[{"corr_author":"1","file":[{"file_id":"14482","date_created":"2023-11-02T17:03:20Z","checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","file_size":737872,"file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","success":1,"date_updated":"2023-11-02T17:03:20Z","access_level":"open_access","creator":"amally","relation":"main_file","content_type":"application/pdf"}],"day":"01","oa":1,"language":[{"iso":"eng"}],"issue":"10","date_updated":"2025-09-09T12:54:16Z","oa_version":"Submitted Version","doi":"10.1016/j.pbi.2023.102443","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","date_published":"2023-10-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling."}],"publication_status":"published","ddc":["580"],"type":"journal_article","isi":1,"intvolume":"        75","publisher":"Elsevier","author":[{"last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas","full_name":"Fiedler, Lukas"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"_id":"14313","file_date_updated":"2023-11-02T17:03:20Z","has_accepted_license":"1","article_number":"102443","quality_controlled":"1","scopus_import":"1","citation":{"chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>.","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","apa":"Fiedler, L., &#38; Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>","ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. 2023;75(10). doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10. Elsevier, 2023.","mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10, 102443, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>.","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443."},"department":[{"_id":"JiFr"}],"acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology.","date_created":"2023-09-10T22:01:11Z","article_processing_charge":"No","publication_identifier":{"issn":["1369-5266"]},"article_type":"review","title":"Rapid auxin signaling: Unknowns old and new","external_id":{"pmid":["37666097"],"isi":["001080095300001"]},"volume":75,"year":"2023","publication":"Current Opinion in Plant Biology"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"doi":"10.1016/j.celrep.2023.113015","month":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","date_published":"2023-09-26T00:00:00Z","ddc":["570"],"publication_status":"published","abstract":[{"text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.","lang":"eng"}],"file":[{"creator":"dernst","access_level":"open_access","date_updated":"2023-09-15T07:12:46Z","content_type":"application/pdf","relation":"main_file","checksum":"ca77a304fb813c292550b8604b0fb41d","date_created":"2023-09-15T07:12:46Z","file_id":"14337","success":1,"file_name":"2023_CellPress_Nardin.pdf","file_size":4879455}],"corr_author":"1","license":"https://creativecommons.org/licenses/by/4.0/","day":"26","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-09-09T12:53:32Z","oa_version":"Published Version","issue":"9","department":[{"_id":"JoCs"}],"publication_identifier":{"eissn":["2211-1247"]},"article_processing_charge":"Yes","acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","date_created":"2023-09-10T22:01:11Z","publication":"Cell Reports","project":[{"grant_number":"607616","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"inter-and intracellular signalling in schizophrenia"}],"year":"2023","volume":42,"external_id":{"pmid":["37632747"],"isi":["001068779200001"]},"article_type":"original","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","isi":1,"type":"journal_article","publisher":"Elsevier","intvolume":"        42","_id":"14314","file_date_updated":"2023-09-15T07:12:46Z","author":[{"first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","full_name":"Nardin, Michele"},{"full_name":"Käfer, Karola","first_name":"Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stella, Federico","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","last_name":"Stella","orcid":"0000-0001-9439-3148"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"citation":{"chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","apa":"Nardin, M., Käfer, K., Stella, F., &#38; Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. 2023;42(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” <i>Cell Reports</i>, vol. 42, no. 9. Elsevier, 2023.","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>, vol. 42, no. 9, 113015, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>.","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015."},"quality_controlled":"1","scopus_import":"1","article_number":"113015","has_accepted_license":"1"},{"year":"2023","publication":"eLife","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","external_id":{"pmid":["37665327"]},"article_type":"original","volume":12,"department":[{"_id":"MaHe"}],"publication_identifier":{"eissn":["2050-084X"]},"acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","date_created":"2023-09-10T22:01:11Z","article_processing_charge":"Yes","author":[{"last_name":"Cho","first_name":"Ukrae H.","full_name":"Cho, Ukrae H."},{"orcid":"0000-0002-2111-992X","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"Hetzer, Martin W"}],"file_date_updated":"2023-09-15T06:59:10Z","_id":"14315","citation":{"ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>.","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>.","apa":"Cho, U. H., &#38; Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>","short":"U.H. Cho, M. Hetzer, ELife 12 (2023)."},"has_accepted_license":"1","scopus_import":"1","article_number":"RP89066","quality_controlled":"1","type":"journal_article","publisher":"eLife Sciences Publications","intvolume":"        12","status":"public","date_published":"2023-09-04T00:00:00Z","abstract":[{"text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.","lang":"eng"}],"publication_status":"published","ddc":["570"],"doi":"10.7554/eLife.89066","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_updated":"2024-10-09T21:06:57Z","file":[{"checksum":"db24bf3d595507387b48d3799c33e289","date_created":"2023-09-15T06:59:10Z","file_id":"14336","success":1,"file_size":3703097,"file_name":"2023_eLife_Cho.pdf","creator":"dernst","access_level":"open_access","date_updated":"2023-09-15T06:59:10Z","content_type":"application/pdf","relation":"main_file"}],"corr_author":"1","day":"04"},{"issue":"17","oa_version":"Preprint","date_updated":"2025-09-09T12:56:46Z","language":[{"iso":"eng"}],"oa":1,"day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway."