[{"publication":"PRX Quantum","citation":{"ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>.","mla":"Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>.","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024).","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” <i>PRX Quantum</i>, vol. 5, no. 1. American Physical Society, 2024."},"year":"2024","date_created":"2024-06-27T10:58:06Z","date_updated":"2026-10-20T22:31:26Z","author":[{"orcid":"0000-0001-7641-8348","full_name":"Sett, Riya","last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"full_name":"Phan, Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"last_name":"Vukics","first_name":"Andras","full_name":"Vukics, Andras"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"das_tickbox":"0","acknowledged_ssus":[{"_id":"M-Shop"}],"date_published":"2024-02-16T00:00:00Z","DOAJ_listed":"1","day":"16","doi":"10.1103/prxquantum.5.010327","scopus_import":"1","abstract":[{"lang":"eng","text":"The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength 𝑔 to a superconducting cavity that is in situ bandwidth 𝜅 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of 𝑔/𝜅. For the highest realized 𝑔/𝜅 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology."}],"department":[{"_id":"JoFi"},{"_id":"AnHi"}],"_id":"17183","acknowledgement":"This work has received funding from the Austrian Science Fund (FWF) through BeyondC (F7105) and the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 862644 (FETopen QUARTET). A.V. acknowledges support from the National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary. The authors thank the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility for technical support. We are grateful to HUN-REN Cloud for providing us with suitable computational infrastructure for the simulations.","external_id":{"arxiv":["2210.14182"],"isi":["001171652500001"]},"publisher":"American Physical Society","oa_version":"Published Version","month":"02","article_type":"original","publication_identifier":{"eissn":["2691-3399"]},"volume":5,"researchdata_availability":"yes","intvolume":"         5","article_number":"010327","issue":"1","quality_controlled":"1","type":"journal_article","OA_type":"gold","APC_amount":"3782,54","ddc":["530"],"ec_funded":1,"status":"public","arxiv":1,"fulldoi":"https://doi.org/10.1103/prxquantum.5.010327","isi":1,"publication_status":"published","file":[{"file_size":1443351,"file_id":"17185","creator":"cchlebak","checksum":"0833880d47f74ad1deda93a1d8ffa5a7","success":1,"relation":"main_file","date_updated":"2024-06-28T12:04:43Z","date_created":"2024-06-28T12:04:43Z","content_type":"application/pdf","file_name":"2024_PRXQuantum_Sett.pdf","access_level":"open_access"}],"title":"Emergent macroscopic bistability induced by a single superconducting qubit","project":[{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-06-28T12:04:43Z","related_material":{"record":[{"relation":"research_data","id":"18978","status":"public"},{"id":"19533","status":"public","relation":"dissertation_contains"}]},"oa":1,"corr_author":"1","OA_place":"publisher","license":"https://creativecommons.org/licenses/by/4.0/","supplementarymaterial":"yes"},{"supplementarymaterial":"yes","dataavailabilitystatement":"The RNA-seq data for this study are available online at the NCBI Sequence Read Archive (accession number: PRJNA1116831). Uncropped images of the DNA gels are provided in the Supplementary Figs. 21 to 22. The source data used to generate the plots are provided in the Supplementary Data 2.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-09-17T09:44:29Z","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"20117","status":"public"}]},"fulldoi":"https://doi.org/10.1038/s42003-024-06747-9","isi":1,"file":[{"creator":"dernst","checksum":"7d66af41c90e73d1b8a375eb652a9561","file_id":"18084","file_size":7718758,"content_type":"application/pdf","date_created":"2024-09-17T09:44:29Z","file_name":"2024_CommBiology_Peng.pdf","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2024-09-17T09:44:29Z"}],"title":"Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"publication_status":"published","type":"journal_article","ddc":["570"],"status":"public","researchdata_availability":"yes (supplementary data)","volume":7,"article_type":"original","publication_identifier":{"eissn":["2399-3642"]},"intvolume":"         7","pmid":1,"article_number":"1085","quality_controlled":"1","_id":"18063","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"acknowledgement":"We thank Drs. Erika Isono (University of Constance), Grégory Vert (University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong) for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University), and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported by grants to S.T. from the National Natural Science Foundation of China (32321001), the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, the Division of Life Sciences and Medicine, the University of Science and Technology of China (QYPY20220012), the Fundamental Research Funds for the Central Universities (WK9100000021), and start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026, KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science Fund (FWF; projects I6123 and P37051-B).","external_id":{"pmid":["39232040"],"isi":["001306499600002"]},"oa_version":"Published Version","month":"09","publisher":"Springer Nature","das_tickbox":"1","doi":"10.1038/s42003-024-06747-9","date_published":"2024-09-04T00:00:00Z","day":"04","scopus_import":"1","abstract":[{"text":"The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters.","lang":"eng"}],"publication":"Communications Biology","date_created":"2024-09-15T22:01:38Z","year":"2024","citation":{"chicago":"Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” <i>Communications Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s42003-024-06747-9\">https://doi.org/10.1038/s42003-024-06747-9</a>.","mla":"Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” <i>Communications Biology</i>, vol. 7, 1085, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s42003-024-06747-9\">10.1038/s42003-024-06747-9</a>.","short":"Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková, J. Friml, S. Tan, Communications Biology 7 (2024).","ieee":"Y. Peng <i>et al.</i>, “Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis,” <i>Communications Biology</i>, vol. 7. Springer Nature, 2024.","ama":"Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. <i>Communications Biology</i>. 2024;7. doi:<a href=\"https://doi.org/10.1038/s42003-024-06747-9\">10.1038/s42003-024-06747-9</a>","ista":"Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085.","apa":"Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024). Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-024-06747-9\">https://doi.org/10.1038/s42003-024-06747-9</a>"},"date_updated":"2026-10-20T22:31:28Z","author":[{"full_name":"Peng, Yakun","first_name":"Yakun","last_name":"Peng"},{"full_name":"Ji, Kangkang","first_name":"Kangkang","last_name":"Ji"},{"first_name":"Yanbo","last_name":"Mao","full_name":"Mao, Yanbo"},{"last_name":"Wang","id":"82F537F2-B517-11E9-84D7-6433E6697425","first_name":"Yiqun","full_name":"Wang, Yiqun"},{"full_name":"Korbei, Barbara","first_name":"Barbara","last_name":"Korbei"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"first_name":"Jinbo","last_name":"Shen","full_name":"Shen, Jinbo"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"}]},{"page":"283-299","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"article_processing_charge":"No","related_material":{"record":[{"id":"20212","status":"public","relation":"dissertation_contains"}]},"corr_author":"1","supplementarymaterial":"yes","type":"book_chapter","status":"public","fulldoi":"https://doi.org/10.1007/978-1-0716-3969-6_19","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","project":[{"grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"publication_status":"published","_id":"17425","alternative_title":["Methods in Molecular Biology"],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","external_id":{"pmid":["39134857"]},"edition":"1","month":"08","oa_version":"None","publisher":"Springer Nature","volume":2831,"researchdata_availability":"no","publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"eisbn":["9781071639696"],"isbn":["9781071639689"]},"place":"New York, NY","intvolume":"      2831","pmid":1,"quality_controlled":"1","publication":"Neuronal Morphogenesis","date_created":"2024-08-13T12:16:41Z","year":"2024","series_title":"MIMB","citation":{"chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>"},"date_updated":"2026-10-20T22:31:27Z","author":[{"full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo","last_name":"Miranda"},{"first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"das_tickbox":"0","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1007/978-1-0716-3969-6_19","editor":[{"full_name":"Toyooka, Kazuhito","first_name":"Kazuhito","last_name":"Toyooka"}],"day":"13","date_published":"2024-08-13T00:00:00Z","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology.","lang":"eng"}],"scopus_import":"1"},{"OA_type":"gold","type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.10518320","open_access":"1"}],"date_created":"2025-01-30T08:30:03Z","year":"2024","ddc":["530"],"citation":{"ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Data Analysis Files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>.","mla":"Sett, Riya, et al. <i>Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>.","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024).","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024."