[{"file_date_updated":"2026-01-21T09:38:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1-22","publication_status":"published","publisher":"Association for Computing Machinery","OA_place":"publisher","oa":1,"quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","OA_type":"hybrid","department":[{"_id":"VlKo"}],"corr_author":"1","type":"journal_article","scopus_import":"1","year":"2025","file":[{"date_updated":"2026-01-21T09:38:09Z","file_id":"21031","success":1,"file_size":2208302,"date_created":"2026-01-21T09:38:09Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_name":"2025_ACMToA_Kolmogorov.pdf","relation":"main_file","checksum":"4a80fdb1e3711b9a2768d2bb8f6d3b4e"}],"publication":"ACM Transactions on Algorithms","date_published":"2025-10-01T00:00:00Z","author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"_id":"21007","date_created":"2026-01-20T10:04:02Z","arxiv":1,"title":"A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT","article_type":"original","article_processing_charge":"Yes (via OA deal)","date_updated":"2026-10-21T13:45:27Z","month":"10","day":"01","oa_version":"Published Version","external_id":{"arxiv":["2307.00115"]},"issue":"4","citation":{"ista":"Kolmogorov V. 2025. A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. ACM Transactions on Algorithms. 21(4), 1–22.","apa":"Kolmogorov, V. (2025). A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3748723\">https://doi.org/10.1145/3748723</a>","chicago":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for SPARSEST CUT.” <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3748723\">https://doi.org/10.1145/3748723</a>.","short":"V. Kolmogorov, ACM Transactions on Algorithms 21 (2025) 1–22.","ama":"Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. <i>ACM Transactions on Algorithms</i>. 2025;21(4):1-22. doi:<a href=\"https://doi.org/10.1145/3748723\">10.1145/3748723</a>","ieee":"V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT,” <i>ACM Transactions on Algorithms</i>, vol. 21, no. 4. Association for Computing Machinery, pp. 1–22, 2025.","mla":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for SPARSEST CUT.” <i>ACM Transactions on Algorithms</i>, vol. 21, no. 4, Association for Computing Machinery, 2025, pp. 1–22, doi:<a href=\"https://doi.org/10.1145/3748723\">10.1145/3748723</a>."},"status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1145/3748723","publication_identifier":{"eissn":["1549-6333"],"issn":["1549-6325"]},"language":[{"iso":"eng"}],"abstract":[{"text":"Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain \"chaining\" algorithm that combines results of multiple calls to the maxflow algorithm. We present an alternative approach that avoids solving the multicommodity flow problem and instead computes \"violating paths\". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors. We also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.","lang":"eng"}],"PlanS_conform":"1","related_material":{"record":[{"relation":"shorter_version","id":"17236","status":"public"}]},"fulldoi":"https://doi.org/10.1145/3748723","intvolume":"        21","volume":21,"ddc":["510"]},{"status":"public","oa_version":"Preprint","external_id":{"isi":["001415246000001"],"arxiv":["2407.15314"]},"day":"06","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2407.15314","open_access":"1"}],"citation":{"apa":"Puglia, D., Odessey, R. H., Burns, P., Luhmann, N., Schmid, S., &#38; Higginbotham, A. P. (2025). Room temperature, cavity-free capacitive strong coupling to mechanical motion. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">https://doi.org/10.1021/acs.nanolett.4c05796</a>","ista":"Puglia D, Odessey RH, Burns P, Luhmann N, Schmid S, Higginbotham AP. 2025. Room temperature, cavity-free capacitive strong coupling to mechanical motion. Nano Letters. 25(7), 2749–2755.","mla":"Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” <i>Nano Letters</i>, vol. 25, no. 7, American Chemical Society, 2025, pp. 2749–55, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">10.1021/acs.nanolett.4c05796</a>.","ieee":"D. Puglia, R. H. Odessey, P. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical motion,” <i>Nano Letters</i>, vol. 25, no. 7. American Chemical Society, pp. 2749–2755, 2025.","chicago":"Puglia, Denise, Rachel H Odessey, Peter Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” <i>Nano Letters</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">https://doi.org/10.1021/acs.nanolett.4c05796</a>.","ama":"Puglia D, Odessey RH, Burns P, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical motion. <i>Nano Letters</i>. 2025;25(7):2749-2755. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">10.1021/acs.nanolett.4c05796</a>","short":"D. Puglia, R.H. Odessey, P. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, Nano Letters 25 (2025) 2749–2755."},"issue":"7","acknowledgement":"We thank Carissa Kumar and Vibha Padmanabhan for assistance in comparing performance with devices across the literature. We thank Andrew Cleland for helpful comments on this work. We are grateful for support from the Miba Machine Shop and Nanofabrication facility at IST Austria. This work was supported by the Austrian FWF grant P33692–N and includes a recipient of a DOC Fellowship of the Austrian Academy of Sciences (DOC – No. 26088) at the Institute of Science and Technology, Austria.","intvolume":"        25","related_material":{"record":[{"relation":"earlier_version","id":"18143","status":"public"}]},"fulldoi":"https://doi.org/10.1021/acs.nanolett.4c05796","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"volume":25,"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"doi":"10.1021/acs.nanolett.4c05796","abstract":[{"lang":"eng","text":"The back-action damping of mechanical motion by electromagnetic radiation is typically overwhelmed by internal loss channels unless demanding experimental ingredients such as superconducting resonators, high-quality optical cavities, or large magnetic fields are employed. Here we demonstrate the first room temperature, cavity-free, all-electric device where back-action damping exceeds internal loss, enabled by a mechanically compliant parallel-plate capacitor with a nanoscale plate separation and an aspect ratio exceeding 1,000. The device has 4 orders of magnitude lower insertion loss than a comparable commercial quartz crystal and achieves a position imprecision rivaling optical interferometers. With the help of a back-action isolation scheme, we observe radiative cooling of mechanical motion by a remote cryogenic load. This work provides a technologically accessible route to high-precision sensing, transduction, and signal processing."}],"isi":1,"language":[{"iso":"eng"}],"corr_author":"1","year":"2025","type":"journal_article","scopus_import":"1","project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"},{"name":"Surface Charge and Tunneling Multi-Mode Imaging","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","grant_number":"26088"}],"OA_type":"green","department":[{"_id":"AnHi"}],"publication_status":"published","publisher":"American Chemical Society","page":"2749-2755","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","quality_controlled":"1","oa":1,"title":"Room temperature, cavity-free capacitive strong coupling to mechanical motion","article_type":"original","date_created":"2025-02-16T23:02:34Z","arxiv":1,"date_updated":"2026-10-21T14:08:09Z","month":"02","article_processing_charge":"No","date_published":"2025-02-06T00:00:00Z","author":[{"full_name":"Puglia, Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise","last_name":"Puglia","orcid":"0000-0003-1144-2763"},{"id":"9a7a5123-8972-11ed-ae7b-dd1f2af457bd","full_name":"Odessey, Rachel H","last_name":"Odessey","first_name":"Rachel H"},{"full_name":"Burns, Peter","last_name":"Burns","first_name":"Peter"},{"last_name":"Luhmann","first_name":"Niklas","full_name":"Luhmann, Niklas"},{"last_name":"Schmid","first_name":"Silvan","full_name":"Schmid, Silvan"},{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nano Letters","_id":"19026"},{"file_date_updated":"2025-11-24T10:55:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"6138-6150.e17","publication_status":"published","publisher":"Cell Press","OA_place":"publisher","quality_controlled":"1","oa":1,"pmid":1,"project":[{"name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739","grant_number":"101142681"},{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"},{"name":"Cell surface receptor complexes for auxin signaling in