}],"date_published":"2023-09-01T00:00:00Z","status":"public","month":"09","main_file_link":[{"url":"https://doi.org/10.1101/2023.03.27.534325","open_access":"1"}],"pmid":1,"doi":"10.1242/jcs.261448","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","article_number":"jcs261448","quality_controlled":"1","citation":{"ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” <i>Journal of Cell Science</i>, vol. 136, no. 17. The Company of Biologists, 2023.","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448.","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>.","ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. 2023;136(17). doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &#38; Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>."},"author":[{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Aoshima, Kaito","last_name":"Aoshima","first_name":"Kaito"},{"last_name":"Shimamura","first_name":"Hiroki","full_name":"Shimamura, Hiroki"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"last_name":"Toshima","first_name":"Junko Y.","full_name":"Toshima, Junko Y."},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"_id":"14316","intvolume":"       136","publisher":"The Company of Biologists","type":"journal_article","isi":1,"external_id":{"pmid":["37539494"],"isi":["001112832300005"]},"title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","article_type":"original","volume":136,"year":"2023","publication":"Journal of Cell Science","date_created":"2023-09-10T22:01:12Z","article_processing_charge":"No","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"department":[{"_id":"DaSi"}]},{"file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2023-09-20T08:46:43Z","access_level":"open_access","creator":"dernst","file_name":"2023_LNCS_Akshay.pdf","file_size":531745,"success":1,"file_id":"14349","date_created":"2023-09-20T08:46:43Z","checksum":"f143c8eedf609f20f2aad2eeb496d53f"}],"day":"17","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"oa_version":"Published Version","alternative_title":["LNCS"],"date_updated":"2025-09-09T12:56:00Z","doi":"10.1007/978-3-031-37709-9_5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"07","status":"public","date_published":"2023-07-17T00:00:00Z","abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"publication_status":"published","ddc":["000"],"type":"conference","isi":1,"publisher":"Springer Nature","intvolume":"     13966","author":[{"last_name":"Akshay","first_name":"S.","full_name":"Akshay, S."},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias"},{"full_name":"Zikelic, Dorde","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","orcid":"0000-0002-4681-1699"}],"file_date_updated":"2023-09-20T08:46:43Z","_id":"14317","citation":{"chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>.","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112."},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","department":[{"_id":"KrCh"}],"conference":{"end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification"},"publication_identifier":{"isbn":["9783031377082"],"issn":["0302-9743"],"eissn":["1611-3349"]},"date_created":"2023-09-10T22:01:12Z","acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","article_processing_charge":"Yes (in subscription journal)","year":"2023","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"}],"publication":"International Conference on Computer Aided Verification","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","external_id":{"isi":["001310805600005"]},"volume":13966,"page":"86-112"},{"date_updated":"2025-09-09T12:55:28Z","oa_version":"Published Version","alternative_title":["LNCS"],"oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"day":"17","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2023-09-20T08:24:47Z","access_level":"open_access","creator":"dernst","file_size":624647,"file_name":"2023_LNCS_Sun.pdf","success":1,"file_id":"14348","date_created":"2023-09-20T08:24:47Z","checksum":"42917e086f8c7699f3bccf84f74fe000"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice."}],"ddc":["000"],"date_published":"2023-07-17T00:00:00Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"07","doi":"10.1007/978-3-031-37709-9_2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","citation":{"ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 16–39.","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” <i>Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>.","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: <i>Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:16-39. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>","apa":"Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In <i>Computer Aided Verification</i> (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In <i>Computer Aided Verification</i>, 13966:16–39. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>."},"author":[{"full_name":"Sun, Yican","last_name":"Sun","first_name":"Yican"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-09-20T08:24:47Z","_id":"14318","intvolume":"     13966","publisher":"Springer Nature","type":"conference","isi":1,"page":"16-39","related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"external_id":{"isi":["001310805600002"]},"title":"Automated tail bound analysis for probabilistic recurrence relations","volume":13966,"year":"2023","publication":"Computer Aided Verification","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"date_created":"2023-09-10T22:01:12Z","acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]},"conference":{"start_date":"2023-07-17","end_date":"2023-07-22","location":"Paris, France","name":"CAV: Computer Aided Verification"},"department":[{"_id":"KrCh"}]},{"type":"journal_article","isi":1,"publisher":"Electronic Journal of Combinatorics","intvolume":"        30","author":[{"full_name":"Anastos, Michael","last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael"},{"full_name":"Fabian, David","last_name":"Fabian","first_name":"David"},{"full_name":"Müyesser, Alp","first_name":"Alp","last_name":"Müyesser"},{"full_name":"Szabó, Tibor","last_name":"Szabó","first_name":"Tibor"}],"_id":"14319","file_date_updated":"2023-09-15T08:02:09Z","citation":{"ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. 2023;30(3). doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>.","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2023. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>.","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","apa":"Anastos, M., Fabian, D., Müyesser, A., &#38; Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>"},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"P3.10","department":[{"_id":"MaKw"}],"publication_identifier":{"eissn":["1077-8926"]},"date_created":"2023-09-10T22:01:12Z","acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","article_processing_charge":"Yes","year":"2023","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"publication":"Electronic Journal of Combinatorics","external_id":{"isi":["001042382200001"],"arxiv":["2212.03100"]},"title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","article_type":"original","volume":30,"file":[{"creator":"dernst","access_level":"open_access","date_updated":"2023-09-15T08:02:09Z","content_type":"application/pdf","relation":"main_file","checksum":"52c46c8cb329f9aaee9ade01525f317b","date_created":"2023-09-15T08:02:09Z","file_id":"14338","success":1,"file_size":247917,"file_name":"2023_elecJournCombinatorics_Anastos.pdf"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","day":"28","language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"arxiv":1,"issue":"3","oa_version":"Published Version","date_updated":"2025-09-09T12:54:51Z","doi":"10.37236/11714","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"month":"07","status":"public","date_published":"2023-07-28T00:00:00Z","abstract":[{"text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities.","lang":"eng"}],"publication_status":"published","ddc":["510"]},{"department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"date_created":"2023-09-12T07:12:12Z","acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","article_processing_charge":"No","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"external_id":{"arxiv":["2210.06310"]},"article_type":"original","title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","volume":108,"year":"2023","publication":"Physical Review B","type":"journal_article","intvolume":"       108","publisher":"American Physical Society","author":[{"first_name":"Paul M","orcid":"0000-0002-5198-7445","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"last_name":"Zibrov","first_name":"Alexander A.","full_name":"Zibrov, Alexander A."},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym"}],"_id":"14320","quality_controlled":"1","article_number":"125411","scopus_import":"1","citation":{"ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. 2023;108(12). doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>.","ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” <i>Physical Review B</i>, vol. 108, no. 12. American Physical Society, 2023.","chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>.","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., &#38; Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>"},"doi":"10.1103/physrevb.108.125411","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06310","open_access":"1"}],"date_published":"2023-09-15T00:00:00Z","status":"public","abstract":[{"text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance.","lang":"eng"}],"publication_status":"published","day":"15","language":[{"iso":"eng"}],"oa":1,"issue":"12","date_updated":"2023-09-20T09:38:24Z","oa_version":"Preprint","arxiv":1},{"publisher":"AIP Publishing","intvolume":"       159","type":"journal_article","isi":1,"citation":{"ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. 2023;159(10). doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>.","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10. AIP Publishing, 2023.","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>.","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023)."},"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"104103","author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","last_name":"Al Hyder","first_name":"Ragheed","full_name":"Al Hyder, Ragheed"},{"full_name":"Cappellaro, Alberto","first_name":"Alberto","last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"file_date_updated":"2023-09-13T09:34:20Z","_id":"14321","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","date_created":"2023-09-13T09:25:09Z","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"MiLe"}],"year":"2023","project":[{"grant_number":"101062862","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","name":"Non-Equilibrium Field Theory of Molecular Rotations"},{"grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"publication":"The Journal of Chemical Physics","title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","article_type":"original","external_id":{"isi":["001133333600011"],"pmid":["37694742"],"arxiv":["2306.17592"]},"volume":159,"day":"11","file":[{"date_updated":"2023-09-13T09:34:20Z","creator":"acappell","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2023-09-13T09:34:20Z","file_id":"14322","checksum":"507ab65ab29e2c987c94cabad7c5370b","success":1,"file_name":"104103_1_5.0165806.pdf","file_size":5749653}],"corr_author":"1","arxiv":1,"issue":"10","date_updated":"2025-09-09T12:57:42Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09","doi":"10.1063/5.0165806","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"ddc":["530"],"status":"public","date_published":"2023-09-11T00:00:00Z"},{"article_number":"2307.09552","oa_version":"Preprint","date_updated":"2024-10-14T12:31:20Z","citation":{"ieee":"P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing, “Self-compatibility: Evaluating causal discovery without ground truth,” <i>arXiv</i>. .","ista":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552.","mla":"Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, 2307.09552, doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>.","ama":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>","apa":"Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., &#38; Janzing, D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>","short":"P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.).","chicago":"Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri, Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>."},"arxiv":1,"author":[{"last_name":"Faller","first_name":"Philipp M.","full_name":"Faller, Philipp M."},{"last_name":"Vankadara","first_name":"Leena Chennuru","full_name":"Vankadara, Leena Chennuru"},{"full_name":"Mastakouri, Atalanti A.","last_name":"Mastakouri","first_name":"Atalanti A."