},"date_updated":"2026-10-20T22:31:26Z","status":"public","author":[{"orcid":"0000-0001-7641-8348","full_name":"Sett, Riya","last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"full_name":"Phan, Duc T","last_name":"Phan","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"full_name":"Vukics, Andras","first_name":"Andras","last_name":"Vukics"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"fulldoi":"https://doi.org/10.5281/ZENODO.10518320","doi":"10.5281/ZENODO.10518320","day":"16","date_published":"2024-01-16T00:00:00Z","title":"Data Analysis files for \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\"","abstract":[{"lang":"eng","text":"Data analysis files for the manuscript \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\".\r\n\r\nThis contains the raw data and the data analysis files for generating the figures in the manuscript.\r\n\r\n Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.\r\n Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file\r\n Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.\r\nFigure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included.  "}],"_id":"18978","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","article_processing_charge":"No","oa":1,"oa_version":"Published Version","month":"01","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"17183"},{"id":"19533","status":"public","relation":"used_in_publication"}]},"publisher":"Zenodo","OA_place":"repository","corr_author":"1"},{"citation":{"apa":"Lukic, K. (2024). <i>Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>","ista":"Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.","ama":"Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>","ieee":"K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.","short":"K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.","mla":"Lukic, Kristina. <i>Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>.","chicago":"Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>."},"date_created":"2024-07-26T09:05:55Z","year":"2024","supervisor":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"author":[{"full_name":"Lukic, Kristina","orcid":"0000-0003-1581-881X","first_name":"Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","last_name":"Lukic"}],"date_updated":"2026-10-16T08:50:36Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"das_tickbox":"0","abstract":[{"text":"This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor.","lang":"eng"}],"day":"26","date_published":"2024-07-26T00:00:00Z","doi":"10.15479/at:ista:17319","department":[{"_id":"LeSa"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"_id":"17319","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","month":"07","publication_identifier":{"issn":["2663-337X"]},"researchdata_availability":"no","degree_awarded":"PhD","ddc":["580"],"type":"dissertation","status":"public","fulldoi":"https://doi.org/10.15479/at:ista:17319","publication_status":"published","title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","file":[{"access_level":"open_access","file_name":"Thesis_Kristina_Lukic.pdf","embargo":"2025-01-26","date_created":"2024-07-26T13:14:24Z","content_type":"application/pdf","date_updated":"2025-01-26T23:30:04Z","relation":"main_file","checksum":"95517e697ea6a87e267e649cad560989","creator":"cchlebak","file_size":24639084,"file_id":"17320"},{"checksum":"74325746a9a05078fb9935dbf2aef752","creator":"cchlebak","file_id":"17321","file_size":96334272,"file_name":"Thesis_Kristina_Lukic.docx","access_level":"closed","date_created":"2024-07-26T13:14:50Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_updated":"2025-01-26T23:30:04Z","embargo_to":"open_access"}],"doi_confirm":"1","language":[{"iso":"eng"}],"page":"224","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2025-01-26T23:30:04Z","corr_author":"1","OA_place":"publisher","supplementarymaterial":"no"},{"supplementarymaterial":"yes","corr_author":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41594-025-01721-3"}]},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2025-01-01T23:30:03Z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"1061-1071","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","dataavailabilitystatement":"Structures of the three SCs were deposited in PDB (accessions 8PW5, 8PW6 and 8PW7) with corresponding cryo-EM density maps in EMDB (IDs 17989, 17990 and 17991). As the models were built on composite maps, the consensus and focused maps for all components of the three SCs have also been deposited on EMDB (18023, 18022, 18025, 18024, 18027, 18026, 18017, 18018, 18019, 18021, 18020, 18015, 18011, 18012, 18013 and 18014). Similarly, structures of complex I were deposited in PDB (accessions 8RGR, 8RGQ, 8RGP and 8RGT) with corresponding composite cryo-EM density maps (19147, 19146, 19145 and 19148) and consensus/focused maps (19085, 19086, 19087, 19091, 19092, 19093, 19088, 19089, 19090, 19105, 19106 and 19107) in EMDB. The following previously deposited models (PDB codes) have been used in the manuscript: 5gup, 5xth, 5iy5, 1ooc, 5z62, 3cx5, 7o3c, 5j4z, 5j7y, 7o37 and 6g2j. Uncropped gels and western blot, as well as the raw data for the activity assays summarized in Extended Data Fig. 8h, have been provided as Source data in this publication. Source data are provided with this paper.","publication_status":"published","file":[{"file_id":"15392","file_size":24424729,"checksum":"21f05d188762acd7f49a97f3d09c8d9f","creator":"lsazanov","date_updated":"2025-01-01T23:30:03Z","relation":"main_file","access_level":"open_access","file_name":"megacomplex_submit_NSMB_withFigures.pdf","embargo":"2025-01-01","date_created":"2024-05-14T11:57:56Z","content_type":"application/pdf"}],"title":"SCAF1 drives the compositional diversity of mammalian respirasomes","project":[{"call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines"}],"isi":1,"fulldoi":"https://doi.org/10.1038/s41594-024-01255-0","status":"public","ddc":["572"],"ec_funded":1,"type":"journal_article","quality_controlled":"1","pmid":1,"intvolume":"        31","article_type":"original","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"researchdata_availability":"yes","volume":31,"publisher":"Springer Nature","oa_version":"Submitted Version","month":"07","external_id":{"isi":["001196897300001"],"pmid":["38575788"]},"acknowledgement":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.","department":[{"_id":"LeSa"}],"_id":"15323","abstract":[{"lang":"eng","text":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions."}],"scopus_import":"1","date_published":"2024-07-01T00:00:00Z","day":"01","doi":"10.1038/s41594-024-01255-0","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"ScienComp"}],"das_tickbox":"1","author":[{"full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-10-16T08:43:37Z","citation":{"mla":"Vercellino, Irene, and Leonid A. Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1061–71, doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>.","short":"I. Vercellino, L.A. Sazanov, Nature Structural and Molecular Biology 31 (2024) 1061–1071.","ieee":"I. Vercellino and L. A. Sazanov, “SCAF1 drives the compositional diversity of mammalian respirasomes,” <i>Nature Structural and Molecular Biology</i>, vol. 31. Springer Nature, pp. 1061–1071, 2024.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” <i>Nature Structural and Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2024). SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01255-0\">https://doi.org/10.1038/s41594-024-01255-0</a>","ama":"Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. <i>Nature Structural and Molecular Biology</i>. 2024;31:1061-1071. doi:<a href=\"https://doi.org/10.1038/s41594-024-01255-0\">10.1038/s41594-024-01255-0</a>","ista":"Vercellino I, Sazanov LA. 2024. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 31, 1061–1071."},"date_created":"2024-04-14T22:01:03Z","year":"2024","publication":"Nature Structural and Molecular Biology"},{"intvolume":"        20","researchdata_availability":"yes","volume":20,"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"article_type":"original","quality_controlled":"1","pmid":1,"article_number":"e1012508","acknowledgement":"We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","_id":"18481","department":[{"_id":"AnKi"}],"oa_version":"Published Version","month":"10","publisher":"Public Library of Science","external_id":{"pmid":["39401260"],"isi":["001331700300003"]},"das_tickbox":"1","abstract":[{"text":"A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.","lang":"eng"}],"scopus_import":"1","doi":"10.1371/journal.pcbi.1012508","DOAJ_listed":"1","day":"14","date_published":"2024-10-14T00:00:00Z","year":"2024","date_created":"2024-10-27T23:01:45Z","citation":{"apa":"Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., &#38; Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>","ista":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508.","ama":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. 