plants","grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"OA_type":"hybrid","department":[{"_id":"JiFr"},{"_id":"XiFe"}],"corr_author":"1","type":"journal_article","year":"2025","publication":"Cell","file":[{"file_size":17825465,"date_created":"2025-11-24T10:55:18Z","file_id":"20679","success":1,"date_updated":"2025-11-24T10:55:18Z","file_name":"2025_Cell_Rodriguez.pdf","creator":"dernst","checksum":"8ac396a0806ad7f2e4e7a0c1eed712ce","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"date_published":"2025-10-30T00:00:00Z","author":[{"full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas"},{"first_name":"Minxia","last_name":"Zou","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline"},{"first_name":"Dmitrii","last_name":"Vladimirtsev","full_name":"Vladimirtsev, Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d"},{"first_name":"Marek","last_name":"Randuch","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"first_name":"Yongfan","last_name":"Yu","full_name":"Yu, Yongfan"},{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","orcid":"0000-0003-4783-1752","last_name":"Gelová"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"orcid":"0000-0003-2140-7195","last_name":"Hajny","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"full_name":"Chen, Meng","last_name":"Chen","first_name":"Meng"},{"first_name":"Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer"},{"first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marques-Bueno, Maria Mar","first_name":"Maria Mar","last_name":"Marques-Bueno"},{"last_name":"Quddoos","first_name":"Zainab","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","full_name":"Quddoos, Zainab"},{"first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kulich, Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan","last_name":"Kulich"},{"first_name":"Yvon","last_name":"Jaillais","full_name":"Jaillais, Yvon"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"ec_funded":1,"_id":"20656","date_created":"2025-11-19T09:44:31Z","article_type":"original","title":"ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism","article_processing_charge":"Yes (via OA deal)","date_updated":"2026-10-22T09:15:44Z","month":"10","day":"30","oa_version":"Published Version","external_id":{"isi":["001616077900005"],"pmid":["41043433"]},"issue":"22","citation":{"mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>Cell</i>, vol. 188, no. 22, Cell Press, 2025, p. 6138–6150.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">10.1016/j.cell.2025.08.026</a>.","chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">https://doi.org/10.1016/j.cell.2025.08.026</a>.","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. <i>Cell</i>. 2025;188(22):6138-6150.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">10.1016/j.cell.2025.08.026</a>","short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, I. Kulich, Y. Jaillais, J. Friml, Cell 188 (2025) 6138–6150.e17.","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism,” <i>Cell</i>, vol. 188, no. 22. Cell Press, p. 6138–6150.e17, 2025.","apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (2025). ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">https://doi.org/10.1016/j.cell.2025.08.026</a>","ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Kulich I, Jaillais Y, Friml J. 2025. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell. 188(22), 6138–6150.e17."},"status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.cell.2025.08.026","publication_identifier":{"issn":["0092-8674"]},"language":[{"iso":"eng"}],"abstract":[{"text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a prerequisite for (1) self-organizing processes, including vascular tissue formation, and (2) directional growth responses such as gravitropism. Here, we identify a mechanism by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (TMK1) receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE 3 (ABL3) auxin receptor. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably for other self-organizing developmental phenomena.","lang":"eng"}],"isi":1,"PlanS_conform":"1","related_material":{"record":[{"status":"public","id":"19399","relation":"earlier_version"},{"relation":"dissertation_contains","id":"23145","status":"public"}]},"fulldoi":"https://doi.org/10.1016/j.cell.2025.08.026","acknowledgement":"We gratefully acknowledge Tongda Xu for experimental, material, and conceptual support. We thank William Gray for providing material, Nataliia Gnyliukh and Ema Cervenova for help with manuscript preparation, and Julia Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at the Institute of Science and Technology Austria (ISTA) for their excellent service and assistance. The research leading to these results has received funding from the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF; I 6123-B) to J.F., and Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by the FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985-2016). S.T. was supported by the National Natural Science Foundation of China (32321001, 32570366). The work of J.H. was supported by the project JG_2024_003 implemented within the Palacký University Young Researcher Grant.","intvolume":"       188","volume":188,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["580"]},{"_id":"23174","publication":"bioRxiv","date_published":"2025-10-17T00:00:00Z","author":[{"last_name":"Randuch","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek"},{"last_name":"Kulich","first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","full_name":"Kulich, Ivan"},{"first_name":"Dmitrii","last_name":"Vladimirtsev","full_name":"Vladimirtsev, Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d"},{"full_name":"Huang, Shouguang","first_name":"Shouguang","last_name":"Huang"},{"last_name":"Hedrich","first_name":"Rainer","full_name":"Hedrich, Rainer"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"article_processing_charge":"No","date_updated":"2026-10-22T09:15:44Z","month":"10","date_created":"2026-10-19T11:44:48Z","title":"Cytosolic Ca2+ as a universal signal for rapid root growth regulation","OA_place":"repository","oa":1,"biorxivid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","project":[{"grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"OA_type":"green","department":[{"_id":"JiFr"}],"corr_author":"1","type":"preprint","year":"2025","language":[{"iso":"eng"}],"abstract":[{"text":"Roots must continuously adapt their growth and have evolved the ability to rapidly respond to diverse environmental and hormonal cues, including the phytohormone auxin. Auxin-induced cellular responses involve membrane depolarization, cytosolic calcium (Ca²⁺) elevation, and extracellular pH increase, but how these processes lead to rapid growth regulation remains unclear. Here, we show that cytosolic Ca²⁺ acts as a universal signal integrating diverse cues for rapid regulation of root growth. Using live imaging, microfluidics, and optogenetics in Arabidopsis, we demonstrate that a swift rise in cytosolic Ca²⁺ is the primary target of auxin signaling affecting growth inhibition. Disruption of Ca²⁺ influx abolishes these responses, whereas light-gated Ca²⁺ influx from the apoplast or endoplasmic reticulum stores inhibits growth. Multiple unrelated stimuli—including auxin, extracellular ATP, RALF peptides, and hydrogen peroxide—converge on this Ca²⁺-dependent mechanism. Cytosolic Ca²⁺ elevation thus represents a necessary and sufficient step for rapid growth inhibition, revealing a unifying principle of root signaling.","lang":"eng"}],"doi":"10.1101/2025.10.17.683082","related_material":{"record":[{"status":"public","id":"23145","relation":"dissertation_contains"}]},"fulldoi":"https://doi.org/10.1101/2025.10.17.683082","acknowledgement":"We gratefully acknowledge Dr. Andrea Bleckmann, creator of pBLAX000 vector and Dr. Shiqiang Gao for donation of template used in XXM-ER cloning. This research was supported by the Laboratory Support Facility, the Plant Facility, the IT Facility and the Imaging and Optical Facility of the Institute of Science and Technology Austria. The graphical elements used in Fig. 5 were adapted and modified from Servier, https://smart.servier.com, and are used under CC BY 3.0 licence. The authors acknowledge the use of AI-tools (Microsoft Copilot, Gemini) for language refinement. All content was critically reviewed by authors.