},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Janzing, Dominik","first_name":"Dominik","last_name":"Janzing"}],"language":[{"iso":"eng"}],"_id":"14333","oa":1,"day":"18","type":"preprint","publication_status":"submitted","abstract":[{"text":"As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly only evaluated on simulated data. This is concerning, given that\r\nsimulations reflect common preconceptions about generating processes regarding\r\nnoise distributions, model classes, and more. In this work, we propose a novel\r\nmethod for falsifying the output of a causal discovery algorithm in the absence\r\nof ground truth. Our key insight is that while statistical learning seeks\r\nstability across subsets of data points, causal learning should seek stability\r\nacross subsets of variables. Motivated by this insight, our method relies on a\r\nnotion of compatibility between causal graphs learned on different subsets of\r\nvariables. We prove that detecting incompatibilities can falsify wrongly\r\ninferred causal relations due to violation of assumptions or errors from finite\r\nsample effects. Although passing such compatibility tests is only a necessary\r\ncriterion for good performance, we argue that it provides strong evidence for\r\nthe causal models whenever compatibility entails strong implications for the\r\njoint distribution. We also demonstrate experimentally that detection of\r\nincompatibilities can aid in causal model selection.","lang":"eng"}],"extern":"1","title":"Self-compatibility: Evaluating causal discovery without ground truth","external_id":{"arxiv":["2307.09552"]},"date_published":"2023-07-18T00:00:00Z","year":"2023","status":"public","publication":"arXiv","date_created":"2023-09-13T12:44:59Z","month":"07","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.09552"}],"department":[{"_id":"FrLo"}],"doi":"10.48550/arXiv.2307.09552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","orcid":"0000-0002-7969-2729","first_name":"Pietro","full_name":"Brighi, Pietro"},{"full_name":"Ljubotina, Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","orcid":"0000-0003-0038-7068","first_name":"Marko"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"file_date_updated":"2023-09-20T10:46:10Z","_id":"14334","citation":{"ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. 2023;15(3). doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>","mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>.","ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” <i>SciPost Physics</i>, vol. 15, no. 3. SciPost Foundation, 2023.","ista":"Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>.","short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).","apa":"Brighi, P., Ljubotina, M., &#38; Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>"},"keyword":["General Physics and Astronomy"],"has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"093","type":"journal_article","publisher":"SciPost Foundation","intvolume":"        15","year":"2023","publication":"SciPost Physics","project":[{"grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"external_id":{"arxiv":["2210.15607"]},"title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","article_type":"original","volume":15,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12750"}]},"department":[{"_id":"MaSe"}],"publication_identifier":{"issn":["2542-4653"]},"date_created":"2023-09-14T13:08:23Z","acknowledgement":"We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI).","article_processing_charge":"No","language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"arxiv":1,"issue":"3","date_updated":"2025-04-14T07:52:05Z","oa_version":"Published Version","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2023-09-20T10:46:10Z","content_type":"application/pdf","relation":"main_file","checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","date_created":"2023-09-20T10:46:10Z","file_id":"14350","success":1,"file_size":4866506,"file_name":"2023_SciPostPhysics_Brighi.pdf"}],"corr_author":"1","day":"13","status":"public","date_published":"2023-09-13T00:00:00Z","abstract":[{"text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.","lang":"eng"}],"publication_status":"published","ddc":["530"],"doi":"10.21468/scipostphys.15.3.093","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09"},{"author":[{"first_name":"S","last_name":"Roychoudhry","full_name":"Roychoudhry, S"},{"full_name":"Sageman-Furnas, K","last_name":"Sageman-Furnas","first_name":"K"},{"full_name":"Wolverton, C","first_name":"C","last_name":"Wolverton"},{"full_name":"Grones, Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","orcid":"0000-0002-0471-8285"},{"last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","full_name":"Molnar, Gergely"},{"full_name":"De Angelis, M","first_name":"M","last_name":"De Angelis"},{"last_name":"Goodman","first_name":"HL","full_name":"Goodman, HL"},{"full_name":"Capstaff, N","first_name":"N","last_name":"Capstaff"},{"full_name":"JPB, Lloyd","first_name":"Lloyd","last_name":"JPB"},{"last_name":"Mullen","first_name":"J","full_name":"Mullen, J"},{"full_name":"Hangarter, R","last_name":"Hangarter","first_name":"R"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Kepinski, S","first_name":"S","last_name":"Kepinski"}],"file_date_updated":"2023-09-20T10:51:31Z","_id":"14339","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","citation":{"short":"S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513.","apa":"Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>","chicago":"Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>.","ista":"Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513.","ieee":"S. Roychoudhry <i>et al.</i>, “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” <i>Nature Plants</i>, vol. 9. Springer Nature, pp. 1500–1513, 2023.","mla":"Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>.","ama":"Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. 2023;9:1500-1513. doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>"},"type":"journal_article","isi":1,"intvolume":"         9","publisher":"Springer Nature","external_id":{"isi":["001069238800014"],"pmid":["37666965"]},"title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","article_type":"original","volume":9,"year":"2023","publication":"Nature Plants","page":"1500-1513","department":[{"_id":"JiFr"}],"date_created":"2023-09-15T09:56:01Z","acknowledgement":"We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.).","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["2055-0278"]},"oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-10-21T06:01:33Z","oa_version":"Published Version","file":[{"date_updated":"2023-09-20T10:51:31Z","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"14351","date_created":"2023-09-20T10:51:31Z","checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","file_size":9647103,"file_name":"2023_NaturePlants_Roychoudhry.pdf","success":1}],"day":"01","date_published":"2023-09-01T00:00:00Z","status":"public","abstract":[{"text":"Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.","lang":"eng"}],"publication_status":"published","ddc":["580"],"doi":"10.1038/s41477-023-01478-x","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09"},{"status":"public","date_published":"2023-09-07T00:00:00Z","ddc":["530"],"abstract":[{"lang":"eng","text":"Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines."}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/s41586-023-06399-5","pmid":1,"month":"09","language":[{"iso":"eng"}],"oa":1,"oa_version":"Submitted Version","date_updated":"2025-09-09T12:59:04Z","issue":"7977","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2024-06-04T09:24:34Z","content_type":"application/pdf","relation":"main_file","checksum":"9c9f172ba0a9a301d76fff4229812464","date_created":"2024-06-04T09:24:34Z","file_id":"17118","success":1,"file_size":3247252,"file_name":"2023_submittedversion.pdf"}],"corr_author":"1","day":"07","publication":"Nature","project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics"},{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow in complex fluids","call_identifier":"FWF","grant_number":"I04188"}],"year":"2023","volume":621,"title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","external_id":{"isi":["001168947700009"],"pmid":["37673988"]},"article_type":"original","related_material":{"link":[{"description":"News on ISTA website","url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/","relation":"press_release"}]},"page":"71-74","department":[{"_id":"BjHo"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"article_processing_charge":"No","date_created":"2023-09-17T22:01:09Z","acknowledgement":"We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.","file_date_updated":"2024-06-04T09:24:34Z","_id":"14341","author":[{"full_name":"Scarselli, Davide","first_name":"Davide","orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli"},{"full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","first_name":"Jose M"},{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"citation":{"ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. 2023;621(7977):71-74. doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>","ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” <i>Nature</i>, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023.","ista":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.","mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>.","chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>.","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., &#38; Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>"},"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","isi":1,"type":"journal_article","publisher":"Springer Nature","intvolume":"       621"},{"volume":123,"external_id":{"isi":["001145465400004"],"arxiv":["2306.09043"]},"article_type":"original","title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","publication":"Applied Physics Letters","year":"2023","department":[{"_id":"ZhAl"}],"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","date_created":"2023-09-17T22:01:09Z","publication_identifier":{"issn":["0003-6951"]},"_id":"14342","file_date_updated":"2023-09-20T11:36:16Z","author":[{"full_name":"Lorenc, Dusan","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc"},{"full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","first_name":"Zhanybek"}],"article_number":"091104","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","citation":{"ama":"Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. 2023;123(9). doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>","ista":"Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.","ieee":"D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” <i>Applied Physics Letters</i>, vol. 123, no. 9. AIP Publishing, 2023.","mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>.","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>.","apa":"Lorenc, D., &#38; Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023)."},"isi":1,"type":"journal_article","intvolume":"       123","publisher":"AIP Publishing","date_published":"2023-08-28T00:00:00Z","status":"public","ddc":["530"],"publication_status":"published","abstract":[{"text":"We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1063/5.0161713","month":"08","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_updated":"2025-09-09T12:58:23Z","issue":"9","arxiv":1,"corr_author":"1","file":[{"access_level":"open_access","creator":"dernst","date_updated":"2023-09-20T11:36:16Z","relation":"main_file","content_type":"application/pdf","checksum":"89a1b604d58b209fec66c6b6f919ac98","file_id":"14353","date_created":"2023-09-20T11:36:16Z","file_size":1486715,"file_name":"2023_ApplPhysLetter_Lorenc.pdf","success":1}],"day":"28"},{"date_published":"2023-01-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and  respectively, each being best possible in its own setting."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1137/1.9781611977554.ch88","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2111.14759"}],"oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:07:01Z","oa_version":"Preprint","arxiv":1,"corr_author":"1","day":"01","volume":2023,"title":"Fast algorithms for solving the Hamilton cycle problem with high probability","external_id":{"arxiv":["2111.14759"]},"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","year":"2023","page":"2286-2323","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2023-01-22","end_date":"2023-01-25","location":"Florence, Italy"},"department":[{"_id":"MaKw"}],"article_processing_charge":"No","date_created":"2023-09-17T22:01:10Z","publication_identifier":{"isbn":["9781611977554"]},"_id":"14344","author":[{"full_name":"Anastos, Michael","last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael"}],"scopus_import":"1","quality_controlled":"1","citation":{"ama":"Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>","ieee":"M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Florence, Italy, 2023, vol. 2023, pp. 2286–2323.","mla":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>.","ista":"Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.","chicago":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>.","apa":"Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>","short":"M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323."