2024;20. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>","short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","ieee":"R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” <i>PLoS Computational Biology</i>, vol. 20. Public Library of Science, 2024.","mla":"Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>, vol. 20, e1012508, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>.","chicago":"Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>."},"publication":"PLoS Computational Biology","author":[{"full_name":"Ho, Richard D.J.G.","first_name":"Richard D.J.G.","last_name":"Ho"},{"first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","full_name":"Kishi, Kasumi","orcid":"0000-0001-6060-4795"},{"full_name":"Majka, Maciej","first_name":"Maciej","last_name":"Majka"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","last_name":"Zagórski"}],"date_updated":"2026-10-20T22:31:31Z","OA_place":"publisher","corr_author":"1","supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"dataavailabilitystatement":"Custom software in C++ used to run the computational screen is available as S1 Simulation code. Custom script in Python used to analyze Shh profiles is available as S1 Script code. All data are in the manuscript and/or supporting information files","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20393"}]},"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2024-10-29T11:59:09Z","isi":1,"fulldoi":"https://doi.org/10.1371/journal.pcbi.1012508","file":[{"date_updated":"2024-10-29T11:59:09Z","success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2024-10-29T11:59:09Z","access_level":"open_access","file_name":"2024_PloSComBio_Ho.pdf","file_id":"18487","file_size":3732443,"creator":"dernst","checksum":"42fa714459943cb3961b40fab8fd82c8"}],"title":"Dynamics of morphogen source formation in a growing tissue","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"}],"publication_status":"published","ddc":["570"],"OA_type":"gold","APC_amount":"3197,23 EUR","type":"journal_article","status":"public"},{"publication":"Chemical Engineering Journal","citation":{"apa":"Liu, Y., Lee, S., Fiedler, C.,  Spadaro, M. C., Chang, C., Li, M., … Ibáñez, M. (2024). Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals. <i>Chemical Engineering Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cej.2024.151405\">https://doi.org/10.1016/j.cej.2024.151405</a>","ama":"Liu Y, Lee S, Fiedler C, et al. Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals. <i>Chemical Engineering Journal</i>. 2024;490. doi:<a href=\"https://doi.org/10.1016/j.cej.2024.151405\">10.1016/j.cej.2024.151405</a>","ista":"Liu Y, Lee S, Fiedler C,  Spadaro MC, Chang C, Li M, Hong M, Arbiol J, Ibáñez M. 2024. Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals. Chemical Engineering Journal. 490, 151405.","mla":"Liu, Yu, et al. “Enhancing Thermoelectric Performance of SolutionpProcessed Polycrystalline SnSe with PbSe Nanocrystals.” <i>Chemical Engineering Journal</i>, vol. 490, 151405, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.cej.2024.151405\">10.1016/j.cej.2024.151405</a>.","ieee":"Y. Liu <i>et al.</i>, “Enhancing thermoelectric performance of solutionpProcessed polycrystalline SnSe with PbSe nanocrystals,” <i>Chemical Engineering Journal</i>, vol. 490. Elsevier, 2024.","short":"Y. Liu, S. Lee, C. Fiedler, M.C.  Spadaro, C. Chang, M. Li, M. Hong, J. Arbiol, M. Ibáñez, Chemical Engineering Journal 490 (2024).","chicago":"Liu, Yu, Seungho Lee, Christine Fiedler, Maria Chiara  Spadaro, Cheng Chang, Mingquan Li, Min Hong, Jordi Arbiol, and Maria Ibáñez. “Enhancing Thermoelectric Performance of SolutionpProcessed Polycrystalline SnSe with PbSe Nanocrystals.” <i>Chemical Engineering Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cej.2024.151405\">https://doi.org/10.1016/j.cej.2024.151405</a>."},"year":"2024","date_created":"2024-05-05T22:01:03Z","date_updated":"2026-10-20T22:31:32Z","author":[{"full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee"},{"id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","first_name":"Christine","last_name":"Fiedler","full_name":"Fiedler, Christine"},{"full_name":" Spadaro, Maria Chiara","first_name":"Maria Chiara","last_name":" Spadaro"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"first_name":"Mingquan","last_name":"Li","full_name":"Li, Mingquan"},{"full_name":"Hong, Min","last_name":"Hong","first_name":"Min"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"das_tickbox":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"day":"15","date_published":"2024-06-15T00:00:00Z","doi":"10.1016/j.cej.2024.151405","abstract":[{"lang":"eng","text":"There is a growing interest in cost-effective polycrystalline SnSe-based thermoelectric (TE) materials, which are able to replace the high performance but mechanically fragile and costly single-crystalline SnSe. In this study, we present a low-temperature solution-based approach to produce SnSe-PbSe nanocomposites with outstanding TE performance. Our method involves combining surfactant-free SnSe particles with oleate-capped PbSe nanocrystals in specific ratios, followed by thermal annealing and consolidation using spark plasma sintering. These nanocomposites are characterized by distinct compositional and structural properties that significantly impact their transport properties. In particular, the addition of oleate-capped PbSe nanocrystals results in: i) a reduction in the electrostatically adsorbed Na at the surface of the SnSe particles; ii) a reduction of Sn vacancies due to alloying with Pb; iii) an increase in grain boundary density; and iv) the formation of PbSnSe secondary phases. Notably, the SnSe-2.5 %PbSe nanocomposites demonstrate a 30 % decrease in thermal conductivity compared to that of the SnSe matrix. This reduction contributes to a maximum figure of merit (zT) of 1.75 at 788 K with a high average zT value of ca. 1.2 in the medium temperature range of 573–773 K. These values represent one of the highest reported in polycrystalline SnSe materials, showcasing the potential of our fabricated SnSe-PbSe nanocomposites for cost-effective TE applications."}],"scopus_import":"1","department":[{"_id":"MaIb"}],"_id":"15357","acknowledgement":"The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility, and the Lab Support Facility (LSF). Y.L., S.L., C.F., C.C. and M.I. acknowledge financial support from ISTA and the Werner Siemens Foundation. Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). C.C. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 12374023). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. The authors thank support from the project NANOGEN(PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF Away of making Europe”, by the “European Union”. ICN2 is supported by the Severo Ochoaprogram from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme / Generalitat de Catalunya. ICN2 is founding member of e-DREAM [70].","external_id":{"isi":["001234835500001"]},"publisher":"Elsevier","oa_version":"Published Version","month":"06","article_type":"original","publication_identifier":{"issn":["1385-8947"]},"researchdata_availability":"upon request","volume":490,"intvolume":"       490","article_number":"151405","quality_controlled":"1","type":"journal_article","OA_type":"hybrid","ddc":["540"],"status":"public","fulldoi":"https://doi.org/10.1016/j.cej.2024.151405","isi":1,"publication_status":"published","file":[{"relation":"main_file","date_updated":"2025-01-09T09:24:29Z","success":1,"file_name":"2024_ChemEngineeringJour_Liu.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-09T09:24:29Z","file_size":12233704,"file_id":"18800","checksum":"6609232a208b9a89d055a270ef0af1fe","creator":"dernst"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat 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S2.","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","OA_place":"publisher","author":[{"last_name":"Krammer","first_name":"Teresa","full_name":"Krammer, Teresa"},{"first_name":"Hannah T.","last_name":"Stuart","full_name":"Stuart, Hannah T."},{"full_name":"Gromberg, Elena","last_name":"Gromberg","first_name":"Elena"},{"first_name":"Keisuke","last_name":"Ishihara","full_name":"Ishihara, Keisuke"},{"full_name":"Cislo, Dillon","first_name":"Dillon","last_name":"Cislo"},{"full_name":"Melchionda, Manuela","last_name":"Melchionda","first_name":"Manuela"},{"last_name":"Becerril Perez","first_name":"Fernando","full_name":"Becerril Perez, Fernando"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"first_name":"Elena","last_name":"Costantini","full_name":"Costantini, Elena"},{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie"},{"first_name":"Laura","last_name":"Arbanas","full_name":"Arbanas, Laura"},{"last_name":"Hörmann","first_name":"Alexandra","full_name":"Hörmann, Alexandra"},{"last_name":"Neumüller","first_name":"Ralph A.","full_name":"Neumüller, Ralph A."