\r\n\r\nFunder Information Declared\r\nEuropean Research Council, 101142681 CYNIPS\r\nAustrian Science Fund, P 37051-B","citation":{"ieee":"M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, and J. Friml, “Cytosolic Ca2+ as a universal signal for rapid root growth regulation,” <i>bioRxiv</i>. .","ama":"Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic Ca2+ as a universal signal for rapid root growth regulation. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.10.17.683082\">10.1101/2025.10.17.683082</a>","chicago":"Randuch, Marek, Ivan Kulich, Dmitrii Vladimirtsev, Shouguang Huang, Rainer Hedrich, and Jiří Friml. “Cytosolic Ca2+ as a Universal Signal for Rapid Root Growth Regulation.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.10.17.683082\">https://doi.org/10.1101/2025.10.17.683082</a>.","short":"M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, J. Friml, BioRxiv (n.d.).","mla":"Randuch, Marek, et al. “Cytosolic Ca2+ as a Universal Signal for Rapid Root Growth Regulation.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.10.17.683082\">10.1101/2025.10.17.683082</a>.","ista":"Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic Ca2+ as a universal signal for rapid root growth regulation. bioRxiv, <a href=\"https://doi.org/10.1101/2025.10.17.683082\">10.1101/2025.10.17.683082</a>.","apa":"Randuch, M., Kulich, I., Vladimirtsev, D., Huang, S., Hedrich, R., &#38; Friml, J. (n.d.). Cytosolic Ca2+ as a universal signal for rapid root growth regulation. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.10.17.683082\">https://doi.org/10.1101/2025.10.17.683082</a>"},"day":"17","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.10.17.683082"}],"oa_version":"Preprint","external_id":{"biorxivid":["10.1101/2025.10.17.683082"]},"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"corr_author":"1","type":"dissertation","year":"2025","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"MaDe"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-10-23T22:30:02Z","page":"155","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","oa":1,"title":"Dissecting gap junction biology using the C. elegans nervous system","date_created":"2025-10-17T16:15:09Z","date_updated":"2026-10-23T22:30:03Z","month":"10","article_processing_charge":"No","date_published":"2025-10-23T00:00:00Z","author":[{"first_name":"Michaela","orcid":"0000-0003-2427-6856","last_name":"Misova","full_name":"Misova, Michaela","id":"495A3C32-F248-11E8-B48F-1D18A9856A87"}],"file":[{"relation":"source_file","checksum":"e042ea314e7e13fce76c6c95e126779a","creator":"mmisova","file_name":"2025-Misova-Michaela-Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access","date_created":"2025-10-23T08:22:35Z","file_size":75070995,"date_updated":"2026-10-23T22:30:02Z","file_id":"20518"},{"content_type":"application/pdf","access_level":"open_access","checksum":"fcd8973d6a025256eb0eb1a82c02172c","relation":"main_file","file_name":"2025-Misova-Michaela-Thesis.pdf","creator":"mmisova","embargo":"2026-10-23","file_id":"20519","date_updated":"2026-10-23T22:30:02Z","file_size":10974630,"date_created":"2025-10-23T08:21:21Z"}],"ec_funded":1,"_id":"20485","degree_awarded":"PhD","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","oa_version":"Published Version","day":"23","supervisor":[{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443"}],"citation":{"apa":"Misova, M. (2025). <i>Dissecting gap junction biology using the C. elegans nervous system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>","ista":"Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria.","mla":"Misova, Michaela. <i>Dissecting Gap Junction Biology Using the C. Elegans Nervous System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>.","ama":"Misova M. Dissecting gap junction biology using the C. elegans nervous system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>","short":"M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System, Institute of Science and Technology Austria, 2025.","chicago":"Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans Nervous System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>.","ieee":"M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,” Institute of Science and Technology Austria, 2025."},"acknowledgement":"I would also like to acknowledge the funding that I received from the European Union’s\r\nHorizon 2020 research and Innovation programme under the Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been possible without the contribution and support of people\r\nbehind the scientific service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit. I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC) Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. ","alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20485","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"ddc":["570"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-068-8"]},"doi":"10.15479/AT-ISTA-20485","language":[{"iso":"eng"}]},{"article_processing_charge":"No","month":"04","date_updated":"2026-10-15T22:30:03Z","date_created":"2025-04-14T06:59:06Z","title":"Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution","_id":"19557","file":[{"date_updated":"2026-10-15T22:30:02Z","file_id":"19561","file_size":21783427,"date_created":"2025-04-15T08:43:36Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access","checksum":"50290a8604edb0a720387f01e9d59fe4","relation":"source_file","creator":"lschwarz","file_name":"Schwarz_Thesis_2025_FINAL.docx"},{"file_size":11432175,"date_created":"2025-04-15T08:43:42Z","file_id":"19562","date_updated":"2026-10-15T22:30:02Z","creator":"lschwarz","embargo":"2026-10-15","file_name":"Schwarz_Thesis_2025_FINALpdfa.pdf","relation":"main_file","checksum":"ed028488180ac4901e018ef1c330cf01","access_level":"open_access","content_type":"application/pdf"}],"date_published":"2025-04-14T00:00:00Z","author":[{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","last_name":"Schwarz"}],"project":[{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964"},{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"corr_author":"1","type":"dissertation","year":"2025","OA_place":"publisher","oa":1,"file_date_updated":"2026-10-15T22:30:02Z","page":"124","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","publisher":"Institute of Science and Technology Austria","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","id":"12802","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9429","status":"public"}]},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19557","alternative_title":["ISTA Thesis"],"acknowledgement":"The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses.","language":[{"iso":"eng"}],"doi":"10.15479/AT-ISTA-19557","publication_identifier":{"issn":["2663-337X"]},"status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","citation":{"ieee":"L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025.","ama":"Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>","short":"L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025.","chicago":"Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>.","mla":"Schwarz, Lena A. <i>Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>.","ista":"Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria.","apa":"Schwarz, L. A. (2025). <i>Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>"},"supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"day":"14","oa_version":"Published Version"},{"_id":"20798","date_published":"2025-12-11T00:00:00Z","author":[{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","full_name":"Wald, Sebastian","last_name":"Wald","orcid":"0000-0002-5869-1604","first_name":"Sebastian"}],"file":[{"relation":"main_file","checksum":"1be72faf529a5e8a2d03cb3d5f808b77","embargo":"2026-06-15","file_name":"2025_Wald_Sebastian_Thesis.pdf","creator":"swald","content_type":"application/pdf","access_level":"open_access","date_created":"2025-12-12T11:53:42Z","file_size":47536855,"date_updated":"2026-06-15T22:30:03Z","file_id":"20809"},{"embargo_to":"open_access","content_type":"application/x-zip-compressed","access_level":"closed","checksum":"8c3a1904dceb4bcd04bc9f14b2594bab","relation":"source_file","file_name":"2025_Wald_Sebastian_Thesis.zip","creator":"swald","file_id":"20810","date_updated":"2026-06-15T22:30:03Z","file_size":40127601,"date_created":"2025-12-12T11:54:55Z"}],"OA_embargo":"6","month":"12","date_updated":"2026-07-24T08:07:28Z","article_processing_charge":"No","title":"Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry","date_created":"2025-12-11T11:48:11Z","OA_place":"publisher","oa":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-06-15T22:30:03Z","page":"152","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","corr_author":"1","type":"dissertation","year":"2025","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"lang":"eng","text":"Atom interferometers measure the relative phase shifts between coherent matter-wave paths\r\nthat arise from interactions with external fields or inertial forces. Due to their exceptional\r\nphase sensitivity, atom interferometers became an essential tool for precision measurements\r\nand fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However, their measurement precision is limited by quantum projection noise,\r\nwhich arises from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates with absolute precision. The generation of entanglement between the atoms offers a\r\npath to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis thesis reports on the development of an atom interferometer experiment designed to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity that mediates all relevant atom-light interactions. The\r\ncavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates on the fundamental theoretical framework, the cavity design, and the full\r\noptical setup, including the detailed configuration of the developed laser stabilization methods.