},"type":"conference","intvolume":"      2023","publisher":"Society for Industrial and Applied Mathematics"},{"oa_version":"Published Version","date_updated":"2025-04-14T13:10:03Z","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"day":"13","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2023-09-25T08:32:37Z","content_type":"application/pdf","relation":"main_file","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","date_created":"2023-09-25T08:32:37Z","file_id":"14366","success":1,"file_size":2317272,"file_name":"2023_NatureComm_Riedl.pdf"}],"corr_author":"1","ddc":["530","570"],"abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"publication_status":"published","status":"public","date_published":"2023-09-13T00:00:00Z","month":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1038/s41467-023-41432-1","citation":{"apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>.","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>.","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>"},"quality_controlled":"1","scopus_import":"1","article_number":"5633","has_accepted_license":"1","_id":"14361","file_date_updated":"2023-09-25T08:32:37Z","author":[{"full_name":"Riedl, Michael","first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mayer, Isabelle D","first_name":"Isabelle D","last_name":"Mayer","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4"},{"full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"publisher":"Springer Nature","intvolume":"        14","isi":1,"type":"journal_article","publication":"Nature Communications","project":[{"grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients"}],"year":"2023","volume":14,"article_type":"original","title":"Synchronization in collectively moving inanimate and living active matter","external_id":{"isi":["001087583700030"],"pmid":["37704595"]},"publication_identifier":{"eissn":["2041-1723"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"article_processing_charge":"Yes","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","date_created":"2023-09-24T22:01:10Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}]},{"department":[{"_id":"HeEd"}],"date_created":"2023-09-24T22:01:11Z","article_processing_charge":"No","publication_identifier":{"issn":["0304-3975"]},"title":"Weakly weighted generalised quasi-metric spaces and semilattices","external_id":{"arxiv":["2212.08424"],"isi":["001076934000001"]},"article_type":"original","volume":977,"year":"2023","publication":"Theoretical Computer Science","type":"journal_article","isi":1,"intvolume":"       977","publisher":"Elsevier","author":[{"last_name":"Castellano","first_name":"Ilaria","full_name":"Castellano, Ilaria"},{"first_name":"Anna","last_name":"Giordano Bruno","full_name":"Giordano Bruno, Anna"},{"id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","last_name":"Zava","orcid":"0000-0001-8686-1888","first_name":"Nicolò","full_name":"Zava, Nicolò"}],"_id":"14362","quality_controlled":"1","scopus_import":"1","article_number":"114129","citation":{"chicago":"Castellano, Ilaria, Anna Giordano Bruno, and Nicolò Zava. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>.","short":"I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977 (2023).","apa":"Castellano, I., Giordano Bruno, A., &#38; Zava, N. (2023). Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>","ama":"Castellano I, Giordano Bruno A, Zava N. Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. 2023;977. doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>","ista":"Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129.","ieee":"I. Castellano, A. Giordano Bruno, and N. Zava, “Weakly weighted generalised quasi-metric spaces and semilattices,” <i>Theoretical Computer Science</i>, vol. 977. Elsevier, 2023.","mla":"Castellano, Ilaria, et al. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>, vol. 977, 114129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>."},"doi":"10.1016/j.tcs.2023.114129","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.08424 "}],"date_published":"2023-10-25T00:00:00Z","status":"public","abstract":[{"text":"Motivated by recent applications to entropy theory in dynamical systems, we generalise notions introduced by Matthews and define weakly weighted and componentwise weakly weighted (generalised) quasi-metrics. We then systematise and extend to full generality the correspondences between these objects and other structures arising in theoretical computer science and dynamics. In particular, we study the correspondences with weak partial metrics and, if the underlying space is a semilattice, with invariant (generalised) quasi-metrics satisfying the descending path condition, and with strictly monotone semi(-co-)valuations.\r\nWe conclude discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation of both the known intrinsic semilattice entropy and the semigroup entropy.","lang":"eng"}],"publication_status":"published","corr_author":"1","day":"25","oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:07:00Z","oa_version":"Preprint","arxiv":1},{"corr_author":"1","file":[{"date_updated":"2023-11-07T08:53:21Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2023-11-07T08:53:21Z","file_id":"14497","checksum":"be1a560efdd96d20712311f4fc54aac2","success":1,"file_size":8197935,"file_name":"2023_iScience_Maes.pdf"}],"day":"20","oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:07:01Z","oa_version":"Published Version","issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1016/j.isci.2023.107780","month":"10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2023-10-20T00:00:00Z","status":"public","ddc":["570"],"abstract":[{"text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies.","lang":"eng"}],"publication_status":"published","isi":1,"type":"journal_article","intvolume":"        26","publisher":"Elsevier","_id":"14363","file_date_updated":"2023-11-07T08:53:21Z","author":[{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","orcid":"0000-0001-9642-1085","first_name":"Margaret E","full_name":"Maes, Margaret E"},{"first_name":"Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria"},{"full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","last_name":"Schoot Uiterkamp","first_name":"Florianne E"},{"last_name":"Sternberg","first_name":"Felix","full_name":"Sternberg, Felix"},{"orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro","full_name":"Venturino, Alessandro"},{"last_name":"Pohl","first_name":"Elena E.","full_name":"Pohl, Elena E."},{"full_name":"Siegert, Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra"}],"scopus_import":"1","quality_controlled":"1","article_number":"107780","has_accepted_license":"1","citation":{"short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023).","apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., &#38; Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>","chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>.","ieee":"M. E. Maes <i>et al.</i>, “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” <i>iScience</i>, vol. 26, no. 10. Elsevier, 2023.","mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>, vol. 26, no. 10, 107780, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>.","ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780.","ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>iScience</i>. 