},{"full_name":"Elvassore, Nicola","last_name":"Elvassore","first_name":"Nicola"},{"full_name":"Siggia, Eric","last_name":"Siggia","first_name":"Eric"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"},{"full_name":"Tanaka, Elly M.","first_name":"Elly M.","last_name":"Tanaka"}],"date_updated":"2026-10-20T22:31:34Z","year":"2024","date_created":"2024-06-16T22:01:07Z","citation":{"mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>.","ieee":"T. Krammer <i>et al.</i>, “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” <i>Developmental Cell</i>, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10.","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>.","apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. 2024;59(15):1940-1953.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>"},"publication":"Developmental Cell","abstract":[{"text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.","lang":"eng"}],"scopus_import":"1","doi":"10.1016/j.devcel.2024.04.021","day":"01","date_published":"2024-08-01T00:00:00Z","das_tickbox":"1","month":"08","oa_version":"Published Version","publisher":"Elsevier","external_id":{"pmid":["38776925"],"isi":["001289684800001"]},"acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","_id":"17148","department":[{"_id":"AnKi"}],"quality_controlled":"1","issue":"15","pmid":1,"intvolume":"        59","researchdata_availability":"yes","volume":59,"article_type":"original","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]}},{"supplementarymaterial":"unclear","corr_author":"1","OA_place":"publisher","article_processing_charge":"No","file_date_updated":"2025-06-12T22:30:02Z","has_accepted_license":"1","related_material":{"record":[{"id":"8707","status":"public","relation":"part_of_dissertation"},{"id":"18648","status":"public","relation":"part_of_dissertation"}]},"oa":1,"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"138","doi_confirm":"1","publication_status":"published","file":[{"checksum":"d45e4d170f9a70a1f69b44b99bd058e4","creator":"nmachnik","file_size":12845009,"file_id":"18649","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","access_level":"open_access","embargo":"2025-06-12","date_created":"2024-12-11T11:59:54Z","content_type":"application/pdf","relation":"main_file","date_updated":"2025-06-12T22:30:02Z"},{"embargo_to":"open_access","relation":"source_file","date_updated":"2025-06-12T22:30:02Z","content_type":"application/zip","date_created":"2024-12-11T11:59:34Z","file_name":"thesis.zip","access_level":"closed","file_id":"18650","file_size":14189810,"creator":"nmachnik","checksum":"f88c9acc62002395ec4dcbdb5eea8b82"}],"project":[{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"}],"title":"Algorithms for causal learning and comparative analysis for genomic data","fulldoi":"https://doi.org/10.15479/at:ista:18642","status":"public","type":"dissertation","degree_awarded":"PhD","ddc":["576"],"publication_identifier":{"issn":["2663-337X"]},"researchdata_availability":"unclear","publisher":"Institute of Science and Technology Austria","month":"12","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"_id":"18642","acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","day":"11","date_published":"2024-12-11T00:00:00Z","doi":"10.15479/at:ista:18642","abstract":[{"lang":"eng","text":"This thesis consists of two pieces of work in the broader field of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefficient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fine-map genetic effects, find the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal effect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe effects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specific genetic effects, and how the error rates of this recovery are influenced\r\nby missing data due to different censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size differences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand finally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n"}],"date_updated":"2026-10-16T11:01:16Z","author":[{"orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N","last_name":"Machnik","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","first_name":"Nick N"}],"supervisor":[{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"}],"citation":{"chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>.","mla":"Machnik, Nick N. <i>Algorithms for Causal Learning and Comparative Analysis for Genomic Data</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>.","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","apa":"Machnik, N. N. (2024). <i>Algorithms for causal learning and comparative analysis for genomic data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>"},"year":"2024","date_created":"2024-12-10T13:49:15Z"},{"year":"2024","date_created":"2024-12-01T23:01:53Z","citation":{"ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>","ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., &#38; Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>.","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” <i>STAR Protocols</i>, vol. 5, no. 4. Elsevier, 2024.","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>, vol. 5, no. 4, 103187, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>."},"publication":"STAR Protocols","author":[{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin"},{"id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","first_name":"Monika Aleksandra","last_name":"Kulig","full_name":"Kulig, Monika Aleksandra"},{"first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","full_name":"Minchington, Thomas"},{"last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"date_updated":"2026-10-20T22:31:34Z","acknowledged_ssus":[{"_id":"NanoFab"}],"das_tickbox":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1"}],"doi":"10.1016/j.xpro.2024.103187","date_published":"2024-12-20T00:00:00Z","DOAJ_listed":"1","day":"20","acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","_id":"18601","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"month":"12","oa_version":"Published Version","publisher":"Elsevier","external_id":{"pmid":["39602310"]},"intvolume":"         5","volume":5,"researchdata_availability":"no","article_type":"original","publication_identifier":{"eissn":["2666-1667"]},"quality_controlled":"1","article_number":"103187","issue":"4","pmid":1,"ddc":["570"],"OA_type":"gold","APC_amount":"804 EUR","type":"journal_article","status":"public","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103187","file":[{"access_level":"open_access","file_name":"2024_STARProtoc_Lehr.pdf","date_created":"2024-12-03T10:53:23Z","content_type":"application/pdf","success":1,"date_updated":"2024-12-03T10:53:23Z","relation":"main_file","checksum":"0c61a6f9978608a103865905e06f4581","creator":"dernst","file_id":"18610","file_size":4989169}],"title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011"}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"dataavailabilitystatement":"This study did not generate datasets or code.","oa":1,"related_material":{"record":[{"id":"19763","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2024-12-03T10:53:23Z","OA_place":"publisher","corr_author":"1","supplementarymaterial":"no"},{"corr_author":"1","OA_place":"repository","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"relation":"later_version","id":"23043","status":"public"},{"relation":"dissertation_contains","id":"18642","status":"public"}]},"oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.1101/2023.12.06.570392","publication_status":"published","title":"Causal inference for multiple risk factors and diseases from genomics data","project":[{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"},{"name":"Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation","grant_number":"590359","_id":"bd936e6f-d553-11ed-ba76-a82299f63e8c"}],"type":"preprint","OA_type":"free access","status":"public","researchdata_availability":"not applicable","acknowledgement":"We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). ","department":[{"_id":"MaRo"}],"_id":"18648","oa_version":"Preprint","month":"08","acknowledged_ssus":[{"_id":"ScienComp"}],"das_tickbox":"0","abstract":[{"lang":"eng","text":"Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n"}],"date_published":"2024-08-10T00:00:00Z","day":"10","doi":"10.1101/2023.12.06.570392","citation":{"mla":"Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” <i>BioRxiv</i>, 2024, doi:<a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>.","short":"N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024).","ieee":"N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” <i>bioRxiv</i>. 