"0000-0001-8635-0877","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","last_name":"Siegert"}],"file":[{"file_size":6251945,"success":1,"date_created":"2023-01-23T09:50:51Z","content_type":"application/pdf","date_updated":"2023-01-23T09:50:51Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_name":"2022_STARProtocols_Huebschmann.pdf","file_id":"12340","checksum":"3c71b8a60633d42c2f77c49025d5559b"}],"date_published":"2022-12-16T00:00:00Z","external_id":{"pmid":["36595902"]},"publication":"STAR Protocols","abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"date_created":"2023-01-12T11:56:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2666-1667"]},"year":"2022","article_number":"101866","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"doi":"10.1016/j.xpro.2022.101866","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for their insights into functional assays and data analysis, Verena Seiboth for insights into necessary institutional permission, and ISTA imaging & optics facility (IOF) especially Bernhard Hochreiter for their support.","article_type":"letter_note","publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425"},{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation"}],"title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","type":"journal_article","has_accepted_license":"1","citation":{"ieee":"V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay,” <i>STAR Protocols</i>, vol. 3, no. 4. Elsevier, 2022.","ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>","chicago":"Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>.","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>, vol. 3, no. 4, 101866, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>.","apa":"Hübschmann, V., Korkut, M., &#38; Siegert, S. (2022). Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>"},"volume":3,"quality_controlled":"1","ec_funded":1,"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)"},"month":"12","publisher":"Elsevier","intvolume":"         3","oa":1,"related_material":{"record":[{"relation":"other","status":"public","id":"11478"}]},"date_updated":"2025-06-11T13:58:47Z","_id":"12117","corr_author":"1","status":"public","ddc":["570"],"file_date_updated":"2023-01-23T09:50:51Z","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"scopus_import":"1"},{"date_created":"2023-01-16T10:04:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2022","doi":"10.1038/s41586-022-05187-x","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","article_type":"original","publication_status":"published","isi":1,"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","issue":"7927","pmid":1,"oa_version":"Submitted Version","day":"15","author":[{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"last_name":"Gelová","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","orcid":"0000-0003-4783-1752"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","orcid":"0000-0002-2739-8843"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer"},{"last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","orcid":"0000-0002-7244-7237"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"full_name":"Živanović, Branka D.","last_name":"Živanović","first_name":"Branka D."},{"last_name":"Zou","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia"},{"last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","orcid":"0000-0002-8600-0671"},{"first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek","last_name":"Randuch"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"last_name":"Teplova","full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","first_name":"Anastasiia"},{"last_name":"Kinoshita","full_name":"Kinoshita, Toshinori","first_name":"Toshinori"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"}],"file":[{"creator":"amally","date_updated":"2023-11-02T17:12:37Z","success":1,"date_created":"2023-11-02T17:12:37Z","content_type":"application/pdf","file_size":79774945,"checksum":"a6055c606aefb900bf62ae3e7d15f921","file_name":"Friml Nature 2022_merged.pdf","file_id":"14483","access_level":"open_access","relation":"main_file"}],"date_published":"2022-09-15T00:00:00Z","external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"publication":"Nature","abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"oa":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19395"},{"id":"20364","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-04-07T11:52:15Z","_id":"12291","corr_author":"1","status":"public","ddc":["580"],"file_date_updated":"2023-11-02T17:12:37Z","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"scopus_import":"1","has_accepted_license":"1","citation":{"ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>"},"quality_controlled":"1","volume":609,"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"ec_funded":1,"page":"575-581","month":"09","publisher":"Springer Nature","intvolume":"       609"},{"oa_version":"None","issue":"5","author":[{"full_name":"Shipman, Barbara A.","last_name":"Shipman","first_name":"Barbara A."