2023;26(10). doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>"},"department":[{"_id":"SaSi"}],"article_processing_charge":"Yes","acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","date_created":"2023-09-24T22:01:11Z","publication_identifier":{"eissn":["2589-0042"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"volume":26,"external_id":{"pmid":["37731609"],"isi":["001080403500001"]},"title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","article_type":"original","publication":"iScience","year":"2023"},{"doi":"10.1137/20M1375851","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"month":"07","status":"public","date_published":"2023-07-25T00:00:00Z","abstract":[{"lang":"eng","text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve -set agreement among  processes or approximate agreement on a cycle of length 4 among  processes in a wait-free manner in asynchronous models where processes communicate using objects that can be constructed from shared registers. However, it was unknown whether proofs based on simpler techniques were possible. We show that these impossibility results cannot be obtained by extension-based proofs in the iterated snapshot model and, hence, extension-based proofs are limited in power."}],"publication_status":"published","day":"25","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"arxiv":1,"issue":"4","date_updated":"2025-05-14T11:26:06Z","oa_version":"Preprint","department":[{"_id":"DaAl"}],"publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"date_created":"2023-09-24T22:01:11Z","acknowledgement":"We would like to thank Valerie King, Toniann Pitassi, and Michael Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research was supported by the Natural Science and Engineering Research Council of Canada under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship, and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship; the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385, CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel corporations. Some of the work on this paper was done while Faith Ellen was visiting IST Austria.","article_processing_charge":"No","year":"2023","project":[{"grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication":"SIAM Journal on Computing","article_type":"original","title":"Why extension-based proofs fail","external_id":{"arxiv":["1811.01421"],"isi":["001082972300004"]},"volume":52,"related_material":{"record":[{"relation":"earlier_version","id":"6676","status":"public"}]},"page":"913-944","type":"journal_article","isi":1,"publisher":"Society for Industrial and Applied Mathematics","intvolume":"        52","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"full_name":"Ellen, Faith","last_name":"Ellen","first_name":"Faith"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"full_name":"Zhu, Leqi","last_name":"Zhu","id":"a2117c59-cee4-11ed-b9d0-874ecf0f8ac5","first_name":"Leqi"}],"_id":"14364","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2023). Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. 2023;52(4):913-944. doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” <i>SIAM Journal on Computing</i>, vol. 52, no. 4. Society for Industrial and Applied Mathematics, pp. 913–944, 2023.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>, vol. 52, no. 4, Society for Industrial and Applied Mathematics, 2023, pp. 913–44, doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based proofs fail. SIAM Journal on Computing. 52(4), 913–944."},"scopus_import":"1","quality_controlled":"1"},{"article_type":"original","title":"Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder","volume":25,"year":"2023","publication":"Genetics in Medicine","date_created":"2023-09-25T08:44:29Z","article_processing_charge":"No","publication_identifier":{"issn":["1098-3600"]},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"100938","citation":{"ama":"Accogli A, Lin S-J, Severino M, et al. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. <i>Genetics in Medicine</i>. 2023;25(11). doi:<a href=\"https://doi.org/10.1016/j.gim.2023.100938\">10.1016/j.gim.2023.100938</a>","ieee":"A. Accogli <i>et al.</i>, “Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder,” <i>Genetics in Medicine</i>, vol. 25, no. 11. Elsevier, 2023.","mla":"Accogli, Andrea, et al. “Clinical, Neuroradiological, and Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” <i>Genetics in Medicine</i>, vol. 25, no. 11, 100938, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.gim.2023.100938\">10.1016/j.gim.2023.100938</a>.","ista":"Accogli A, Lin S-J, Severino M, Kim S-H, Huang K, Rocca C, Landsverk M, Zaki MS, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D, Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Sawyer LB, Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingappa L, McDunnah P, Horvath R, Cognè B, Isidor B, Hahn A, Gripp KW, Jafarnejad SM, Østergaard E, Prada CE, Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK, Maroofian R. 2023. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in Medicine. 25(11), 100938.","chicago":"Accogli, Andrea, Sheng-Jia Lin, Mariasavina Severino, Sung-Hoon Kim, Kevin Huang, Clarissa Rocca, Megan Landsverk, et al. “Clinical, Neuroradiological, and Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” <i>Genetics in Medicine</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.gim.2023.100938\">https://doi.org/10.1016/j.gim.2023.100938</a>.","short":"A. Accogli, S.-J. Lin, M. Severino, S.-H. Kim, K. Huang, C. Rocca, M. Landsverk, M.S. Zaki, A. Al-Maawali, V.M. Srinivasan, K. Al-Thihli, G.B. Schaefer, M. Davis, D. Tonduti, C. Doneda, L.M. Marten, C. Mühlhausen, M. Gomez, E. Lamantea, R. Mena, M. Nizon, V. Procaccio, A. Begtrup, A. Telegrafi, H. Cui, H.L. Schulz, J. Mohr, S. Biskup, M.A. Loos, H.V. Aráoz, V. Salpietro, L.D. Keppen, M. Chitre, C. Petree, L. Raymond, J. Vogt, L.B. Sawyer, A.A. Basinger, S.V. Pedersen, T.S. Pearson, D.K. Grange, L. Lingappa, P. McDunnah, R. Horvath, B. Cognè, B. Isidor, A. Hahn, K.W. Gripp, S.M. Jafarnejad, E. Østergaard, C.E. Prada, D. Ghezzi, V.K. Gowda, R.W. Taylor, N. Sonenberg, H. Houlden, M. Sissler, G.K. Varshney, R. Maroofian, Genetics in Medicine 25 (2023).","apa":"Accogli, A., Lin, S.-J., Severino, M., Kim, S.-H., Huang, K., Rocca, C., … Maroofian, R. (2023). Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. <i>Genetics in Medicine</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gim.2023.100938\">https://doi.org/10.1016/j.gim.2023.100938</a>"},"keyword":["Genetics (clinical)"],"author":[{"full_name":"Accogli, Andrea","first_name":"Andrea","last_name":"Accogli"},{"full_name":"Lin, Sheng-Jia","last_name":"Lin","first_name":"Sheng-Jia"},{"last_name":"Severino","first_name":"Mariasavina","full_name":"Severino, Mariasavina"},{"full_name":"Kim, Sung-Hoon","last_name":"Kim","first_name":"Sung-Hoon"},{"full_name":"Huang, Kevin","orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","last_name":"Huang","first_name":"Kevin"},{"full_name":"Rocca, Clarissa","last_name":"Rocca","first_name":"Clarissa"},{"first_name":"Megan","last_name":"Landsverk","full_name":"Landsverk, Megan"},{"first_name":"Maha S.","last_name":"Zaki","full_name":"Zaki, Maha S."