[{"DOAJ_listed":"1","quality_controlled":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","month":"02","acknowledgement":"We thank Pere Rosselló for his contributions to the initial modeling of the presented sensing technique. This work was supported by Institute of Science and Technology Austria, and\r\nthe European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).","scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","year":"2024","external_id":{"arxiv":["2306.12804"]},"date_updated":"2026-07-08T07:52:51Z","citation":{"apa":"Agafonova, S., Mishra, U., Diorico, F. R., &#38; Hosten, O. (2024). Zigzag optical cavity for sensing and controlling torsional motion. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">https://doi.org/10.1103/physrevresearch.6.013141</a>","short":"S. Agafonova, U. Mishra, F.R. Diorico, O. Hosten, Physical Review Research 6 (2024).","mla":"Agafonova, Sofia, et al. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” <i>Physical Review Research</i>, vol. 6, no. 1, 013141, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">10.1103/physrevresearch.6.013141</a>.","ama":"Agafonova S, Mishra U, Diorico FR, Hosten O. Zigzag optical cavity for sensing and controlling torsional motion. <i>Physical Review Research</i>. 2024;6(1). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">10.1103/physrevresearch.6.013141</a>","chicago":"Agafonova, Sofia, Umang Mishra, Fritz R Diorico, and Onur Hosten. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">https://doi.org/10.1103/physrevresearch.6.013141</a>.","ieee":"S. Agafonova, U. Mishra, F. R. Diorico, and O. Hosten, “Zigzag optical cavity for sensing and controlling torsional motion,” <i>Physical Review Research</i>, vol. 6, no. 1. American Physical Society, 2024.","ista":"Agafonova S, Mishra U, Diorico FR, Hosten O. 2024. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 6(1), 013141."},"publisher":"American Physical Society","arxiv":1,"has_accepted_license":"1","publication_identifier":{"eissn":["2643-1564"]},"publication":"Physical Review Research","supplementarymaterial":"no","project":[{"name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","grant_number":"101087907","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6"}],"APC_amount":"2933,65 EUR","file_date_updated":"2024-02-12T11:46:50Z","volume":6,"intvolume":"         6","author":[{"orcid":"0000-0003-0582-2946","last_name":"Agafonova","full_name":"Agafonova, Sofya","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80"},{"full_name":"Mishra, Umang","last_name":"Mishra","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","first_name":"Umang"},{"orcid":"0000-0002-4947-8924","full_name":"Diorico, Fritz R","last_name":"Diorico","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","first_name":"Fritz R"},{"last_name":"Hosten","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_updated":"2024-02-12T11:46:50Z","creator":"dernst","success":1,"content_type":"application/pdf","relation":"main_file","checksum":"3a39ebffb24c1cc1dd0b547a726dc52d","file_size":1437167,"file_name":"2024_PhysicalRevResearch_Agafonova.pdf","access_level":"open_access","file_id":"14981","date_created":"2024-02-12T11:46:50Z"}],"date_published":"2024-02-05T00:00:00Z","doi":"10.1103/physrevresearch.6.013141","publication_status":"published","OA_place":"publisher","language":[{"iso":"eng"}],"day":"05","das_tickbox":"0","oa_version":"Published Version","_id":"14980","ddc":["530"],"researchdata_availability":"no","oa":1,"abstract":[{"text":"Precision sensing and manipulation of milligram-scale mechanical oscillators has attracted growing interest in the fields of table-top explorations of gravity and tests of quantum mechanics at macroscopic scales. Torsional oscillators present an opportunity in this regard due to their remarked isolation from environmental noise. For torsional motion, an effective employment of optical cavities to enhance optomechanical interactions—as already established for linear oscillators—so far faced certain challenges. Here, we propose a concept for sensing and manipulating torsional motion, where exclusively the torsional rotations of a pendulum are mapped onto the path length of a single two-mirror optical cavity. The concept inherently alleviates many limitations of previous approaches. A proof-of-principle experiment is conducted with a rigidly controlled pendulum to explore the sensing aspects of the concept and to identify practical limitations in a potential state-of-the art setup. Based on this study, we anticipate development of precision torque sensors utilizing torsional pendulums that can support sensitivities below 10−19Nm/√Hz, while the motion of the pendulums are dominated by quantum radiation pressure noise at sub-microwatts of incoming laser power. These developments will provide horizons for experiments at the interface of quantum mechanics and gravity.","lang":"eng"}],"OA_type":"gold","issue":"1","date_created":"2024-02-12T11:42:18Z","title":"Zigzag optical cavity for sensing and controlling torsional motion","status":"public","department":[{"_id":"OnHo"}],"corr_author":"1","article_processing_charge":"Yes","article_number":"013141","article_type":"original"},{"publisher":"Optica Publishing Group","external_id":{"isi":["001202817000004"]},"citation":{"ama":"Diorico FR, Zhutov A, Hosten O. Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. <i>Optica</i>. 2024;11(1):26-31. doi:<a href=\"https://doi.org/10.1364/optica.507451\">10.1364/optica.507451</a>","mla":"Diorico, Fritz R., et al. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10<sup>−7</sup> Instability Scale Relative to Cavity Linewidth.” <i>Optica</i>, vol. 11, no. 1, Optica Publishing Group, 2024, pp. 26–31, doi:<a href=\"https://doi.org/10.1364/optica.507451\">10.1364/optica.507451</a>.","ista":"Diorico FR, Zhutov A, Hosten O. 2024. Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. Optica. 11(1), 26–31.","ieee":"F. R. Diorico, A. Zhutov, and O. Hosten, “Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth,” <i>Optica</i>, vol. 11, no. 1. Optica Publishing Group, pp. 26–31, 2024.","chicago":"Diorico, Fritz R, Artem Zhutov, and Onur Hosten. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10<sup>−7</sup> Instability Scale Relative to Cavity Linewidth.” <i>Optica</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/optica.507451\">https://doi.org/10.1364/optica.507451</a>.","apa":"Diorico, F. R., Zhutov, A., &#38; Hosten, O. (2024). Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. <i>Optica</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/optica.507451\">https://doi.org/10.1364/optica.507451</a>","short":"F.R. Diorico, A. Zhutov, O. Hosten, Optica 11 (2024) 26–31."