2024.","chicago":"Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” <i>BioRxiv</i>, 2024. <a href=\"https://doi.org/10.1101/2023.12.06.570392\">https://doi.org/10.1101/2023.12.06.570392</a>.","apa":"Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., &#38; Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.12.06.570392\">https://doi.org/10.1101/2023.12.06.570392</a>","ama":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. <i>bioRxiv</i>. 2024. doi:<a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>","ista":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, <a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>."},"year":"2024","date_created":"2024-12-11T10:42:59Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.12.06.570392"}],"publication":"bioRxiv","author":[{"last_name":"Machnik","first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N"},{"full_name":"Mahmoudi, Seyed Mahdi","first_name":"Seyed Mahdi","id":"b9f6d5ef-7774-11eb-a47f-df2c75c02ee7","last_name":"Mahmoudi"},{"full_name":"Borczyk, Malgorzata","first_name":"Malgorzata","last_name":"Borczyk"},{"id":"30d4014e-7753-11eb-b44b-db6d61112e73","first_name":"Ilse","last_name":"Krätschmer","full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259"},{"full_name":"Bauer, Markus J.","first_name":"Markus J.","last_name":"Bauer"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson"}],"date_updated":"2026-10-20T22:31:33Z"},{"quality_controlled":"1","issue":"13","article_number":"e5029","pmid":1,"intvolume":"        14","researchdata_availability":"no","volume":14,"publication_identifier":{"eissn":["2331-8325"]},"article_type":"original","oa_version":"Published Version","month":"07","publisher":"Bio-Protocol","external_id":{"pmid":["39007160"]},"acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING to E.M.B.).","_id":"17233","department":[{"_id":"MiSi"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene."}],"doi":"10.21769/BioProtoc.5029","date_published":"2024-07-05T00:00:00Z","day":"05","das_tickbox":"0","author":[{"id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","first_name":"Ziqiang","last_name":"Li","full_name":"Li, Ziqiang"},{"last_name":"Huard","first_name":"Jennifer","full_name":"Huard, Jennifer"},{"full_name":"Bayer, Emmanuelle M.","last_name":"Bayer","first_name":"Emmanuelle M."},{"full_name":"Wattelet-Boyer, Valérie","last_name":"Wattelet-Boyer","first_name":"Valérie"}],"date_updated":"2026-10-21T07:57:41Z","date_created":"2024-07-14T22:01:11Z","year":"2024","citation":{"chicago":"LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>. Bio-Protocol, 2024. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>.","short":"Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024).","ieee":"Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” <i>Bio-protocol</i>, vol. 14, no. 13. Bio-Protocol, 2024.","mla":"LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>.","ama":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-protocol</i>. 2024;14(13). doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>","ista":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. 2024. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 14(13), e5029.","apa":"LI, Z., Huard, J., Bayer, E. M., &#38; Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-Protocol</i>. Bio-Protocol. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>"},"publication":"Bio-protocol","supplementarymaterial":"no","oa":1,"article_processing_charge":"Yes","file_date_updated":"2024-07-16T06:16:11Z","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis","file":[{"relation":"main_file","date_updated":"2024-07-16T06:16:11Z","success":1,"access_level":"open_access","file_name":"2024_BioProtocol_Li.pdf","content_type":"application/pdf","date_created":"2024-07-16T06:16:11Z","file_id":"17242","file_size":2896048,"checksum":"c8671c0ad483da6407cb16cc3fef1990","creator":"dernst"}],"publication_status":"published","fulldoi":"https://doi.org/10.21769/BioProtoc.5029","status":"public","ddc":["570"],"type":"journal_article"},{"department":[{"_id":"MiSi"}],"_id":"17191","external_id":{"pmid":["38907047"],"isi":["001251509300001"]},"publisher":"Springer Nature","month":"06","oa_version":"None","publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"article_type":"letter_note","volume":25,"researchdata_availability":"no","intvolume":"        25","pmid":1,"quality_controlled":"1","publication":"Nature Immunology","citation":{"apa":"Lembo, S., &#38; Sixt, M. K. (2024). Nuclear squeezing wakes up dendritic cells. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-024-01881-2\">https://doi.org/10.1038/s41590-024-01881-2</a>","ama":"Lembo S, Sixt MK. Nuclear squeezing wakes up dendritic cells. <i>Nature Immunology</i>. 2024;25:1131–1132. doi:<a href=\"https://doi.org/10.1038/s41590-024-01881-2\">10.1038/s41590-024-01881-2</a>","ista":"Lembo S, Sixt MK. 2024. Nuclear squeezing wakes up dendritic cells. Nature Immunology. 25, 1131–1132.","short":"S. Lembo, M.K. Sixt, Nature Immunology 25 (2024) 1131–1132.","ieee":"S. Lembo and M. K. Sixt, “Nuclear squeezing wakes up dendritic cells,” <i>Nature Immunology</i>, vol. 25. Springer Nature, pp. 1131–1132, 2024.","mla":"Lembo, Sergio, and Michael K. Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” <i>Nature Immunology</i>, vol. 25, Springer Nature, 2024, pp. 1131–1132, doi:<a href=\"https://doi.org/10.1038/s41590-024-01881-2\">10.1038/s41590-024-01881-2</a>.","chicago":"Lembo, Sergio, and Michael K Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” <i>Nature Immunology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41590-024-01881-2\">https://doi.org/10.1038/s41590-024-01881-2</a>."},"date_created":"2024-06-30T22:01:05Z","year":"2024","date_updated":"2026-10-21T07:57:17Z","author":[{"last_name":"Lembo","first_name":"Sergio","id":"d993a7b2-292f-11ed-aaac-fb045a912e31","orcid":"0000-0002-2253-8771","full_name":"Lembo, Sergio"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"das_tickbox":"0","day":"21","date_published":"2024-06-21T00:00:00Z","doi":"10.1038/s41590-024-01881-2","abstract":[{"lang":"eng","text":"Dendritic cells migrate to and from lymph nodes in response to chemokine gradients.Data now show that steady-state migration of these cells can be triggered by a mechanosensitive pathway."}],"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"1131–1132 ","article_processing_charge":"No","corr_author":"1","supplementarymaterial":"no","type":"journal_article","status":"public","fulldoi":"https://doi.org/10.1038/s41590-024-01881-2","isi":1,"publication_status":"published","title":"Nuclear squeezing wakes up dendritic cells"},{"corr_author":"1","_id":"18716","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"None","oa":1,"month":"09","related_material":{"record":[{"relation":"used_in_publication","id":"18710","status":"public"}]},"publisher":"Zenodo","fulldoi":"https://doi.org/10.5281/ZENODO.13833474","doi":"10.5281/ZENODO.13833474","day":"24","date_published":"2024-09-24T00:00:00Z","title":"Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl","abstract":[{"text":"Data for publication 10.1039/d4cp03727h","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.13833474"}],"type":"research_data_reference","ddc":["530"],"date_created":"2025-01-02T08:21:55Z","year":"2024","citation":{"apa":"Hrast, M. (2024). Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13833474\">https://doi.org/10.5281/ZENODO.13833474</a>","ama":"Hrast M. Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.13833474\">10.5281/ZENODO.13833474</a>","ista":"Hrast M. 2024. Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13833474\">10.5281/ZENODO.13833474</a>.","mla":"Hrast, Mateja. <i>Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.13833474\">10.5281/ZENODO.13833474</a>.","ieee":"M. Hrast, “Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl.” Zenodo, 2024.","short":"M. Hrast, (2024).","chicago":"Hrast, Mateja. “Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.13833474\">https://doi.org/10.5281/ZENODO.13833474</a>."},"date_updated":"2026-10-21T07:56:54Z","status":"public","author":[{"full_name":"Hrast, Mateja","first_name":"Mateja","id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d","last_name":"Hrast"}]},{"title":"Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl","date_published":"2024-09-24T00:00:00Z","day":"24","doi":"10.5281/zenodo.13833474","fulldoi":"https://doi.org/10.5281/zenodo.13833474","author":[{"last_name":"Hrast","first_name":"Mateja","full_name":"Hrast, Mateja"}],"status":"public","date_updated":"2026-10-21T07:56:55Z","citation":{"apa":"Hrast, M. (2024). Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. Repository. <a href=\"https://doi.org/10.5281/zenodo.13833474\">https://doi.org/10.5281/zenodo.13833474</a>","ista":"Hrast M. 2024. Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl, Repository, <a href=\"https://doi.org/10.5281/zenodo.13833474\">10.5281/zenodo.13833474</a>.","ama":"Hrast M. Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. 