},{"orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","last_name":"Stephenson","first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"}],"day":"28","publication":"PRIMUS","date_published":"2022-05-28T00:00:00Z","abstract":[{"lang":"eng","text":"Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-01-16T10:07:21Z","keyword":["Education","General Mathematics"],"doi":"10.1080/10511970.2021.1872750","year":"2022","publication_identifier":{"issn":["1051-1970"],"eissn":["1935-4053"]},"publication_status":"published","article_type":"original","title":"Tangible topology through the lens of limits","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","volume":32,"citation":{"short":"B.A. Shipman, E.R. Stephenson, PRIMUS 32 (2022) 593–609.","ista":"Shipman BA, Stephenson ER. 2022. Tangible topology through the lens of limits. PRIMUS. 32(5), 593–609.","mla":"Shipman, Barbara A., and Elizabeth R. Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>, vol. 32, no. 5, Taylor &#38; Francis, 2022, pp. 593–609, doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>.","apa":"Shipman, B. A., &#38; Stephenson, E. R. (2022). Tangible topology through the lens of limits. <i>PRIMUS</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>","ieee":"B. A. Shipman and E. R. Stephenson, “Tangible topology through the lens of limits,” <i>PRIMUS</i>, vol. 32, no. 5. Taylor &#38; Francis, pp. 593–609, 2022.","chicago":"Shipman, Barbara A., and Elizabeth R Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>.","ama":"Shipman BA, Stephenson ER. Tangible topology through the lens of limits. <i>PRIMUS</i>. 2022;32(5):593-609. doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>"},"page":"593-609","article_processing_charge":"No","month":"05","intvolume":"        32","publisher":"Taylor & Francis","date_updated":"2024-10-09T21:03:58Z","status":"public","corr_author":"1","_id":"12307","scopus_import":"1","department":[{"_id":"HeEd"},{"_id":"GradSch"}]},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8385"},{"relation":"part_of_dissertation","status":"public","id":"11736"},{"status":"public","relation":"part_of_dissertation","id":"9818"}]},"oa":1,"date_updated":"2026-06-18T19:57:47Z","status":"public","_id":"12358","corr_author":"1","degree_awarded":"PhD","ddc":["000","620"],"file_date_updated":"2023-02-02T09:39:25Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"has_accepted_license":"1","citation":{"ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>.","apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>"},"page":"138","ec_funded":1,"acknowledged_ssus":[{"_id":"SSU"}],"article_processing_charge":"No","OA_place":"publisher","month":"09","supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"date_created":"2023-01-24T10:49:46Z","doi":"10.15479/at:ista:12103","year":"2022","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-020-6"]},"publication_status":"published","project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"type":"dissertation","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","language":[{"iso":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg","last_name":"Sperl"}],"day":"22","file":[{"title":"Thesis","description":"This is the main PDF file of the thesis. File size: 105 MB","checksum":"083722acbb8115e52e3b0fdec6226769","relation":"main_file","access_level":"open_access","file_name":"thesis_gsperl.pdf","file_id":"12371","date_updated":"2023-02-02T09:29:57Z","creator":"cchlebak","file_size":104497530,"content_type":"application/pdf","date_created":"2023-01-25T12:04:41Z"},{"access_level":"open_access","relation":"main_file","file_name":"thesis_gsperl_compressed.pdf","file_id":"12483","title":"Thesis (compressed 23MB)","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","checksum":"511f82025e5fcb70bff4731d6896ca07","file_size":23183710,"date_created":"2023-02-02T09:33:37Z","content_type":"application/pdf","date_updated":"2023-02-02T09:33:37Z","creator":"cchlebak"},{"file_id":"12484","file_name":"thesis-source.zip","access_level":"open_access","relation":"source_file","checksum":"ed4cb85225eedff761c25bddfc37a2ed","content_type":"application/x-zip-compressed","date_created":"2023-02-02T09:39:25Z","file_size":98382247,"creator":"cchlebak","date_updated":"2023-02-02T09:39:25Z"}],"date_published":"2022-09-22T00:00:00Z","abstract":[{"text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n","lang":"eng"}]}]