},"date_updated":"2026-07-08T08:25:12Z","type":"journal_article","year":"2024","keyword":["Atomic and Molecular Physics","and Optics","Electronic","Optical and Magnetic Materials"],"acknowledgement":"We thank Rishabh Sahu and Sebastian Wald for technical contributions to the experiment. Funding by Institute of Science and Technology Austria.","scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","DOAJ_listed":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","month":"01","date_published":"2024-01-20T00:00:00Z","file":[{"success":1,"content_type":"application/pdf","creator":"dernst","date_updated":"2024-01-17T08:53:16Z","file_size":4558986,"checksum":"eb99ca7d0fe73e22f121875175546ed7","relation":"main_file","date_created":"2024-01-17T08:53:16Z","file_id":"14824","access_level":"open_access","file_name":"2023_Optica_Diorico.pdf"}],"author":[{"last_name":"Diorico","full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924","first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Artem","id":"0f02ed6a-b514-11ee-b891-8379c5f19cb7","last_name":"Zhutov","full_name":"Zhutov, Artem"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","last_name":"Hosten","full_name":"Hosten, Onur"}],"volume":11,"file_date_updated":"2024-01-17T08:53:16Z","intvolume":"        11","APC_amount":"3393,38 EUR","supplementarymaterial":"no","publication":"Optica","dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","has_accepted_license":"1","publication_identifier":{"issn":["2334-2536"]},"OA_type":"gold","researchdata_availability":"upon request","oa":1,"abstract":[{"lang":"eng","text":"Frequency-stable lasers form the back bone of precision measurements in science and technology. Such lasers typically attain their stability through frequency locking to reference cavities. State-of-the-art locking performances to date had been achieved using frequency modulation based methods, complemented with active drift cancellation systems. We demonstrate an all passive, modulation-free laser-cavity locking technique (squash locking) that utilizes changes in spatial beam ellipticity for error signal generation, and a coherent polarization post-selection for noise resilience. By comparing two identically built proof-of-principle systems, we show a frequency locking instability of 5×10<jats:sup>−7</jats:sup> relative to the cavity linewidth at 10 s averaging. The results surpass the demonstrated performances of methods engineered over the last five decades, potentially enabling an advancement in the precision control of lasers, while creating avenues for bridging the performance gaps between industrial grade lasers with scientific ones due to the afforded simplicity and scalability."}],"ddc":["530"],"_id":"14802","OA_place":"publisher","language":[{"iso":"eng"}],"day":"20","oa_version":"Published Version","das_tickbox":"1","publication_status":"published","doi":"10.1364/optica.507451","isi":1,"page":"26-31","article_type":"original","article_processing_charge":"Yes","corr_author":"1","issue":"1","date_created":"2024-01-15T10:25:38Z","status":"public","department":[{"_id":"OnHo"}],"title":"Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth"},{"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-07-08T08:50:57Z","citation":{"short":"V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute of Science and Technology Austria, 2024.","apa":"Li, V. (2024). <i>Towards a quantum entanglement enhanced atom interferomter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>","chicago":"Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>.","ieee":"V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute of Science and Technology Austria, 2024.","ista":"Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria.","mla":"Li, Vyacheslav. <i>Towards a Quantum Entanglement Enhanced Atom Interferomter</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>.","ama":"Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>"},"year":"2024","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2024-07-11T00:00:00Z","file":[{"checksum":"15b2dbe8d2c9ed7ca5dd413827928077","relation":"main_file","file_size":6729761,"file_name":"PhD_Thesis_Vyacheslav_Li_no_signatures_PDFA.pdf","date_created":"2024-07-11T10:26:22Z","file_id":"17228","access_level":"open_access","date_updated":"2024-07-11T10:26:22Z","success":1,"content_type":"application/pdf","creator":"vli"},{"access_level":"closed","file_id":"17229","date_created":"2024-07-11T10:26:22Z","file_name":"PhD Thesis Vyacheslav Li.zip","file_size":9542859,"relation":"source_file","checksum":"16e904a11d8d0ebb167cb654ddfc7fe5","creator":"vli","content_type":"application/x-zip-compressed","date_updated":"2024-07-11T10:26:22Z"}],"author":[{"first_name":"Vyacheslav","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Vyacheslav"}],"file_date_updated":"2024-07-11T10:26:22Z","degree_awarded":"PhD","project":[{"_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11438","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","oa":1,"abstract":[{"lang":"eng","text":"This thesis describes the development of an atom interferometer designed to exploit the\r\nadvantages of utilizing quantum entanglement for enhanced precision measurements beyond\r\nthe standard quantum limit. While the project remains ongoing, significant progress has been\r\nmade.\r\nA key contribution of this work is the development of Quantrol, an experimental control\r\nsystem leveraging the ARTIQ framework. This software enables precise timing and control\r\nwithout requiring prior knowledge of ARTIQ’s implementation details or coding experience.\r\nThe interface offers user friendly visual comprehension of the experimental sequence and\r\nextended capabilities, allowing researchers to scan variables with a simple click of a mouse.\r\nThe main proposed project is to implement atom interferometric sequence with squeezed input\r\nstates inside of a dipole trap generated by a high finesse cavity. The presence of the dipole\r\ntrap allows one dimensional atomic cloud split while maintaining relatively strong confinement\r\nin other directions.\r\nWe are currently able to trap and cool 87Rb atoms to few micro kelvin temperatures, load\r\nthem into the dipole trap and state prepare them to be used for squeezing and interferometric\r\nsequence."}],"_id":"17225","ddc":["530"],"oa_version":"Published Version","language":[{"iso":"eng"}],"OA_place":"publisher","day":"11","publication_status":"published","doi":"10.15479/at:ista:17225","supervisor":[{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X"}],"page":"79","article_processing_charge":"No","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"title":"Towards a quantum entanglement enhanced atom interferomter","date_created":"2024-07-11T09:46:48Z","status":"public"},{"date_published":"2024-10-21T00:00:00Z","article_processing_charge":"No","author":[{"last_name":"Henheik","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"last_name":"Langmann","full_name":"Langmann, Edwin","first_name":"Edwin"},{"full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard"}],"department":[{"_id":"LaEr"},{"_id":"RoSe"}],"date_created":"2025-04-11T11:43:58Z","title":"Multi-band superconductors have enhanced critical temperatures","status":"public","corr_author":"1","related_material":{"record":[{"status":"public","id":"19540","relation":"dissertation_contains"},{"status":"public","relation":"later_version","id":"22290"}]},"publication":"arXiv","arxiv":1,"oa":1,"abstract":[{"text":"We