2024. doi:<a href=\"https://doi.org/10.5281/zenodo.13833474\">10.5281/zenodo.13833474</a>","mla":"Hrast, Mateja. <i>Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl</i>. Repository, 2024, doi:<a href=\"https://doi.org/10.5281/zenodo.13833474\">10.5281/zenodo.13833474</a>.","ieee":"M. Hrast, “Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl.” Repository, 2024.","short":"M. Hrast, (2024).","chicago":"Hrast, Mateja. “Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” Repository, 2024. <a href=\"https://doi.org/10.5281/zenodo.13833474\">https://doi.org/10.5281/zenodo.13833474</a>."},"ddc":["530"],"date_created":"2026-09-09T09:20:36Z","year":"2024","type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.13833475","open_access":"1"}],"OA_type":"green","OA_place":"repository","related_material":{"record":[{"relation":"used_in_publication","id":"18710","status":"public"}]},"publisher":"Repository","month":"09","oa_version":"None","oa":1,"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MiLe"},{"_id":"MaSe"}],"_id":"22866"},{"citation":{"chicago":"Stark, Konstantin, Badr Kilani, Sven Stockhausen, Johanna Busse, Irene Schubert, Thuy Duong Tran, Florian R Gärtner, et al. “Antibodies and Complement Are Key Drivers of Thrombosis.” <i>Immunity</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">https://doi.org/10.1016/j.immuni.2024.08.007</a>.","mla":"Stark, Konstantin, et al. “Antibodies and Complement Are Key Drivers of Thrombosis.” <i>Immunity</i>, vol. 57, no. 9, Elsevier, 2024, pp. 2140–56, doi:<a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">10.1016/j.immuni.2024.08.007</a>.","ieee":"K. Stark <i>et al.</i>, “Antibodies and complement are key drivers of thrombosis,” <i>Immunity</i>, vol. 57, no. 9. Elsevier, pp. 2140–2156, 2024.","short":"K. Stark, B. Kilani, S. Stockhausen, J. Busse, I. Schubert, T.D. Tran, F.R. Gärtner, A. Leunig, K. Pekayvaz, L. Nicolai, V. Fumagalli, J. Stermann, F. Stephan, C. David, M.B. Müller, B. Heyman, A. Lux, A. Da Palma Guerreiro, L.P. Frenzel, C.Q. Schmidt, A. Dopler, M. Moser, S. Chandraratne, M.L. Von Brühl, M. Lorenz, T. Korff, M. Rudelius, O. Popp, M. Kirchner, P. Mertins, F. Nimmerjahn, M. Iannacone, M. Sperandio, B. Engelmann, A. Verschoor, S. Massberg, Immunity 57 (2024) 2140–2156.","ama":"Stark K, Kilani B, Stockhausen S, et al. Antibodies and complement are key drivers of thrombosis. <i>Immunity</i>. 2024;57(9):2140-2156. doi:<a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">10.1016/j.immuni.2024.08.007</a>","ista":"Stark K, Kilani B, Stockhausen S, Busse J, Schubert I, Tran TD, Gärtner FR, Leunig A, Pekayvaz K, Nicolai L, Fumagalli V, Stermann J, Stephan F, David C, Müller MB, Heyman B, Lux A, Da Palma Guerreiro A, Frenzel LP, Schmidt CQ, Dopler A, Moser M, Chandraratne S, Von Brühl ML, Lorenz M, Korff T, Rudelius M, Popp O, Kirchner M, Mertins P, Nimmerjahn F, Iannacone M, Sperandio M, Engelmann B, Verschoor A, Massberg S. 2024. Antibodies and complement are key drivers of thrombosis. Immunity. 57(9), 2140–2156.","apa":"Stark, K., Kilani, B., Stockhausen, S., Busse, J., Schubert, I., Tran, T. D., … Massberg, S. (2024). Antibodies and complement are key drivers of thrombosis. <i>Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">https://doi.org/10.1016/j.immuni.2024.08.007</a>"},"year":"2024","date_created":"2024-09-22T22:01:42Z","publication":"Immunity","author":[{"full_name":"Stark, Konstantin","first_name":"Konstantin","last_name":"Stark"},{"full_name":"Kilani, Badr","last_name":"Kilani","first_name":"Badr"},{"full_name":"Stockhausen, Sven","last_name":"Stockhausen","first_name":"Sven"},{"first_name":"Johanna","last_name":"Busse","full_name":"Busse, Johanna"},{"full_name":"Schubert, Irene","first_name":"Irene","last_name":"Schubert"},{"full_name":"Tran, Thuy Duong","first_name":"Thuy Duong","last_name":"Tran"},{"last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R"},{"full_name":"Leunig, Alexander","last_name":"Leunig","first_name":"Alexander"},{"full_name":"Pekayvaz, Kami","first_name":"Kami","last_name":"Pekayvaz"},{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"last_name":"Fumagalli","first_name":"Valeria","full_name":"Fumagalli, Valeria"},{"last_name":"Stermann","first_name":"Julia","full_name":"Stermann, Julia"},{"full_name":"Stephan, Felix","first_name":"Felix","last_name":"Stephan"},{"first_name":"Christian","last_name":"David","full_name":"David, Christian"},{"first_name":"Martin B.","last_name":"Müller","full_name":"Müller, Martin B."},{"first_name":"Birgitta","last_name":"Heyman","full_name":"Heyman, Birgitta"},{"full_name":"Lux, Anja","first_name":"Anja","last_name":"Lux"},{"full_name":"Da Palma Guerreiro, Alexandra","first_name":"Alexandra","last_name":"Da Palma Guerreiro"},{"first_name":"Lukas P.","last_name":"Frenzel","full_name":"Frenzel, Lukas P."},{"full_name":"Schmidt, Christoph Q.","first_name":"Christoph Q.","last_name":"Schmidt"},{"full_name":"Dopler, Arthur","first_name":"Arthur","last_name":"Dopler"},{"first_name":"Markus","last_name":"Moser","full_name":"Moser, Markus"},{"first_name":"Sue","last_name":"Chandraratne","full_name":"Chandraratne, Sue"},{"first_name":"Marie Luise","last_name":"Von Brühl","full_name":"Von Brühl, Marie Luise"},{"last_name":"Lorenz","first_name":"Michael","full_name":"Lorenz, Michael"},{"last_name":"Korff","first_name":"Thomas","full_name":"Korff, Thomas"},{"last_name":"Rudelius","first_name":"Martina","full_name":"Rudelius, Martina"},{"full_name":"Popp, Oliver","last_name":"Popp","first_name":"Oliver"},{"last_name":"Kirchner","first_name":"Marieluise","full_name":"Kirchner, Marieluise"},{"last_name":"Mertins","first_name":"Philipp","full_name":"Mertins, Philipp"},{"first_name":"Falk","last_name":"Nimmerjahn","full_name":"Nimmerjahn, Falk"},{"first_name":"Matteo","last_name":"Iannacone","full_name":"Iannacone, Matteo"},{"full_name":"Sperandio, Markus","first_name":"Markus","last_name":"Sperandio"},{"last_name":"Engelmann","first_name":"Bernd","full_name":"Engelmann, Bernd"},{"full_name":"Verschoor, Admar","first_name":"Admar","last_name":"Verschoor"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"date_updated":"2026-10-21T08:01:09Z","das_tickbox":"1","abstract":[{"lang":"eng","text":"Venous thromboembolism (VTE) is a common, deadly disease with an increasing incidence despite preventive efforts. Clinical observations have associated elevated antibody concentrations or antibody-based therapies with thrombotic events. However, how antibodies contribute to thrombosis is unknown. Here, we show that reduced blood flow enabled immunoglobulin M (IgM) to bind to FcμR and the polymeric immunoglobulin receptor (pIgR), initiating endothelial activation and platelet recruitment. Subsequently, the procoagulant surface of activated platelets accommodated antigen- and FcγR-independent IgG deposition. This leads to classical complement activation, setting in motion a prothrombotic vicious circle. Key elements of this mechanism were present in humans in the setting of venous stasis as well as in the dysregulated immunothrombosis of COVID-19. This antibody-driven thrombosis can be prevented by pharmacologically targeting complement. Hence, our results uncover antibodies as previously unrecognized central regulators of thrombosis. These findings carry relevance for therapeutic application of antibodies and open innovative avenues to target thrombosis without compromising hemostasis."}],"scopus_import":"1","day":"10","date_published":"2024-09-10T00:00:00Z","doi":"10.1016/j.immuni.2024.08.007","acknowledgement":"We thank Michael Carroll (Harvard Medical School, Boston) for providing Ighmtm1Che, C4−/−, and C3−/− mice; Mark Suter (University of Zurich, Zurich) for providing Aicda−/− mice; Marina Botto (Imperial College London, London) for providing C1q−/− and fB−/− mice; Craig Gerard (Harvard Medical School, Boston) for providing C3aR−/− mice; Falk Nimmerjahn (University Erlangen-Nuernberg, Erlangen) for providing Fcgr−/−Fcgr2b−/− mice; Karl Lang (University of Duisburg-Essen, Essen) for providing Fcmr−/− mice; Hans Hengartner and Rolf Zinkernagel (ETH Zurich, Zurich) for providing KL25 mice; Mark Zabel (University Hospital of Zurich, Zurich) for providing CR2−/− mice; Christie Ballantyne (Baylor College of Medicine, Houston) for providing CD11c−/− mice; and Siamon Gordon (University of Oxford, Oxford) for providing CD11b−/− mice. A.V. wishes to thank Michael Grünaug and dedicates this work to Annette, Rita, and Hans.