\r\nExperimentally, continuous loading methods were explored, resulting in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control\r\nwas verified via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity coupling.\r\nThese presented results establish the experimental groundwork for the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry."}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-075-6"],"issn":["2663-337X"]},"doi":"10.15479/AT-ISTA-20798","ddc":["530"],"das_tickbox":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"14759","status":"public"}]},"fulldoi":"https://doi.org/10.15479/AT-ISTA-20798","alternative_title":["ISTA Thesis"],"citation":{"mla":"Wald, Sebastian. <i>Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>.","short":"S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry, Institute of Science and Technology Austria, 2025.","ama":"Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>","chicago":"Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>.","ieee":"S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry,” Institute of Science and Technology Austria, 2025.","apa":"Wald, S. (2025). <i>Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>","ista":"Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria."},"supervisor":[{"full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten"}],"oa_version":"Published Version","keyword":["entanglement-enhanced atom interferometry","cavity QED","spin-squeezing","dipole trap","quantum optics"],"day":"11","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"status":"public","has_accepted_license":"1","degree_awarded":"PhD","doi_confirm":"1"},{"oa":1,"quality_controlled":"1","article_number":"e1767232024","OA_place":"publisher","publisher":"Society for Neuroscience","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-09-27T22:30:02Z","scopus_import":"1","year":"2025","type":"journal_article","department":[{"_id":"MaDe"}],"OA_type":"hybrid","pmid":1,"_id":"19498","author":[{"full_name":"Stratigi, Aikaterini","last_name":"Stratigi","first_name":"Aikaterini"},{"first_name":"Miguel","last_name":"Soler-García","full_name":"Soler-García, Miguel"},{"first_name":"Mia","last_name":"Krout","full_name":"Krout, Mia"},{"full_name":"Shukla, Shikha","last_name":"Shukla","first_name":"Shikha"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario","last_name":"De Bono","orcid":"0000-0001-8347-0443","first_name":"Mario"},{"last_name":"Richmond","first_name":"Janet E.","full_name":"Richmond, Janet E."},{"full_name":"Laurent, Patrick","last_name":"Laurent","first_name":"Patrick"}],"date_published":"2025-03-26T00:00:00Z","file":[{"date_updated":"2025-09-27T22:30:02Z","file_id":"19525","file_size":3111735,"date_created":"2025-04-07T11:57:19Z","access_level":"open_access","content_type":"application/pdf","file_name":"2025_JourNeuroscience_Stratigi.pdf","embargo":"2025-09-27","creator":"dernst","checksum":"7befc0168f4cd5bd2b0fcff9e2a94784","relation":"main_file"}],"publication":"Journal of Neuroscience","date_updated":"2026-07-28T11:30:41Z","month":"03","OA_embargo":"6 months","article_processing_charge":"No","article_type":"original","title":"Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans","date_created":"2025-04-06T22:01:32Z","citation":{"apa":"Stratigi, A., Soler-García, M., Krout, M., Shukla, S., de Bono, M., Richmond, J. E., &#38; Laurent, P. (2025). Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>","ista":"Stratigi A, Soler-García M, Krout M, Shukla S, de Bono M, Richmond JE, Laurent P. 2025. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 45(13), e1767232024.","mla":"Stratigi, Aikaterini, et al. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>, vol. 45, no. 13, e1767232024, Society for Neuroscience, 2025, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>.","ieee":"A. Stratigi <i>et al.</i>, “Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans,” <i>Journal of Neuroscience</i>, vol. 45, no. 13. Society for Neuroscience, 2025.","ama":"Stratigi A, Soler-García M, Krout M, et al. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. 2025;45(13). doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>","short":"A. Stratigi, M. Soler-García, M. Krout, S. Shukla, M. de Bono, J.E. Richmond, P. Laurent, Journal of Neuroscience 45 (2025).","chicago":"Stratigi, Aikaterini, Miguel Soler-García, Mia Krout, Shikha Shukla, Mario de Bono, Janet E. Richmond, and Patrick Laurent. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2025. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>."},"issue":"13","external_id":{"pmid":["39919830"],"isi":["001460952700001"]},"oa_version":"Published Version","day":"26","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","isi":1,"abstract":[{"lang":"eng","text":"A dynamic interplay between fast synaptic signals and slower neuromodulatory signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits. The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance remain uncertain. We designed a genetic screen to isolate genes involved in the peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin (snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1). We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans, and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies [developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C. elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1 signaling alters the synapsin and actin cytoskeleton and increases neuropeptide release by cholinergic motor neurons, which secondarily affects the presynaptic vesicle cycle. Together, these results clarify the dominant mechanisms of action of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I balance in DEE70."}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"doi":"10.1523/JNEUROSCI.1767-23.2024","ddc":["570"],"volume":45,"intvolume":"        45","acknowledgement":"P.L. is a research associate of the Belgian National Fund for Scientific Research (FRS-FNRS). K.S., M.S.-G., S.S., and P.L. are supported by grants from the FRS-FNRS. This work was supported by an Advanced ERC Grant (269058 ACMO) to M.D.B. We thank the team of Alexander Gottschalk for the snn-1(S9A) strain. We thank the Imaging Facility of the Faculty of Medicine (LiMiF) of the Universite Libre de Bruxelles, supported by FRS-FNRS. This work made use of instruments in the Electron Microscopy Core of the University of Illinois Chicago Research Resources Center as well as the BioCryo facility of Northwestern University's NUANCE Center, which has received support from the SHyNE Resource (NSF ECCS-2025633), the IIN, and Northwestern's MRSEC program (NSF DMR-2308691). Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440).","fulldoi":"https://doi.org/10.1523/JNEUROSCI.1767-23.2024"},{"publication_status":"published","publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-01-29T23:30:03Z","page":"135","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","oa":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","corr_author":"1","type":"dissertation","year":"2025","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"department":[{"_id":"JoFi"},{"_id":"GradSch"}],"date_published":"2025-01-24T00:00:00Z","author":[{"last_name":"Arnold","orcid":"0000-0003-1397-7876","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"}],"file":[{"file_id":"18946","date_updated":"2026-01-29T23:30:03Z","file_size":18856130,"date_created":"2025-01-29T08:38:08Z","embargo_to":"open_access","access_level":"closed","content_type":"application/x-zip-compressed","creator":"cchlebak","file_name":"tex for upload.zip","relation":"source_file","checksum":"71872702e8f46c275eaea44efc4d304f"},{"creator":"cchlebak","file_name":"ISTThesisGA2022_final.pdf","embargo":"2026-01-29","checksum":"dfaa06591970f4bff163705802fad56d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":17344760,"date_created":"2025-01-29T08:38:34Z","date_updated":"2026-01-29T23:30:03Z","file_id":"18947"}],"ec_funded":1,"_id":"18871","title":"Microwave-optic interconnects for superconducting circuits","date_created":"2025-01-24T10:28:39Z","month":"01","date_updated":"2026-04-16T12:20:43Z","article_processing_charge":"No","oa_version":"Published Version","day":"24","supervisor":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"citation":{"mla":"Arnold, Georg M. <i>Microwave-Optic Interconnects for Superconducting Circuits</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>.","short":"G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits, Institute of Science and Technology Austria, 2025.","ama":"Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>","chicago":"Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>.","ieee":"G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,” Institute of Science and Technology Austria, 2025.","apa":"Arnold, G. M. (2025). <i>Microwave-optic interconnects for superconducting circuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>","ista":"Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria."},"degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"has_accepted_license":"1","status":"public","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:18871","abstract":[{"text":"\"Can we do this with a new type of computer - a quantum computer?\". This famous\r\nquotation of the brilliant Richard Feynman within a conference talk on \"Simulating physics\r\nwith computers.” is often reverently praised as the origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical. Now, 43 years later, the theoretical framework of how such\r\na computer can operate has been developed. Two main important concepts for a potential\r\nquantum supremacy, superposition and entanglement, have been exploited to design quantum\r\nalgorithms to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis still far from being certain, in fact the race between the most promising platforms such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well\r\nas spin qubits has recently intensified. If one also includes the most mature applications of\r\nquantum communication technologies, secure quantum key distribution and quantum random\r\nnumber generators, as part of a quantum information technology ecosystem, we are confronted\r\nwith a plethora of different materials, concepts, and also operation frequencies. While\r\nsuperconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently, a quantum frequency converter or microwave-optic transducer is required\r\nto interface the different frequency domains or establish a long-range network connection\r\nwith suitable telecom fibers. In fact, the combination of different frequency regimes is also\r\nan essential part in our classical modern communication network, where computations are\r\nperformed in electrical circuits and the information exchange over longer distances happens\r\nvia optical fibers. However, the specific challenges specific to building a quantum computer,\r\nalso apply to the development of such a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the carrier of information, i.e. the smallest possible quantity, the signal\r\ncan easily be corrupted by other noise sources which needs to be avoided by all means. This\r\nis also the reason why microwave quantum computers operate at temperature environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals cannot be copied which would be a typical\r\nstrategy to account for errors in classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic transducers: While quantum computers are operating in one specific frequency\r\ndomain, microwave-optic transducers combine microwave and optical fields in one device.\r\nThis results in the particular challenge that high-energy optical radiation, which is usually\r\nwell-shielded from superconducting microwave quantum processors, are now an essential part\r\nof the device. The concomitant optical radiation in the operating transducer will inevitably\r\nhave a detrimental effect on the superconducting microwave components. Together with the\r\nrequirement of minimal background noise for quantum-limited operation as described above,\r\nv\r\nheating from the absorption of optical photons within the same device where single microwave\r\nexcitations are processed forms a formidable challenge.\r\nThis thesis aims to address this challenge by developing microwave-optic transducers where\r\nthe impact of optical absorption on superconducting circuits in general and superconducting\r\nqubits specifically can be mitigated. In our first approach, we developed a compact device\r\nwith optimized interaction strengths between the different frequency domains. This minimizes\r\nthe optical powers used for transducer operation and thus the optical absorption heating. This\r\nwork was - to the best of our knowledge - the first comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately, we saw that the optical absorption heating added\r\nnoise way above a single excitation. Consequently, a potential quantum signal would have\r\nbeen buried in the noise, added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional microwave-optic transducer instead\r\nof an integrated device. The larger heat capacity of the macroscopic device with a size\r\nof a few millimeters can absorb a larger fraction of the optical heating before it increases\r\nthe temperature of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat the microwave-optic transducer can be operated in a regime in which optical fields don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic\r\ntransducers in conjunction with microwave quantum processors and brings the integration and\r\nseamless orchestration of different frequency components in a quantum network a step closer.\r\n","lang":"eng"}],"language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020 research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN) and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n","related_material":{"record":[{"status":"public","id":"6609","relation":"part_of_dissertation"},{"status":"public","id":"8529","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"18953"},{"status":"public","relation":"part_of_dissertation","id":"10924"},{"id":"9114","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"13200","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:18871","ddc":["530"],"acknowledged_ssus":[{"_id":"SSU"},{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"ddc":["570"],"related_material":{"record":[{"id":"14274","relation":"part_of_dissertation","status":"public"}]},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19745","alternative_title":["ISTA Thesis"],"acknowledgement":"This project has received funding from the Austrian Science Fund (FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cell migration is a crucial process in animal development and maintenance. It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment, where cells can switch between\r\nmigration modes as they encounter new environmental cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration strategy when encountering geometrically,\r\nmechanically and chemically distinct environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy, extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable. Instead, the cells use topography of the\r\nenvironment to propel their cell body forward. To migrate efficiently in the maze of different\r\npore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions into much denser environments with limited choice of large pores. In such invasive\r\ntransitions it is unclear if the cells can cross tight pores without the use of adhesions and\r\nextracellular proteolysis and whether they maintain the nucleus in the cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen gels, geometrically defined\r\nmicrochannels with constrictions and simplistic under agarose migration assay, we provide\r\na comprehensive characterization of invasive migration of dendritic cells. We show that\r\nduring invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody into the dense environment. In collagen gels, we show that dendritic cells can invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading\r\nto a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile force is simultaneously necessary for reverting the nucleus back to\r\nthe cell front after invasion and maintaining this positioning during permissive migration.