introduce a multi-band BCS free energy functional and prove that for a\r\nmulti-band superconductor the effect of inter-band coupling can only increase\r\nthe critical temperature, irrespective of its attractive or repulsive nature\r\nand its strength. Further, for weak coupling and weaker inter-band coupling, we\r\nprove that the dependence of the increase in critical temperature on the\r\ninter-band coupling is (1) linear, if there are two or more equally strongly\r\nsuperconducting bands, or (2) quadratic, if there is only one dominating band.","lang":"eng"}],"year":"2024","oa_version":"Preprint","day":"21","language":[{"iso":"eng"}],"OA_place":"repository","type":"preprint","_id":"19550","external_id":{"arxiv":["2409.17297"]},"date_updated":"2026-07-13T11:34:07Z","citation":{"short":"S.J. Henheik, E. Langmann, A.B. Lauritsen, ArXiv (n.d.).","apa":"Henheik, S. J., Langmann, E., &#38; Lauritsen, A. B. (n.d.). Multi-band superconductors have enhanced critical temperatures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2409.17297\">https://doi.org/10.48550/arXiv.2409.17297</a>","chicago":"Henheik, Sven Joscha, Edwin Langmann, and Asbjørn Bækgaard Lauritsen. “Multi-Band Superconductors Have Enhanced Critical Temperatures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2409.17297\">https://doi.org/10.48550/arXiv.2409.17297</a>.","ista":"Henheik SJ, Langmann E, Lauritsen AB. Multi-band superconductors have enhanced critical temperatures. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2409.17297\">10.48550/arXiv.2409.17297</a>.","ieee":"S. J. Henheik, E. Langmann, and A. B. Lauritsen, “Multi-band superconductors have enhanced critical temperatures,” <i>arXiv</i>. .","mla":"Henheik, Sven Joscha, et al. “Multi-Band Superconductors Have Enhanced Critical Temperatures.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2409.17297\">10.48550/arXiv.2409.17297</a>.","ama":"Henheik SJ, Langmann E, Lauritsen AB. Multi-band superconductors have enhanced critical temperatures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2409.17297\">10.48550/arXiv.2409.17297</a>"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.48550/arXiv.2409.17297","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2409.17297","open_access":"1"}],"publication_status":"draft","month":"10","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"date_published":"2024-03-14T00:00:00Z","file":[{"file_name":"2024_PLoSCompBio_Chintaluri.pdf","access_level":"open_access","file_id":"19897","date_created":"2025-06-25T05:47:36Z","relation":"main_file","checksum":"c09718d0d09614642d877d0716ce32e8","file_size":2540277,"date_updated":"2025-06-25T05:47:36Z","creator":"dernst","content_type":"application/pdf","success":1}],"author":[{"orcid":"0000-0003-4252-1608","full_name":"Chintaluri, Chaitanya","last_name":"Chintaluri","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","first_name":"Chaitanya"},{"last_name":"Bejtka","full_name":"Bejtka, Marta","first_name":"Marta"},{"first_name":"Wladyslaw","full_name":"Sredniawa, Wladyslaw","last_name":"Sredniawa"},{"full_name":"Czerwinski, Michal","last_name":"Czerwinski","first_name":"Michal"},{"first_name":"Jakub M.","last_name":"Dzik","full_name":"Dzik, Jakub M."},{"full_name":"Jedrzejewska-Szmek, Joanna","last_name":"Jedrzejewska-Szmek","first_name":"Joanna"},{"last_name":"Wojciki","full_name":"Wojciki, Daniel K.","first_name":"Daniel K."}],"intvolume":"        20","volume":20,"file_date_updated":"2025-06-25T05:47:36Z","related_material":{"link":[{"relation":"software","url":"https://github.com/Neuroinflab/kCSD-python"}]},"publication":"PLoS Computational Biology","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"has_accepted_license":"1","publisher":"Public Library of Science","citation":{"apa":"Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., &#38; Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">https://doi.org/10.1371/journal.pcbi.1011941</a>","short":"C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024).","ama":"Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. <i>PLoS Computational Biology</i>. 2024;20(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">10.1371/journal.pcbi.1011941</a>","mla":"Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” <i>PLoS Computational Biology</i>, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">10.1371/journal.pcbi.1011941</a>.","ieee":"C. Chintaluri <i>et al.</i>, “kCSD-python, reliable current source density estimation with quality control,” <i>PLoS Computational Biology</i>, vol. 20, no. 3. Public Library of Science, 2024.","ista":"Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 20(3), e1011941.","chicago":"Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">https://doi.org/10.1371/journal.pcbi.1011941</a>."},"date_updated":"2026-07-13T12:30:33Z","external_id":{"isi":["001190689800001"],"pmid":["38484020"]},"year":"2024","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","acknowledgement":"The Python implementation of kCSD was started by Grzegorz Parka during Google Summer of Code project through the International Neuroinformatics Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class. This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691 to DKW; 2015/17/B/ST7/04123 to DKW). ","month":"03","quality_controlled":"1","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","article_number":"e1011941","article_processing_charge":"Yes","corr_author":"1","title":"kCSD-python, reliable current source density estimation with quality control","department":[{"_id":"TiVo"}],"status":"public","date_created":"2024-03-24T23:00:59Z","issue":"3","OA_type":"gold","oa":1,"abstract":[{"text":"Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results.","lang":"eng"}],"ddc":["000","570"],"_id":"15169","das_tickbox":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"14","OA_place":"publisher","publication_status":"published","doi":"10.1371/journal.pcbi.1011941","isi":1,"pmid":1},{"corr_author":"1","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"title":"Inference of genetic effects via approximate message passing","status":"public","conference":{"location":"Seoul, Korea","start_date":"2024-04-14","end_date":"2024-04-19","name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing"},"date_created":"2024-06-16T22:01:07Z","article_processing_charge":"No","page":"13151-13155","isi":1,"main_file_link":[{"open_access":"1","url":"https://openreview.net/forum?id=aQYCDxfZV0"}],"publication_status":"published","doi":"10.1109/ICASSP48485.2024.10447198","_id":"17147","oa_version":"Submitted Version","language":[{"iso":"eng"}],"OA_place":"repository","day":"19","OA_type":"green","abstract":[{"text":"Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people.","lang":"eng"}],"oa":1,"publication":"2024 IEEE International Conference on Acoustics, Speech, and Signal Processing","publication_identifier":{"issn":["1520-6149"],"isbn":["9798350344851"]},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"author":[{"full_name":"Depope, Al","last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","first_name":"Al"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813"}],"date_published":"2024-04-19T00:00:00Z","month":"04","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by a Lopez-Loreta Prize to MM, an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and core funding from ISTA. The authors thank Philip Schniter, Matthew Stephens and Pragya Sur for valuable suggestions on an early version of the work. The authors acknowledge the participants and investigators of the UK Biobank study. High-performance\r\ncomputing was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","scopus_import":"1","date_updated":"2026-07-13T14:57:55Z","citation":{"apa":"Depope, A., Mondelli, M., &#38; Robinson, M. R. (2024). Inference of genetic effects via approximate message passing. In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i> (pp. 13151–13155). Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>","short":"A. Depope, M. Mondelli, M.R. Robinson, in:, 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–13155.","mla":"Depope, Al, et al. “Inference of Genetic Effects via Approximate Message Passing.” <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, IEEE, 2024, pp. 13151–55, doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>.","ama":"Depope A, Mondelli M, Robinson MR. Inference of genetic effects via approximate message passing. In: <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>. IEEE; 2024:13151-13155. doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>","chicago":"Depope, Al, Marco Mondelli, and Matthew Richard Robinson. “Inference of Genetic Effects via Approximate Message Passing.” In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, 13151–55. IEEE, 2024. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>.","ieee":"A. Depope, M. Mondelli, and M. R. Robinson, “Inference of genetic effects via approximate message passing,” in <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, Seoul, Korea, 2024, pp. 13151–13155.","ista":"Depope A, Mondelli M, Robinson MR. 2024. Inference of genetic effects via approximate message passing. 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP: International Conference on Acoustics, Speech and Signal Processing, 13151–13155."},"external_id":{"isi":["001396233806078"]},"year":"2024","type":"conference","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"IEEE"},{"article_number":"2400408","article_processing_charge":"Yes (via OA deal)","article_type":"original","issue":"22","date_created":"2024-03-25T08:57:40Z","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"status":"public","corr_author":"1","abstract":[{"text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications.","lang":"eng"}],"oa":1,"language":[{"iso":"eng"}],"day":"12","oa_version":"Published Version","_id":"15182","ddc":["530"],"doi":"10.1002/aenm.202400408","publication_status":"published","isi":1,"file":[{"date_updated":"2024-07-22T12:07:56Z","content_type":"application/pdf","success":1,"creator":"dernst","file_name":"2024_AdvancedEnergyMaterials_Kleinhanns.pdf","file_id":"17314","date_created":"2024-07-22T12:07:56Z","access_level":"open_access","checksum":"86b26430e00d5f43ea19e9b610692ab7","relation":"main_file","file_size":8824301}],"date_published":"2024-06-12T00:00:00Z","file_date_updated":"2024-07-22T12:07:56Z","volume":14,"intvolume":"        14","author":[{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","orcid":"0000-0003-1537-7436"},{"id":"38b830db-ea88-11ee-bf9b-929beaf79054","first_name":"Francesco","full_name":"Milillo, Francesco","last_name":"Milillo"},{"first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","last_name":"Calcabrini","full_name":"Calcabrini, Mariano"},{"full_name":"Fiedler, Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","first_name":"Christine"},{"first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","full_name":"Horta, Sharona"},{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel"},{"first_name":"Marissa J.","last_name":"Strumolo","full_name":"Strumolo, Marissa J."},{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"full_name":"Tkadletz, Michael","last_name":"Tkadletz","first_name":"Michael"},{"first_name":"Richard L.","last_name":"Brutchey","full_name":"Brutchey, Richard L."},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"has_accepted_license":"1","publication_identifier":{"issn":["1614-6832"],"eissn":["1614-6840"]},"publication":"Advanced Energy Materials","related_material":{"record":[{"id":"22017","relation":"dissertation_contains","status":"for_moderation"}]},"publisher":"Wiley","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"type":"journal_article","year":"2024","citation":{"ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 14(22), 2400408.","ieee":"T. Kleinhanns <i>et al.</i>, “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” <i>Advanced Energy Materials</i>, vol. 14, no. 22. Wiley, 2024.","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>.","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. 2024;14(22). doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>, vol. 14, no. 22, 2400408, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials 14 (2024).","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>"},"date_updated":"2026-07-14T08:43:40Z","external_id":{"isi":["001184300200001"]},"acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","scopus_import":"1","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","month":"06"},{"ec_funded":1,"date_created":"2024-11-17T23:01:47Z","status":"public","department":[{"_id":"MoHe"}],"conference":{"name":"DISC: Symposium on Distributed Computing","location":"Madrid, Spain","start_date":"2024-10-28","end_date":"2024-11-01"},"title":"Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges","corr_author":"1","article_number":"21","article_processing_charge":"Yes","isi":1,"doi":"10.4230/LIPIcs.DISC.2024.21","publication_status":"published","oa_version":"Published Version","OA_place":"publisher","language":[{"iso":"eng"}],"day":"24","_id":"18557","ddc":["000"],"oa":1,"abstract":[{"text":"Broadcast and Consensus are most fundamental tasks in distributed computing. These tasks are particularly challenging in dynamic networks where communication across the network links may be unreliable, e.g., due to mobility or failures. Over the last years, researchers have derived several impossibility results and high time complexity lower bounds for these tasks. Specifically for the setting where in each round of communication the adversary is allowed to choose one rooted tree along which the information is disseminated, there is a lower as well as an upper bound that is linear in the number n of nodes for Broadcast and for n ≥ 3 the adversary can guarantee that Consensus never happens. This setting is called the oblivious message adversary for rooted trees. Also note that if the adversary is allowed to choose a graph that does not contain a rooted tree, then it can guarantee that Broadcast and Consensus will never happen. However, such