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. \r\n947611) (K.S.). This study was supported by the Deutsche Forschungsgemeinschaft through the collaborative research center 914 project B02 (K.S. and S.M.), project B04 (A.V.), project A01 (M.M.), project B01 (M.S.), the collaborative research center 1123 project B07 (K.S. and S.M.), the collaborative research center 359 (project A03 [K.S.] and B02 [M.S.]), the international research training group 1911 project B09 (A.V.), the clinical research unit 303 project 7 (A.V.), cluster of excellence 2167 (A.V.), collaborative research center 1526 project 05 (A.V.), the ANR-DFG project JAKPOT (K.S.), LMUexcellent (K.S.), and the Deutsche Zentrum für Herz-Kreislauf-Forschung (PostDoc Grant and partner site project [K.S. and S.M.]). M.I. is supported by the European Research Council (ERC) Advanced Grant 101141363, ERC Proof of Concept Grant 101138728, Italian Association for Cancer Research (AIRC) Grants 19891 and \r\n22737, Italian Ministry for University and Research Grants PE00000007 (INF-ACT) and PRIN \r\n2022FMESXL, Funded Research Agreement from Asher Biotherapeutics, VIR Biotechnology, and BlueJay Therapeutics. V.F. is supported by the Italian Ministry for University and Research Grants PE00000007 (INF-ACT) and Fondazione Prossimo Mio.","department":[{"_id":"MiSi"}],"_id":"18109","publisher":"Elsevier","oa_version":"Published Version","month":"09","external_id":{"isi":["001317438500001"],"pmid":["39226900"]},"intvolume":"        57","publication_identifier":{"eissn":["1097-4180"]},"article_type":"original","volume":57,"researchdata_availability":"upon request","quality_controlled":"1","issue":"9","pmid":1,"ddc":["570"],"type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1016/j.immuni.2024.08.007","publication_status":"published","file":[{"file_size":6892750,"file_id":"18162","checksum":"4683de43d06a8fd8e3fc91af4ddc1ba2","creator":"dernst","success":1,"date_updated":"2024-09-30T09:16:03Z","relation":"main_file","file_name":"2024_Immunity_Stark.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-09-30T09:16:03Z"}],"title":"Antibodies and complement are key drivers of thrombosis","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"2140-2156","dataavailabilitystatement":"All data reported in this paper will be shared by the lead contact upon request. This paper does not report original codes. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","oa":1,"file_date_updated":"2024-09-30T09:16:03Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","supplementarymaterial":"yes"},{"supplementarymaterial":"no","corr_author":"1","oa":1,"file_date_updated":"2024-02-26T10:10:48Z","has_accepted_license":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","file":[{"file_id":"15030","file_size":1054754,"creator":"dernst","checksum":"b89716aae6a5599f187897e39de1e53a","success":1,"relation":"main_file","date_updated":"2024-02-26T10:10:48Z","date_created":"2024-02-26T10:10:48Z","content_type":"application/pdf","file_name":"2024_LIPICs_Goranci.pdf","access_level":"open_access"}],"title":"Electrical flows for polylogarithmic competitive oblivious routing","project":[{"call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures"},{"name":"Efficient algorithms","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"isi":1,"arxiv":1,"fulldoi":"https://doi.org/10.4230/LIPIcs.ITCS.2024.55","status":"public","ec_funded":1,"ddc":["000"],"type":"conference","quality_controlled":"1","article_number":"55","intvolume":"       287","publication_identifier":{"isbn":["9783959773096"],"issn":["1868-8969"]},"researchdata_availability":"no","volume":287,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","month":"01","oa_version":"Published Version","external_id":{"isi":["001300389400055"],"arxiv":["2303.02491"]},"conference":{"location":"Berkeley, CA, United States","start_date":"2024-01-30","end_date":"2024-02-02","name":"ITCS: Innovations in Theoretical Computer Science"},"acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets), 2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398 and a Sloan Research Fellowship.","alternative_title":["LIPIcs"],"department":[{"_id":"MoHe"}],"_id":"15008","abstract":[{"lang":"eng","text":"Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. \r\nIn this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth."}],"scopus_import":"1","date_published":"2024-01-24T00:00:00Z","day":"24","doi":"10.4230/LIPIcs.ITCS.2024.55","das_tickbox":"0","author":[{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"first_name":"Sushant","last_name":"Sachdeva","full_name":"Sachdeva, Sushant"},{"first_name":"A. R.","last_name":"Sricharan","full_name":"Sricharan, A. R."}],"date_updated":"2026-10-21T08:02:42Z","citation":{"ama":"Goranci G, Henzinger M, Räcke H, Sachdeva S, Sricharan AR. Electrical flows for polylogarithmic competitive oblivious routing. In: <i>15th Innovations in Theoretical Computer Science Conference</i>. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">10.4230/LIPIcs.ITCS.2024.55</a>","ista":"Goranci G, Henzinger M, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 287, 55.","apa":"Goranci, G., Henzinger, M., Räcke, H., Sachdeva, S., &#38; Sricharan, A. R. (2024). Electrical flows for polylogarithmic competitive oblivious routing. In <i>15th Innovations in Theoretical Computer Science Conference</i> (Vol. 287). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">https://doi.org/10.4230/LIPIcs.ITCS.2024.55</a>","chicago":"Goranci, Gramoz, Monika Henzinger, Harald Räcke, Sushant Sachdeva, and A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” In <i>15th Innovations in Theoretical Computer Science Conference</i>, Vol. 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">https://doi.org/10.4230/LIPIcs.ITCS.2024.55</a>.","ieee":"G. Goranci, M. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical flows for polylogarithmic competitive oblivious routing,” in <i>15th Innovations in Theoretical Computer Science Conference</i>, Berkeley, CA, United States, 2024, vol. 287.","short":"G. Goranci, M. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” <i>15th Innovations in Theoretical Computer Science Conference</i>, vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">10.4230/LIPIcs.ITCS.2024.55</a>."},"year":"2024","date_created":"2024-02-18T23:01:02Z","publication":"15th Innovations in Theoretical Computer Science Conference"},{"file_date_updated":"2025-01-13T10:55:28Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"745-753","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"language":[{"iso":"eng"}],"supplementarymaterial":"yes","OA_place":"publisher","status":"public","OA_type":"hybrid","type":"journal_article","ddc":["570"],"file":[{"file_name":"2024_JourAllergyClinicalImm_Link.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-13T10:55:28Z","success":1,"relation":"main_file","date_updated":"2025-01-13T10:55:28Z","checksum":"6a5af05082e1869d7cad6406fa4eb76c","creator":"dernst","file_id":"18840","file_size":1792425}],"title":"Integrin β1–mediated mast cell immune-surveillance of blood vessel content","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.jaci.2024.03.022","isi":1,"external_id":{"pmid":["38636606"],"isi":["001308886700001"]},"oa_version":"Published Version","month":"09","publisher":"Elsevier","_id":"15408","department":[{"_id":"MiSi"}],"acknowledgement":"This work was funded by Deutsche Forschungsgemeinschaft, Germany, grants RO2133/ 9-1 and RO2133/ 9-2 in the setting of FOR2599 and TR156 project C11 (Project-ID 246807620–TRR 156) to A. Roers and Springboard-to-Postdoc grant of the Dresden International Graduate School for Biomedicine and Bioengineering (DIGS-BB), Dresden, Germany, and Fond zur Förderung der Wissenschaftlichen Forschung (FWF), Austria, Hertha Firnberg grant (project number T-1219) to A. Polikarpova.\r\nWe thank Dr Michael Gerlach, Core Facility Cellular Imaging, Faculty of Medicine Carl Gustav Carus, TU Dresden, for expert support of in vivo imaging experiments; Grace Wurigamule for help with 2-photon imaging and flow cytometric analysis of mouse skin; and Christina Hiller, Livia Schulze, Madelaine Rickauer, and Christa Haase for providing expert technical assistance.","issue":"3","pmid":1,"quality_controlled":"1","volume":154,"researchdata_availability":"no","publication_identifier":{"eissn":["1097-6825"],"issn":["0091-6749"]},"article_type":"original","intvolume":"       154","date_updated":"2026-10-21T08:01:51Z","author":[{"first_name":"Kristina","last_name":"Link","full_name":"Link, Kristina"},{"full_name":"Muhandes, Lina","first_name":"Lina","last_name":"Muhandes"},{"full_name":"Polikarpova, Anastasia","last_name":"Polikarpova","first_name":"Anastasia"},{"first_name":"Tim","last_name":"Lämmermann","full_name":"Lämmermann, Tim"},{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Fässler","first_name":"Reinhard","full_name":"Fässler, Reinhard"},{"full_name":"Roers, Axel","first_name":"Axel","last_name":"Roers"}],"publication":"Journal of Allergy and Clinical Immunology","year":"2024","date_created":"2024-05-19T22:01:13Z","citation":{"ieee":"K. Link <i>et al.</i>, “Integrin β1–mediated mast cell immune-surveillance of blood vessel content,” <i>Journal of Allergy and Clinical Immunology</i>, vol. 154, no. 3. Elsevier, pp. 745–753, 2024.","short":"K. Link, L. Muhandes, A. Polikarpova, T. Lämmermann, M.K. Sixt, R. Fässler, A. Roers, Journal of Allergy and Clinical Immunology 154 (2024) 745–753.","mla":"Link, Kristina, et al. “Integrin Β1–Mediated Mast Cell Immune-Surveillance of Blood Vessel Content.” <i>Journal of Allergy and Clinical Immunology</i>, vol. 154, no. 3, Elsevier, 2024, pp. 745–53, doi:<a href=\"https://doi.org/10.1016/j.jaci.2024.03.022\">10.1016/j.jaci.2024.03.022</a>.","chicago":"Link, Kristina, Lina Muhandes, Anastasia Polikarpova, Tim Lämmermann, Michael K Sixt, Reinhard Fässler, and Axel Roers. “Integrin Β1–Mediated Mast Cell Immune-Surveillance of Blood Vessel Content.” <i>Journal of Allergy and Clinical Immunology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jaci.2024.03.022\">https://doi.org/10.1016/j.jaci.2024.03.022</a>.","apa":"Link, K., Muhandes, L., Polikarpova, A., Lämmermann, T., Sixt, M. K., Fässler, R., &#38; Roers, A. (2024). Integrin β1–mediated mast cell immune-surveillance of blood vessel content. <i>Journal of Allergy and Clinical Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jaci.2024.03.022\">https://doi.org/10.1016/j.jaci.2024.03.022</a>","ista":"Link K, Muhandes L, Polikarpova A, Lämmermann T, Sixt MK, Fässler R, Roers A. 2024. Integrin β1–mediated mast cell immune-surveillance of blood vessel content. Journal of Allergy and Clinical Immunology. 