\r\nA functional role of the reorientation was uncovered in the first collaboration project.\r\nA prominent central actin pool was identified around the MTOC, especially pronounced in\r\ndense and compressive environments. The actin pool was shown to generate pushing forces\r\nto dilate the space for cell translocation. These forces are only necessary in non-permissive\r\nenvironments, where the nucleus reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive environments where space generation is dispensable, the\r\nMTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second collaboration project, we investigated the effects of distinct chemical\r\nenvironments on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas explained by their ability to modulate and even self-generate chemokine gradients. This\r\nallows the cells to migrate faster and more persistent in uniform chemokine fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial\r\nplayer in this process, both sensing the signal and internalizing the chemokine to create a sink."}],"doi":"10.15479/AT-ISTA-19745","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-058-9"]},"has_accepted_license":"1","status":"public","degree_awarded":"PhD","citation":{"ieee":"N. Canigova, “Adaptive strategies of dendritic cell migration in response to environmental cues,” Institute of Science and Technology Austria, 2025.","chicago":"Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>.","ama":"Canigova N. Adaptive strategies of dendritic cell migration in response to environmental cues. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>","short":"N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues, Institute of Science and Technology Austria, 2025.","mla":"Canigova, Nikola. <i>Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>.","ista":"Canigova N. 2025. Adaptive strategies of dendritic cell migration in response to environmental cues. Institute of Science and Technology Austria.","apa":"Canigova, N. (2025). <i>Adaptive strategies of dendritic cell migration in response to environmental cues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>"},"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"}],"day":"27","oa_version":"Published Version","article_processing_charge":"No","OA_embargo":"6","month":"05","date_updated":"2026-06-18T17:34:48Z","date_created":"2025-05-26T08:49:00Z","title":"Adaptive strategies of dendritic cell migration in response to environmental cues","ec_funded":1,"_id":"19745","file":[{"file_size":103879193,"date_created":"2025-05-28T07:38:17Z","file_id":"19748","date_updated":"2025-11-27T23:30:02Z","relation":"source_file","checksum":"1a2d1525d19347fbb879ef57c02951bf","creator":"cchlebak","file_name":"NikolaCanigova_Thesis_final.docx","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"access_level":"open_access","content_type":"application/pdf","creator":"cchlebak","embargo":"2025-11-27","file_name":"NikolaCanigova_Thesis_final_PDFA2a_fixed.pdf","checksum":"c1d8f9a40a8e19fcf895373f4b773a46","relation":"main_file","file_id":"19749","date_updated":"2025-11-27T23:30:02Z","file_size":194530600,"date_created":"2025-05-28T07:39:53Z"}],"date_published":"2025-05-27T00:00:00Z","author":[{"full_name":"Canigova, Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola","last_name":"Canigova","orcid":"0000-0002-8518-5926"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"}],"department":[{"_id":"MiSi"},{"_id":"GradSch"}],"corr_author":"1","year":"2025","type":"dissertation","OA_place":"publisher","oa":1,"file_date_updated":"2025-11-27T23:30:02Z","page":"133","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","publisher":"Institute of Science and Technology Austria"},{"status":"public","has_accepted_license":"1","degree_awarded":"PhD","citation":{"ieee":"A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025.","ama":"Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>","short":"A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025.","chicago":"Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>.","mla":"Hlavata, Annamaria. <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>.","ista":"Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria.","apa":"Hlavata, A. (2025). <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>"},"supervisor":[{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036"}],"oa_version":"Published Version","day":"20","ddc":["572"],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"acknowledgement":"I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.","fulldoi":"https://doi.org/10.15479/10.15479/AT-ISTA-19431","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"],"isbn":["978-3-99078-055-8"]},"doi":"10.15479/10.15479/AT-ISTA-19431","corr_author":"1","type":"dissertation","year":"2025","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"OA_place":"publisher","oa":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-03-20T23:30:04Z","page":"83","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"03","date_updated":"2026-04-07T11:46:32Z","article_processing_charge":"No","title":"Regulation of Cytoplasmic RNA Polymerase II","date_created":"2025-03-20T12:52:47Z","_id":"19431","date_published":"2025-03-20T00:00:00Z","author":[{"last_name":"Hlavata","first_name":"Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria"}],"file":[{"relation":"source_file","checksum":"b7ddf424ffe95f8c767c53c8bb62d4f3","creator":"ahlavata","file_name":"PhD_Thesis_Hlavata_final_submission.docx","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2025-03-24T12:48:36Z","file_size":23506747,"file_id":"19448","date_updated":"2026-03-20T23:30:04Z"},{"access_level":"open_access","content_type":"application/pdf","file_name":"PhD_Thesis_Hlavata_final_submission_update.pdf","embargo":"2026-03-20","creator":"ahlavata","checksum":"6c5a59c9bac467c3d0b3ffb8ea6d9fd4","relation":"main_file","date_updated":"2026-03-20T23:30:04Z","file_id":"19449","date_created":"2025-03-24T12:51:10Z","file_size":9478591}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","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)"},"status":"public","has_accepted_license":"1","degree_awarded":"PhD","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"citation":{"ista":"Sartoris L. 2025. The effect of circadian rhythm on organisational immunity of ant colonies. Institute of Science and Technology Austria.","apa":"Sartoris, L. (2025). <i>The effect of circadian rhythm on organisational immunity of ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>","ieee":"L. Sartoris, “The effect of circadian rhythm on organisational immunity of ant colonies,” Institute of Science and Technology Austria, 2025.","ama":"Sartoris L. The effect of circadian rhythm on organisational immunity of ant colonies. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>","chicago":"Sartoris, Linda. “The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>.","short":"L. Sartoris, The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies, Institute of Science and Technology Austria, 2025.","mla":"Sartoris, Linda. <i>The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>."},"oa_version":"Published Version","day":"24","ddc":["577"],"acknowledged_ssus":[{"_id":"LifeSc"}],"acknowledgement":"Thank you to the Lab Support Facility at ISTA. Thank you to the European Research Council (ERC) for their funding under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grant EPIDEMICSonCHIP, No. 771402, to Sylvia Cremer, and ERC Starting Grant DISEASE, No. 802628, to Nathalie Stroeymeyt).","fulldoi":"https://doi.org/10.15479/AT-ISTA-19302","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Social interaction networks of insect colonies facilitate efficient information exchange and\r\ndemonstrate adaptive changes to mitigate disease transmission. While circadian rhythms\r\ninfluence individual behaviour, their role in shaping colony-level defences against pathogens\r\nremains unexplored. Here, we investigate whether social networks of the black garden ant,\r\nLasius niger, exhibit circadian rhythms and how these rhythms influence disease vulnerability\r\nwhen colonies are exposed to a pathogen during the day or the night.