deterministic adversarial models may be overly pessimistic, as many processes in real-world settings are stochastic in nature rather than worst-case. This paper studies Broadcast on stochastic dynamic networks and shows that the situation is very different to the deterministic case. In particular, we show that if information dissemination occurs along random rooted trees and directed Erdős–Rényi graphs, Broadcast completes in O(log n) rounds of communication with high probability. The fundamental insight in our analysis is that key variables are mutually independent. We then study two adversarial models, (a) one with Byzantine nodes and (b) one where an adversary controls the edges. (a) Our techniques without Byzantine nodes are general enough so that they can be extended to Byzantine nodes. (b) In the spirit of smoothed analysis, we introduce the notion of randomized oblivious message adversary, where in each round, an adversary picks k ≤ 2n/3 edges to appear in the communication network, and then a graph (e.g. rooted tree or directed Erdős–Rényi graph) is chosen uniformly at random among the set of all such graphs that include these edges. We show that Broadcast completes in a finite number of rounds, which is, e.g., O(k+log n) rounds in rooted trees. We then extend these results to All-to-All Broadcast, and Consensus, and give lower bounds that show that most of our upper bounds are tight.","lang":"eng"}],"OA_type":"gold","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773522"]},"has_accepted_license":"1","related_material":{"record":[{"status":"for_moderation","relation":"dissertation_contains","id":"22281"}]},"publication":"38th International Symposium on Distributed Computing","project":[{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"},{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Efficient algorithms","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"}],"intvolume":"       319","volume":319,"file_date_updated":"2024-11-18T08:02:45Z","author":[{"orcid":"0000-0003-4268-7368","last_name":"El-Hayek","full_name":"El-Hayek, Antoine","first_name":"Antoine","id":"888a098e-fcac-11ee-aff7-d347be57b725"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"file":[{"date_created":"2024-11-18T08:02:45Z","file_id":"18561","access_level":"open_access","file_name":"2024_LIPIcs_ElHayek.pdf","file_size":809666,"checksum":"d6c8277331cafa188c33ba1717206cf4","relation":"main_file","content_type":"application/pdf","success":1,"creator":"dernst","date_updated":"2024-11-18T08:02:45Z"}],"date_published":"2024-10-24T00:00:00Z","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","acknowledgement":"Antoine El-Hayek: This project has received funding from the Austrian Science Fund\r\n(FWF) grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung,\r\n2020–2024.\r\nMonika Henzinger: This project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (MoDynStruct,\r\nNo. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI\r\n10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE\r\nStiftung, 2020–2024.\r\nStefan Schmid: This project has received funding from the German Research Foundation (DFG),\r\nSPP 2378 (project ReNO), 2023-2027.","year":"2024","type":"conference","date_updated":"2026-07-15T09:01:38Z","citation":{"apa":"El-Hayek, A., Henzinger, M., &#38; Schmid, S. (2024). Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges. In <i>38th International Symposium on Distributed Computing</i> (Vol. 319). Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">https://doi.org/10.4230/LIPIcs.DISC.2024.21</a>","short":"A. El-Hayek, M. Henzinger, S. Schmid, in:, 38th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ama":"El-Hayek A, Henzinger M, Schmid S. Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges. In: <i>38th International Symposium on Distributed Computing</i>. Vol 319. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">10.4230/LIPIcs.DISC.2024.21</a>","mla":"El-Hayek, Antoine, et al. “Broadcast and Consensus in Stochastic Dynamic Networks with Byzantine Nodes and Adversarial Edges.” <i>38th International Symposium on Distributed Computing</i>, vol. 319, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">10.4230/LIPIcs.DISC.2024.21</a>.","ista":"El-Hayek A, Henzinger M, Schmid S. 2024. Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges. 38th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 319, 21.","ieee":"A. El-Hayek, M. Henzinger, and S. Schmid, “Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges,” in <i>38th International Symposium on Distributed Computing</i>, Madrid, Spain, 2024, vol. 319.","chicago":"El-Hayek, Antoine, Monika Henzinger, and Stefan Schmid. “Broadcast and Consensus in Stochastic Dynamic Networks with Byzantine Nodes and Adversarial Edges.” In <i>38th International Symposium on Distributed Computing</i>, Vol. 319. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">https://doi.org/10.4230/LIPIcs.DISC.2024.21</a>."},"external_id":{"arxiv":["2302.11988"],"isi":["001542467600021"]},"arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"]},{"doi":"10.15479/at:ista:17119","publication_status":"published","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"abstract":[{"text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research.","lang":"eng"}],"oa":1,"day":"20","OA_place":"publisher","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"17119","ddc":["576"],"date_created":"2024-06-07T16:14:13Z","status":"public","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","corr_author":"1","ec_funded":1,"page":"105","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"06","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","type":"dissertation","year":"2024","date_updated":"2026-04-07T13:21:37Z","citation":{"apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria."},"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"degree_awarded":"PhD","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"related_material":{"record":[{"id":"542","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10767"}]},"file":[{"embargo_to":"open_access","date_updated":"2025-01-10T23:30:10Z","creator":"rkelemen","content_type":"application/zip","file_name":"thesis.zip","access_level":"closed","date_created":"2024-06-07T16:09:17Z","file_id":"17121","relation":"source_file","checksum":"fab59146e3b3dc2e5d214576984a2a63","file_size":180557931},{"embargo":"2025-01-10","date_updated":"2025-01-10T23:30:10Z","content_type":"application/pdf","creator":"rkelemen","file_name":"thesis_to_archive.pdf","file_id":"17213","date_created":"2024-07-10T08:00:20Z","access_level":"open_access","checksum":"91cc4c25a792239e8a7688e8aec7c62a","relation":"main_file","file_size":19405484}],"date_published":"2024-06-20T00:00:00Z","file_date_updated":"2025-01-10T23:30:10Z","author":[{"first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281"}]},{"degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"has_accepted_license":"1","file":[{"embargo_to":"open_access","date_updated":"2025-10-29T23:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"bkaczmar","file_name":"20241029_PhD_thesis_BKaczmarek.docx","file_id":"18485","date_created":"2024-10-29T11:56:36Z","access_level":"closed","checksum":"2053294ea4d770c495e4cc501e2a218b","relation":"source_file","file_size":23136626},{"content_type":"application/pdf","creator":"bkaczmar","embargo":"2025-10-29","date_updated":"2025-10-29T23:30:02Z","date_created":"2024-10-29T11:56:44Z","file_id":"18486","access_level":"open_access","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","file_size":11707360,"checksum":"8ce857a4cd44b776791eaf180ac9dbb3","relation":"main_file"}],"date_published":"2024-10-29T00:00:00Z","file_date_updated":"2025-10-29T23:30:02Z","author":[{"last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"year":"2024","type":"dissertation","citation":{"short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>."