154(3), 745–753.","ama":"Link K, Muhandes L, Polikarpova A, et al. Integrin β1–mediated mast cell immune-surveillance of blood vessel content. <i>Journal of Allergy and Clinical Immunology</i>. 2024;154(3):745-753. doi:<a href=\"https://doi.org/10.1016/j.jaci.2024.03.022\">10.1016/j.jaci.2024.03.022</a>"},"doi":"10.1016/j.jaci.2024.03.022","day":"01","date_published":"2024-09-01T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Background: IgE-mediated degranulation of mast cells (MCs) provides rapid protection against environmental hazards, including animal venoms. A fraction of tissue-resident MCs intimately associates with blood vessels. These perivascular MCs were reported to extend projections into the vessel lumen and to be the first MCs to acquire intravenously injected IgE, suggesting that IgE loading of MCs depends on their vascular association.\r\nObjective: We sought to elucidate the molecular basis of the MC–blood vessel interaction and to determine its relevance for IgE-mediated immune responses.\r\nMethods: We selectively inactivated the Itgb1 gene, encoding the β1 chain of integrin adhesion molecules (ITGB1), in MCs by conditional gene targeting in mice. We analyzed skin MCs for blood vessel association, surface IgE density, and capability to bind circulating antibody specific for MC surface molecules, as well as in vivo responses to antigen administered via different routes.\r\nResults: Lack of ITGB1 expression severely compromised MC–blood vessel association. ITGB1-deficient MCs showed normal densities of surface IgE but reduced binding of intravenously injected antibodies. While their capacity to degranulate in response to IgE ligation in vivo was unimpaired, anaphylactic responses to antigen circulating in the vasculature were largely abolished.\r\nConclusions: ITGB1-mediated association of MCs with blood vessels is key for MC immune surveillance of blood vessel content, but is dispensable for slow steady-state loading of endogenous IgE onto tissue-resident MCs."}],"das_tickbox":"0"},{"supplementarymaterial":"yes","dataavailabilitystatement":"This study includes no data deposited in external repositories.","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"102-127","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2024-02-05T12:35:03Z","oa":1,"fulldoi":"https://doi.org/10.1038/s44319-023-00020-6","publication_status":"published","file":[{"relation":"main_file","date_updated":"2024-02-05T12:35:03Z","success":1,"file_name":"2023_EmboReports_PimentaMarques.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-02-05T12:35:03Z","file_id":"14941","file_size":9645056,"checksum":"53c3ef43d9bd6d7bff3ffcf57d763cac","creator":"dernst"}],"title":"Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM","type":"journal_article","ddc":["570"],"status":"public","article_type":"original","publication_identifier":{"eissn":["1469-3178"]},"volume":25,"researchdata_availability":"not applicable","intvolume":"        25","pmid":1,"issue":"1","quality_controlled":"1","department":[{"_id":"MiSi"}],"_id":"14933","acknowledgement":"We thank all members of the Cell Cycle and Regulation Lab for the discussions and for the critical reading of the manuscript. We thank Tomer Avidor-Reiss (University of Toledo, Toledo, OH), Daniel St. Johnston (The Gurdon Institute, Cambridge, UK), David Glover (University of Cambridge, Cambridge, UK), Jingyan Fu (Agricultural University, Beijing, China) Jordan Raff (University of Oxford, Oxford, UK) and Timothy Megraw (Florida State University, Tallahassee, FL) for sharing tools. We acknowledge the technical support of Instituto Gulbenkian de Ciência (IGC)‘s Advanced Imaging Facility, in particular Gabriel Martins, Nuno Pimpão Martins and José Marques. We also thank Tiago Paixão from the IGC’s Quantitative & Digital Science Unit and Marco Louro from the CCR lab for the support provided on statistical analysis. IGC’s Advanced Imaging Facility (AIF-UIC) is supported by the national Portuguese funding ref# PPBI-POCI-01-0145-FEDER -022122. We thank the IGC’s Fly Facility, supported by CONGENTO (LISBOA-01-0145-FEDER-022170). This work was supported by an ERC grant (ERC-2015-CoG-683258) awarded to MBD and a grant from the Portuguese Research Council (FCT) awarded to APM (PTDC/BIA-BID/32225/2017).","external_id":{"pmid":["38200359"]},"publisher":"Embo Press","oa_version":"Published Version","month":"01","das_tickbox":"1","date_published":"2024-01-10T00:00:00Z","day":"10","doi":"10.1038/s44319-023-00020-6","scopus_import":"1","abstract":[{"lang":"eng","text":"Centrioles are part of centrosomes and cilia, which are microtubule organising centres (MTOC) with diverse functions. Despite their stability, centrioles can disappear during differentiation, such as in oocytes, but little is known about the regulation of their structural integrity. Our previous research revealed that the pericentriolar material (PCM) that surrounds centrioles and its recruiter, Polo kinase, are downregulated in oogenesis and sufficient for maintaining both centrosome structural integrity and MTOC activity. We now show that the expression of specific components of the centriole cartwheel and wall, including ANA1/CEP295, is essential for maintaining centrosome integrity. We find that Polo kinase requires ANA1 to promote centriole stability in cultured cells and eggs. In addition, ANA1 expression prevents the loss of centrioles observed upon PCM-downregulation. However, the centrioles maintained by overexpressing and tethering ANA1 are inactive, unlike the MTOCs observed upon tethering Polo kinase. These findings demonstrate that several centriole components are needed to maintain centrosome structure. Our study also highlights that centrioles are more dynamic than previously believed, with their structural stability relying on the continuous expression of multiple components."}],"publication":"EMBO Reports","citation":{"chicago":"Pimenta-Marques, Ana, Tania Perestrelo, Patricia Dos Reis Rodrigues, Paulo Duarte, Ana Ferreira-Silva, Mariana Lince-Faria, and Mónica Bettencourt-Dias. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” <i>EMBO Reports</i>. Embo Press, 2024. <a href=\"https://doi.org/10.1038/s44319-023-00020-6\">https://doi.org/10.1038/s44319-023-00020-6</a>.","mla":"Pimenta-Marques, Ana, et al. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” <i>EMBO Reports</i>, vol. 25, no. 1, Embo Press, 2024, pp. 102–27, doi:<a href=\"https://doi.org/10.1038/s44319-023-00020-6\">10.1038/s44319-023-00020-6</a>.","short":"A. Pimenta-Marques, T. Perestrelo, P. Dos Reis Rodrigues, P. Duarte, A. Ferreira-Silva, M. Lince-Faria, M. Bettencourt-Dias, EMBO Reports 25 (2024) 102–127.","ieee":"A. Pimenta-Marques <i>et al.</i>, “Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM,” <i>EMBO Reports</i>, vol. 25, no. 1. Embo Press, pp. 102–127, 2024.","ista":"Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, Duarte P, Ferreira-Silva A, Lince-Faria M, Bettencourt-Dias M. 2024. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO Reports. 25(1), 102–127.","ama":"Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, et al. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. <i>EMBO Reports</i>. 2024;25(1):102-127. doi:<a href=\"https://doi.org/10.1038/s44319-023-00020-6\">10.1038/s44319-023-00020-6</a>","apa":"Pimenta-Marques, A., Perestrelo, T., Dos Reis Rodrigues, P., Duarte, P., Ferreira-Silva, A., Lince-Faria, M., &#38; Bettencourt-Dias, M. (2024). Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. <i>EMBO Reports</i>. Embo Press. <a href=\"https://doi.org/10.1038/s44319-023-00020-6\">https://doi.org/10.1038/s44319-023-00020-6</a>"},"year":"2024","date_created":"2024-02-04T23:00:53Z","date_updated":"2026-10-21T08:00:18Z","author":[{"full_name":"Pimenta-Marques, Ana","last_name":"Pimenta-Marques","first_name":"Ana"},{"full_name":"Perestrelo, Tania","first_name":"Tania","last_name":"Perestrelo"},{"first_name":"Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","last_name":"Dos Reis Rodrigues","full_name":"Dos Reis Rodrigues, Patricia","orcid":"0000-0003-1681-508X"},{"full_name":"Duarte, Paulo","first_name":"Paulo","last_name":"Duarte"},{"first_name":"Ana","last_name":"Ferreira-Silva","full_name":"Ferreira-Silva, Ana"},{"first_name":"Mariana","last_name":"Lince-Faria","full_name":"Lince-Faria, Mariana"},{"full_name":"Bettencourt-Dias, Mónica","last_name":"Bettencourt-Dias","first_name":"Mónica"}]}]