\r\nWe first establish baseline daily variations in activity and network dynamics in pathogen-free\r\ncolonies, revealing constitutive daily fluctuations in disease susceptibility. Subsequently, we\r\nexamine pathogen-induced changes in sanitary care and network dynamics by exposing\r\nforagers to a natural pathogen (Metarhizium brunneum) during either the day or the night.\r\nIndividual pathogen loads were measured after a nine-hour post-exposure period to evaluate\r\ntransmission outcomes.\r\nOur results demonstrate that diurnal ant colonies maintain robust circadian patterns in network\r\nproperties while flexibly adapting to pathogen exposure. Ants upregulate sanitary care\r\nirrespective of exposure timing, prioritising the protection of the valuable colony centre\r\nconsisting of nurses and the queen. These findings underscore the robustness and adaptability\r\nof ant colonies in balancing circadian rhythms with effective social immune responses.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"doi":"10.15479/AT-ISTA-19302","type":"dissertation","year":"2025","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"OA_type":"closed access","project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa":1,"publisher":"Institute of Science and Technology Austria","publication_status":"published","page":"85","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2026-03-02T23:31:13Z","date_updated":"2026-03-02T23:31:14Z","month":"02","article_processing_charge":"No","title":"The effect of circadian rhythm on organisational immunity of ant colonies","date_created":"2025-03-06T12:16:54Z","_id":"19302","ec_funded":1,"author":[{"last_name":"Sartoris","first_name":"Linda","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","full_name":"Sartoris, Linda"}],"date_published":"2025-02-24T00:00:00Z","file":[{"file_name":"Thesis_Linda_Sartoris.docx","creator":"lsartori","relation":"source_file","checksum":"7e9466dcf3681454211b74b5107e9f7b","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2025-03-07T10:16:11Z","file_size":7129583,"date_updated":"2026-02-23T23:30:03Z","file_id":"19310"},{"embargo_to":"open_access","content_type":"application/pdf","access_level":"closed","checksum":"2ccfcf32f0590bb0ec1a488e606a73f5","relation":"other","file_name":"thesis_Sartoris_for_print.pdf","creator":"lsartori","file_id":"19384","description":"for printing purposes only","date_updated":"2026-03-02T23:31:13Z","date_created":"2025-03-11T10:42:20Z","file_size":3199703},{"file_id":"19385","date_updated":"2026-02-23T23:30:03Z","file_size":3183186,"date_created":"2025-03-11T10:52:00Z","access_level":"open_access","content_type":"application/pdf","creator":"lsartori","embargo":"2026-02-23","file_name":"Thesis_Linda_Sartoris.pdf","checksum":"1d1f3c1279065b1a7f407ff6d1ee1503","relation":"main_file"}]},{"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"ddc":["612"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-19456","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"abstract":[{"text":"Making decisions requires flexibly adapting to changing environments, a process that\r\ndepends on accurately interpreting current contingencies and integrating them with\r\npast experience. Two brain regions are particularly critical for this process, the medial\r\nprefrontal cortex (mPFC) and the hippocampus. Using contextual information from the\r\nhippocampus, the mPFC selects relevant cognitive frameworks and suppresses\r\nirrelevant ones to guide appropriate actions. Several studies have shown that some\r\nmPFC pyramidal neurons become spatially tuned when spatial information is required\r\nto guide goal-directed behavior. However, the role of prefrontal spatial representations\r\nin learning and decision making is not well understood. This work aims to characterize\r\nthe role of mPFC spatial tuning in supporting a contextual association task. Rats were\r\ntrained to learn two cue–location associations on a radial arm maze over multiple days,\r\nwhile we simultaneously recorded from dorsal CA1 of the hippocampus and the\r\nprelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and\r\nprefrontal pyramidal neurons that “flicker” between multiple spatial representations on\r\ndifferent trials, suggesting dynamic, context-dependent coding. This flickering may\r\nprovide a substrate for how the network reorganizes in response to task demands,\r\nlikely by enabling the flexible evaluation of competing representations. ","lang":"eng"}],"doi":"10.15479/AT-ISTA-19456","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-056-5"]},"has_accepted_license":"1","status":"public","degree_awarded":"PhD","citation":{"apa":"Cumpelik, A. D. (2025). <i>The role of prefrontal spatial coding in supporting a contextual association task</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>","ista":"Cumpelik AD. 2025. The role of prefrontal spatial coding in supporting a contextual association task. Institute of Science and Technology Austria.","mla":"Cumpelik, Andrea D. <i>The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>.","chicago":"Cumpelik, Andrea D. “The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>.","short":"A.D. Cumpelik, The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task, Institute of Science and Technology Austria, 2025.","ama":"Cumpelik AD. The role of prefrontal spatial coding in supporting a contextual association task. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>","ieee":"A. D. Cumpelik, “The role of prefrontal spatial coding in supporting a contextual association task,” Institute of Science and Technology Austria, 2025."},"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"day":"18","keyword":["neuroscience","decision making","learning","cognitive flexibility","medial prefrontal cortex","hippocampus","electrophysiology"],"oa_version":"Published Version","article_processing_charge":"No","month":"02","date_updated":"2026-04-07T12:37:58Z","OA_embargo":"6 months","date_created":"2025-03-25T11:22:38Z","title":"The role of prefrontal spatial coding in supporting a contextual association task","_id":"19456","file":[{"date_updated":"2025-09-30T22:30:02Z","file_id":"19457","file_size":11869040,"date_created":"2025-03-25T11:07:55Z","access_level":"open_access","content_type":"application/pdf","creator":"acumpeli","file_name":"2025_Thesis_Cumpelik_corrections_PDFA.pdf","embargo":"2025-09-30","checksum":"1c7573303d8e5f6da3eb03d59055390f","relation":"main_file"},{"date_created":"2025-03-25T11:08:05Z","file_size":20436467,"file_id":"19458","date_updated":"2025-09-30T22:30:02Z","file_name":"2025_Thesis_Cumpelik_corrections.docx","creator":"acumpeli","relation":"source_file","checksum":"b93265ebd9a53f7a14100d0d48b4ff5b","embargo_to":"open_access","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"author":[{"last_name":"Cumpelik","orcid":"0000-0003-1727-6612","first_name":"Andrea D","id":"3F158B32-F248-11E8-B48F-1D18A9856A87","full_name":"Cumpelik, Andrea D"}],"date_published":"2025-02-18T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"year":"2025","type":"dissertation","corr_author":"1","oa":1,"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"96","file_date_updated":"2025-09-30T22:30:02Z","publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"year":"2025","type":"dissertation","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"138","file_date_updated":"2026-01-15T23:30:03Z","oa":1,"OA_place":"publisher","title":"Social immunity in a tri-partite host-pathogen relationship","date_created":"2025-07-10T14:12:20Z","date_updated":"2026-04-07T12:39:58Z","month":"07","article_processing_charge":"No","author":[{"last_name":"Strahodinsky","first_name":"Florian","id":"979E35EE-C996-11E9-8C7C-CF13E6697425","full_name":"Strahodinsky, Florian"}],"date_published":"2025-07-11T00:00:00Z","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access","relation":"source_file","checksum":"df3a02f0d937ea9a3d79d5fb94fff097","creator":"fstrahod","file_name":"Thesis_Florian_Strahodinsky_DOCX.docx","date_updated":"2026-01-15T23:30:03Z","file_id":"20021","file_size":9857392,"date_created":"2025-07-14T13:18:37Z"},{"date_created":"2025-07-14T13:18:38Z","file_size":6439602,"file_id":"20022","date_updated":"2026-01-15T23:30:03Z","file_name":"Thesis_Florian_Strahodinsky_PDF.pdf","creator":"fstrahod","embargo":"2026-01-15","relation":"main_file","checksum":"7164c21fe1946e839f7b8acd255ce803","access_level":"open_access","content_type":"application/pdf"}],"_id":"19993","degree_awarded":"PhD","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","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)"},"has_accepted_license":"1","status":"public","oa_version":"Published Version","day":"11","citation":{"apa":"Strahodinsky, F. (2025). <i>Social immunity in a tri-partite host-pathogen relationship</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>","ista":"Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria.","mla":"Strahodinsky, Florian. <i>Social Immunity in a Tri-Partite Host-Pathogen Relationship</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>.","ieee":"F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025.","chicago":"Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>.","ama":"Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>","short":"F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025."