},"date_updated":"2026-04-07T13:23:59Z","date_created":"2024-10-27T07:35:13Z","status":"public","title":"Biochemical and structural insights into ADAR1 RNA editing","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"corr_author":"1","page":"124","article_processing_charge":"No","doi":"10.15479/at:ista:18477","publication_status":"published","supervisor":[{"orcid":"0000-0003-0893-7036","last_name":"Bernecky","full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"oa_version":"Published Version","OA_place":"publisher","language":[{"iso":"eng"}],"day":"29","ddc":["572"],"_id":"18477"},{"oa_version":"Published Version","OA_place":"publisher","day":"02","language":[{"iso":"eng"}],"ddc":["570"],"_id":"15352","abstract":[{"text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. ","lang":"eng"}],"oa":1,"supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert"}],"doi":"10.15479/at:ista:15352","publication_status":"published","article_processing_charge":"No","page":"54","date_created":"2024-05-02T08:31:38Z","status":"public","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","corr_author":"1","year":"2024","type":"dissertation","citation":{"short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>"},"date_updated":"2026-04-07T13:05:00Z","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Master's Thesis"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"month":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2025-05-02T22:30:04Z","author":[{"last_name":"Murmann","full_name":"Murmann, Julie Stefanie","first_name":"Julie Stefanie","id":"1d390868-f128-11eb-9611-a0ca5f7833b5"}],"file":[{"creator":"cchlebak","content_type":"application/pdf","date_updated":"2025-05-02T22:30:04Z","embargo":"2025-05-02","access_level":"open_access","date_created":"2024-05-02T12:26:13Z","file_id":"15354","file_name":"Murmann_Thesis_final_2024_2.pdf","file_size":5936142,"relation":"main_file","checksum":"095817a6c944954ac3f277e547031a33"},{"access_level":"closed","date_created":"2024-05-02T12:37:56Z","file_id":"15355","file_name":"Murmann_Thesis_final_2024.zip","file_size":20645510,"relation":"source_file","checksum":"43b632255372973a437ac87739cfd4db","embargo_to":"open_access","creator":"cchlebak","content_type":"application/x-zip-compressed","date_updated":"2025-05-02T22:30:04Z"}],"date_published":"2024-05-02T00:00:00Z","publication_identifier":{"issn":["2791-4585"]},"has_accepted_license":"1","degree_awarded":"MS"},{"ec_funded":1,"issue":"5","date_created":"2024-01-21T23:00:56Z","status":"public","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"corr_author":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","page":"755-771.e9","pmid":1,"isi":1,"doi":"10.1016/j.neuron.2023.12.002","publication_status":"published","language":[{"iso":"eng"}],"day":"06","OA_place":"publisher","oa_version":"Published Version","_id":"14843","ddc":["570"],"oa":1,"abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"OA_type":"hybrid","has_accepted_license":"1","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"publication":"Neuron","related_material":{"record":[{"status":"public","id":"15101","relation":"dissertation_contains"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","relation":"press_release"}]},"project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"PlanS_conform":"1","file_date_updated":"2025-04-23T14:02:08Z","volume":112,"intvolume":"       112","author":[{"last_name":"Chen","full_name":"Chen, JingJing","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chen, Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru","full_name":"Arai, Itaru","last_name":"Arai"},{"last_name":"Kim","full_name":"Kim, Olena","orcid":"0000-0003-2344-1039","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"file":[{"file_name":"2024_Neuron_Chen.pdf","access_level":"open_access","date_created":"2025-04-23T14:02:08Z","file_id":"19614","relation":"main_file","checksum":"30098b4f0209556ddfb3540a23d07ca5","file_size":8192355,"date_updated":"2025-04-23T14:02:08Z","creator":"dernst","success":1,"content_type":"application/pdf"}],"date_published":"2024-03-06T00:00:00Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","scopus_import":"1","acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","year":"2024","external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"citation":{"short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>."},"date_updated":"2026-07-16T22:30:20Z","publisher":"Elsevier","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}]},{"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>"},"date_updated":"2026-04-07T13:21:56Z","type":"dissertation","year":"2024","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","date_published":"2024-01-19T00:00:00Z","file":[{"embargo_to":"open_access","date_updated":"2025-01-19T23:30:04Z","creator":"hchiossi","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_Thesis_190124.docx","access_level":"closed","date_created":"2024-01-19T11:04:05Z","file_id":"14838","relation":"source_file","checksum":"d3fa3de1abd5af5204c13e9d55375615","file_size":8656268},{"checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","relation":"main_file","file_size":6567275,"file_name":"PhD_Thesis_190124.pdf","date_created":"2024-01-19T11:03:59Z","file_id":"14839","access_level":"open_access","embargo":"2025-01-19","date_updated":"2025-01-19T23:30:04Z","content_type":"application/pdf","creator":"hchiossi"}],"author":[{"last_name":"Chiossi","full_name":"Chiossi, Heloisa","orcid":"0009-0004-2973-278X","first_name":"Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2025-01-19T23:30:04Z","degree_awarded":"PhD","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"oa":1,"abstract":[{"lang":"eng","text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour."}],"ddc":["570"],"_id":"14821","language":[{"iso":"eng"}],"OA_place":"publisher","day":"19","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:14821","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"page":"89","article_processing_charge":"No","corr_author":"1","status":"public","title":"Adaptive hierarchical representations in the hippocampus","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"date_created":"2024-01-16T14:25:21Z","ec_funded":1},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"03","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"EM-Fac"}],"type":"dissertation","year":"2024","citation":{"short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>","mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>."