},{"first_name":"Almundher","last_name":"Al-Maawali","full_name":"Al-Maawali, Almundher"},{"full_name":"Srinivasan, Varunvenkat M.","last_name":"Srinivasan","first_name":"Varunvenkat M."},{"first_name":"Khalid","last_name":"Al-Thihli","full_name":"Al-Thihli, Khalid"},{"full_name":"Schaefer, G. Bradly","first_name":"G. Bradly","last_name":"Schaefer"},{"full_name":"Davis, Monica","last_name":"Davis","first_name":"Monica"},{"full_name":"Tonduti, Davide","first_name":"Davide","last_name":"Tonduti"},{"first_name":"Chiara","last_name":"Doneda","full_name":"Doneda, Chiara"},{"first_name":"Lara M.","last_name":"Marten","full_name":"Marten, Lara M."},{"first_name":"Chris","last_name":"Mühlhausen","full_name":"Mühlhausen, Chris"},{"first_name":"Maria","last_name":"Gomez","full_name":"Gomez, Maria"},{"last_name":"Lamantea","first_name":"Eleonora","full_name":"Lamantea, Eleonora"},{"first_name":"Rafael","last_name":"Mena","full_name":"Mena, Rafael"},{"first_name":"Mathilde","last_name":"Nizon","full_name":"Nizon, Mathilde"},{"last_name":"Procaccio","first_name":"Vincent","full_name":"Procaccio, Vincent"},{"full_name":"Begtrup, Amber","first_name":"Amber","last_name":"Begtrup"},{"first_name":"Aida","last_name":"Telegrafi","full_name":"Telegrafi, Aida"},{"first_name":"Hong","last_name":"Cui","full_name":"Cui, Hong"},{"full_name":"Schulz, Heidi L.","last_name":"Schulz","first_name":"Heidi L."},{"first_name":"Julia","last_name":"Mohr","full_name":"Mohr, Julia"},{"first_name":"Saskia","last_name":"Biskup","full_name":"Biskup, Saskia"},{"full_name":"Loos, Mariana Amina","first_name":"Mariana Amina","last_name":"Loos"},{"last_name":"Aráoz","first_name":"Hilda Verónica","full_name":"Aráoz, Hilda Verónica"},{"first_name":"Vincenzo","last_name":"Salpietro","full_name":"Salpietro, Vincenzo"},{"full_name":"Keppen, Laura Davis","first_name":"Laura Davis","last_name":"Keppen"},{"last_name":"Chitre","first_name":"Manali","full_name":"Chitre, Manali"},{"full_name":"Petree, Cassidy","first_name":"Cassidy","last_name":"Petree"},{"last_name":"Raymond","first_name":"Lucy","full_name":"Raymond, Lucy"},{"first_name":"Julie","last_name":"Vogt","full_name":"Vogt, Julie"},{"full_name":"Sawyer, Lindsey B.","last_name":"Sawyer","first_name":"Lindsey B."},{"full_name":"Basinger, Alice A.","first_name":"Alice A.","last_name":"Basinger"},{"first_name":"Signe Vandal","last_name":"Pedersen","full_name":"Pedersen, Signe Vandal"},{"first_name":"Toni S.","last_name":"Pearson","full_name":"Pearson, Toni S."},{"full_name":"Grange, Dorothy K.","first_name":"Dorothy K.","last_name":"Grange"},{"full_name":"Lingappa, Lokesh","last_name":"Lingappa","first_name":"Lokesh"},{"full_name":"McDunnah, Paige","last_name":"McDunnah","first_name":"Paige"},{"full_name":"Horvath, Rita","first_name":"Rita","last_name":"Horvath"},{"first_name":"Benjamin","last_name":"Cognè","full_name":"Cognè, Benjamin"},{"last_name":"Isidor","first_name":"Bertrand","full_name":"Isidor, Bertrand"},{"first_name":"Andreas","last_name":"Hahn","full_name":"Hahn, Andreas"},{"full_name":"Gripp, Karen W.","last_name":"Gripp","first_name":"Karen W."},{"first_name":"Seyed Mehdi","last_name":"Jafarnejad","full_name":"Jafarnejad, Seyed Mehdi"},{"full_name":"Østergaard, Elsebet","last_name":"Østergaard","first_name":"Elsebet"},{"full_name":"Prada, Carlos E.","last_name":"Prada","first_name":"Carlos E."},{"full_name":"Ghezzi, Daniele","first_name":"Daniele","last_name":"Ghezzi"},{"first_name":"Vykuntaraju K.","last_name":"Gowda","full_name":"Gowda, Vykuntaraju K."},{"first_name":"Robert W.","last_name":"Taylor","full_name":"Taylor, Robert W."},{"last_name":"Sonenberg","first_name":"Nahum","full_name":"Sonenberg, Nahum"},{"full_name":"Houlden, Henry","first_name":"Henry","last_name":"Houlden"},{"last_name":"Sissler","first_name":"Marie","full_name":"Sissler, Marie"},{"full_name":"Varshney, Gaurav K.","last_name":"Varshney","first_name":"Gaurav K."},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"}],"file_date_updated":"2023-09-25T08:48:54Z","_id":"14368","intvolume":"        25","publisher":"Elsevier","type":"journal_article","abstract":[{"lang":"eng","text":"Purpose: \r\nBiallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase, have been reported in a small group of individuals displaying a neurodevelopmental phenotype but with limited neuroradiological data and insufficient evidence for causality of the variants.\r\nMethods:\r\nExome or genome sequencing was carried out in 15 families. Clinical and neuroradiological evaluation was performed for all affected individuals, including review of 10 previously reported individuals. The pathogenicity of TARS2 variants was evaluated using in vitro assays and a zebrafish model.\r\nResults:\r\nWe report 18 new individuals harboring biallelic TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual disability, regression, cerebellar and cerebral atrophy, basal ganglia signal alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro studies showed that variants within the TARS2301-381 region had decreased binding to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated key features of the human phenotype and unraveled dysregulation of downstream targets of mTORC1 signaling. Functional testing of the variants confirmed the pathogenicity in a zebrafish model.\r\nConclusion:\r\nWe define the clinico-radiological spectrum of TARS2-related mitochondrial disease, unveil the likely involvement of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish a TARS2 zebrafish model as an important tool to study variant pathogenicity."}],"publication_status":"published","ddc":["570"],"extern":"1","date_published":"2023-11-01T00:00:00Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","doi":"10.1016/j.gim.2023.100938","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"11","oa_version":"Published Version","date_updated":"2023-09-25T08:50:10Z","language":[{"iso":"eng"}],"oa":1,"day":"01","file":[{"checksum":"440f0cd8a2ffcbe03c015c1746728387","date_created":"2023-09-25T08:48:54Z","file_id":"14369","success":1,"file_size":4105513,"file_name":"2023_GeneticsMedicine_Accogli.pdf","creator":"dernst","access_level":"open_access","date_updated":"2023-09-25T08:48:54Z","content_type":"application/pdf","relation":"main_file"}]}]