},"date_updated":"2026-04-07T13:24:22Z","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"},{"grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383"}],"degree_awarded":"PhD","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"14843","status":"public"}]},"file":[{"relation":"source_file","checksum":"db4947474ffa271e66c254b6fe876a55","file_size":11271363,"file_name":"Thesis_Jingjing CHEN.docx","access_level":"closed","file_id":"15104","date_created":"2024-03-11T14:10:58Z","date_updated":"2024-04-02T22:30:03Z","creator":"jchen","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"relation":"main_file","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_size":16627311,"file_name":"Thesis_Jingjing CHEN_merged.pdf","access_level":"open_access","date_created":"2024-03-11T14:11:06Z","file_id":"15105","date_updated":"2024-04-02T22:30:03Z","embargo":"2024-04-01","creator":"jchen","content_type":"application/pdf"}],"date_published":"2024-03-11T00:00:00Z","file_date_updated":"2024-04-02T22:30:03Z","author":[{"full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing"}],"doi":"10.15479/at:ista:15101","publication_status":"published","supervisor":[{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission."}],"oa":1,"language":[{"iso":"eng"}],"day":"11","OA_place":"publisher","oa_version":"Published Version","_id":"15101","ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"PeJo"}],"status":"public","date_created":"2024-03-11T10:09:54Z","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","corr_author":"1","ec_funded":1,"page":"84","article_processing_charge":"No"},{"publication_status":"published","doi":"10.15479/at:ista:18471","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973"}],"abstract":[{"lang":"eng","text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. "}],"oa":1,"ddc":["570"],"_id":"18471","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"28","OA_place":"publisher","corr_author":"1","status":"public","date_created":"2024-10-26T20:02:42Z","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"title":"Visualizing the neuronal transcriptional landscape with tissue context","ec_funded":1,"page":"97","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-14T08:34:37Z","citation":{"short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>"},"year":"2024","type":"dissertation","degree_awarded":"PhD","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232"}],"publication_identifier":{"isbn":["978-3-99078-044-2"],"issn":["2663-337X"]},"has_accepted_license":"1","date_published":"2024-10-28T00:00:00Z","file":[{"embargo_to":"open_access","date_updated":"2025-05-05T22:30:04Z","creator":"nagudelo","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","access_level":"closed","date_created":"2024-10-26T22:29:06Z","file_id":"18475","relation":"source_file","checksum":"6d7c7725d040d8debc070dcb35ac965d","file_size":183077763},{"creator":"nagudelo","content_type":"application/pdf","date_updated":"2025-05-05T22:30:04Z","embargo":"2025-05-05","file_size":47027710,"relation":"main_file","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","access_level":"open_access","file_id":"18476","date_created":"2024-10-26T23:13:33Z","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf"}],"author":[{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas"}],"file_date_updated":"2025-05-05T22:30:04Z"},{"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"title":"Visual adaptations to natural statistics","date_created":"2024-11-20T21:30:44Z","status":"public","corr_author":"1","ec_funded":1,"page":"86","article_processing_charge":"No","OA_embargo":"12","doi":"10.15479/at:ista:18574","publication_status":"published","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330"}],"abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"oa":1,"oa_version":"Published Version","day":"22","OA_place":"publisher","language":[{"iso":"eng"}],"_id":"18574","ddc":["573"],"project":[{"_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","name":"Circuits of Visual Attention"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-050-3"]},"has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"12349","status":"public"},{"status":"public","relation":"research_data","id":"12370"}]},"file":[{"relation":"source_file","checksum":"ebb000d361c36b22ed6e639a931c6b7c","file_size":75512262,"file_name":"PhD Thesis - Divyansh Gupta.zip","access_level":"closed","date_created":"2024-11-25T14:44:03Z","file_id":"18589","date_updated":"2025-11-11T23:30:02Z","creator":"dgupta","content_type":"application/zip","embargo_to":"open_access"},{"date_updated":"2025-11-11T23:30:02Z","embargo":"2025-11-11","creator":"dgupta","content_type":"application/pdf","relation":"main_file","checksum":"1282401eb71598bc311058b0fcefc6a1","file_size":6412619,"file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","access_level":"open_access","date_created":"2024-11-26T11:43:19Z","file_id":"18591"}],"date_published":"2024-11-22T00:00:00Z","file_date_updated":"2025-11-11T23:30:02Z","author":[{"first_name":"Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","last_name":"Gupta","full_name":"Gupta, Divyansh"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","month":"11","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"year":"2024","type":"dissertation","citation":{"mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024."},"date_updated":"2026-04-07T13:24:48Z"},{"file":[{"embargo":"2025-01-01","date_updated":"2025-01-01T23:30:03Z","content_type":"application/pdf","creator":"lsazanov","checksum":"21f05d188762acd7f49a97f3d09c8d9f","relation":"main_file","file_size":24424729,"file_name":"megacomplex_submit_NSMB_withFigures.pdf","file_id":"15392","date_created":"2024-05-14T11:57:56Z","access_level":"open_access"}],"date_published":"2024-07-01T00:00:00Z","file_date_updated":"2025-01-01T23:30:03Z","volume":31,"intvolume":"        31","author":[{"first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","last_name":"Vercellino","full_name":"Vercellino, Irene"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines"}],"has_accepted_license":"1","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"publication":"Nature Structural and Molecular Biology","related_material":{"link":[{"url":"https://doi.org/10.1038/s41594-025-01721-3","relation":"erratum"}]},"publisher":"Springer Nature","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"ScienComp"}],"type":"journal_article","year":"2024","date_updated":"2025-11-24T08:35:04Z","external_id":{"isi":["001196897300001"],"pmid":["38575788"]},"citation":{"ista":"Vercellino I, Sazanov LA. 2024. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 31, 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>.","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>","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.","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>"},"scopus_import":"1","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.","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","page":"1061-1071","article_processing_charge":"No","article_type":"original","date_created":"2024-04-14T22:01:03Z","title":"SCAF1 drives the compositional diversity of mammalian respirasomes","status":"public","department":[{"_id":"LeSa"}],"corr_author":"1","ec_funded":1,"oa":1,"abstract":[{"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.","lang":"eng"}],"day":"01","language":[{"iso":"eng"}],"oa_version":"Submitted Version","_id":"15323","ddc":["572"],"doi":"10.1038/s41594-024-01255-0","publication_status":"published","pmid":1,"isi":1},{"status":"public","date_created":"2024-11-11T08:40:45Z","title":"Early stages of sex chromosome evolution","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"corr_author":"1","article_processing_charge":"No","page":"181","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"doi":"10.15479/at:ista:18531","OA_embargo":"6","publication_status":"published","OA_place":"publisher","day":"11","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"18531","ddc":["576"],"oa":1,"abstract":[{"text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. ","lang":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"12521","relation":"part_of_dissertation","status":"public"},{"id":"18549","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","file_date_updated":"2025-05-11T22:30:04Z","author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"}],"file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"amrnjava","date_updated":"2025-05-11T22:30:04Z","file_id":"18551","date_created":"2024-11-13T12:15:28Z","title":"Early stages of sex chromosome evolution","access_level":"closed","file_name":"AMrnjavac_thesis_library.docx","file_size":26870629,"checksum":"3e48b163c22114ef5d5371f758668289","relation":"source_file"},{"date_updated":"2025-05-11T22:30:04Z","embargo":"2025-05-11","creator":"amrnjava","content_type":"application/pdf","file_name":"AMrnjavac_thesis_library.pdf","access_level":"open_access","title":"Early stages of sex chromosome evolution","file_id":"18552","date_created":"2024-11-13T12:15:54Z","relation":"main_file","checksum":"3ead60c1b678e7dcf018043aef3b5db2","file_size":4228766}],"date_published":"2024-11-11T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"11","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"keyword":["Sex chromosomes","evolution","selection","sheltering"],"type":"dissertation","year":"2024","citation":{"apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024."},"date_updated":"2026-04-07T13:22:45Z","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}]},{"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"doi":"10.1101/2024.07.02.601697","publication_status":"draft","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.07.02.601697"}],"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"lang":"eng","text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n"}],"year":"2024","oa_version":"Preprint","day":"04","type":"preprint","language":[{"iso":"eng"}],"OA_place":"repository","_id":"18549","date_updated":"2026-07-16T22:30:22Z","citation":{"chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>.","ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, <a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” <i>bioRxiv</i>. .","mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>","short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","apa":"Mrnjavac, A., &#38; Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>"},"status":"public","date_created":"2024-11-13T09:12:08Z","department":[{"_id":"BeVi"}],"title":"Evidence of a Slower-Z effect in Schistosoma japonicum","corr_author":"1","related_material":{"record":[{"relation":"later_version","id":"19370","status":"public"},{"status":"public","id":"18531","relation":"dissertation_contains"}]},"publication":"bioRxiv","date_published":"2024-07-04T00:00:00Z","article_processing_charge":"No","author":[{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}]},{"oa_version":"Published Version","language":[{"iso":"eng"}],"day":"11","OA_place":"publisher","ddc":["576"],"_id":"18642","abstract":[{"lang":"eng","text":"This thesis consists of two pieces of work in the broader feld of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefcient 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 fne-map genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal efect 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 efects 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 specifc genetic efects, and how the error rates of this recovery are infuenced\r\nby missing data due to diferent 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 diferences 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 fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n"}],"oa":1,"supervisor":[{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"doi":"10.15479/at:ista:18642","publication_status":"published","article_processing_charge":"No","page":"138","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"status":"public","date_created":"2024-12-10T13:49:15Z","title":"Algorithms for causal learning and comparative analysis for genomic data","corr_author":"1","year":"2024","type":"dissertation","date_updated":"2026-04-07T13:23:06Z","citation":{"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>","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>.","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","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>.","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>","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024."},"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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.","file_date_updated":"2025-06-12T22:30:02Z","author":[{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","first_name":"Nick N","full_name":"Machnik, Nick N","last_name":"Machnik","orcid":"0000-0001-6617-9742"}],"file":[{"content_type":"application/pdf","creator":"nmachnik","embargo":"2025-06-12","date_updated":"2025-06-12T22:30:02Z","file_id":"18649","date_created":"2024-12-11T11:59:54Z","access_level":"open_access","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","file_size":12845009,"checksum":"d45e4d170f9a70a1f69b44b99bd058e4","relation":"main_file"},{"file_size":14189810,"relation":"source_file","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","access_level":"closed","file_id":"18650","date_created":"2024-12-11T11:59:34Z","file_name":"thesis.zip","creator":"nmachnik","content_type":"application/zip","date_updated":"2025-06-12T22:30:02Z","embargo_to":"open_access"}],"date_published":"2024-12-11T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"18648","status":"public"},{"status":"public","id":"8707","relation":"part_of_dissertation"}]},"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181"}],"degree_awarded":"PhD"}]