},"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-19993","alternative_title":["ISTA Thesis"],"ddc":["570"],"acknowledged_ssus":[{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT-ISTA-19993","abstract":[{"lang":"eng","text":"Ants are frequently challenged by different pathogens, which they counter with\r\nindividual and collective responses. Usually, the pathogens like fungi or viruses are\r\nsolitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These\r\nentomopathogenic nematodes are active parasites with an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated the basic biology of the host-pathogen relationship.\r\nWe tested different ant life stages and found that adult ants display defense behaviors\r\nand are generally resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker presence significantly reduces transmission risk. In the end, we were also able\r\nto disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial and nematode components.\r\nIn the second chapter, we studied the effect of multiple infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect of combined fungal and nematode\r\nexposure to better understand how the pathogens interact with each other in an ant\r\nhost. We found instances where combined exposure lead to higher mortality in a given\r\ntime frame in both, adult queens and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model to study worm infections\r\nin ants which extend our knowledge on collective disease defense."}],"language":[{"iso":"eng"}]},{"type":"dissertation","year":"2025","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","page":"113","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2026-05-23T22:30:02Z","oa":1,"OA_place":"publisher","title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","date_created":"2025-05-23T15:21:29Z","date_updated":"2026-06-12T08:34:29Z","month":"05","OA_embargo":"12","article_processing_charge":"No","author":[{"full_name":"Inumella, Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala","last_name":"Inumella","orcid":"0009-0002-5890-120X"}],"date_published":"2025-05-23T00:00:00Z","file":[{"file_size":8292363,"date_created":"2025-05-28T11:59:11Z","file_id":"19757","date_updated":"2026-05-23T22:30:02Z","creator":"sinumell","file_name":"Final Thesis_Syamala Inumella.pdf","embargo":"2026-05-23","checksum":"847ec70b2e40f50e0ddc7b8da201d52c","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_size":7145703,"date_created":"2025-05-28T11:59:11Z","file_id":"19758","date_updated":"2026-05-23T22:30:02Z","file_name":"Final Thesis_Syamala Inumella.docx","creator":"sinumell","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","relation":"source_file","embargo_to":"open_access","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"_id":"19722","degree_awarded":"PhD","status":"public","has_accepted_license":"1","oa_version":"Published Version","day":"23","supervisor":[{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"citation":{"mla":"Inumella, Syamala. <i>Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>.","ama":"Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>","chicago":"Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>.","short":"S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025.","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025.","apa":"Inumella, S. (2025). <i>Molecular mechanisms of microtubule reorganization in elongating root epidermal cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>","ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria."},"acknowledgement":"Special thanks to the Plant Facility.","alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-19722","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["580"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-059-6"]},"doi":"10.15479/AT-ISTA-19722","abstract":[{"lang":"eng","text":"As root epidermal cells progress from a phase of elongation to differentiation, their\r\ncortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The\r\nhormone cytokinin, a key regulator of root development, facilitates these cytoskeletal\r\nchanges. However, the molecular mechanisms underlying hormone-mediated MT\r\nreorientation during root development are still unknown. Here, we find that MT reorientation\r\nin root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell\r\ndifferentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s\r\nassociation with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end\r\ncreated by katanin-mediated severing at crossovers. Notably, our findings suggest that\r\ndynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning\r\nof the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets\r\nof cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1\r\nassociation in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it\r\nincreases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives\r\nMT reorganization during cell development by simultaneously modulating several\r\nmicrotubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool\r\nduring this process."}],"language":[{"iso":"eng"}]},{"article_processing_charge":"No","month":"10","date_updated":"2026-05-06T08:01:28Z","date_created":"2025-10-15T13:30:21Z","title":"An examination on phages as a naturally composable system","_id":"20470","file":[{"date_created":"2025-10-21T17:33:27Z","file_size":10603235,"date_updated":"2026-04-30T22:30:02Z","file_id":"20516","checksum":"d32ea83f259f6b0506325cd57b1d44c3","relation":"source_file","creator":"brwu","file_name":"2025_Wu_Bryan_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access"},{"date_created":"2025-10-21T17:33:26Z","file_size":6251936,"date_updated":"2026-04-30T22:30:02Z","file_id":"20517","file_name":"2025_Wu_Bryan_Thesis.pdf","creator":"brwu","embargo":"2026-04-30","relation":"main_file","checksum":"53590046fd3244c5550b4022282449d2","access_level":"open_access","content_type":"application/pdf"}],"author":[{"last_name":"Wu","first_name":"Bryan","id":"3C521EBA-F248-11E8-B48F-1D18A9856A87","full_name":"Wu, Bryan"}],"date_published":"2025-10-30T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"CaGu"}],"type":"dissertation","year":"2025","corr_author":"1","oa":1,"OA_place":"publisher","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"102","file_date_updated":"2026-04-30T22:30:02Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","ddc":["579"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20470","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems."}],"doi":"10.15479/AT-ISTA-20470","publication_identifier":{"issn":["2663-337X"]},"status":"public","has_accepted_license":"1","degree_awarded":"PhD","citation":{"mla":"Wu, Bryan. <i>An Examination on Phages as a Naturally Composable System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>.","ieee":"B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025.","short":"B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025.","chicago":"Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>.","ama":"Wu B. An examination on phages as a naturally composable system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>","apa":"Wu, B. (2025). <i>An examination on phages as a naturally composable system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>","ista":"Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria."},"supervisor":[{"first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"day":"30","oa_version":"Published Version"},{"has_accepted_license":"1","status":"public","doi_confirm":"1","degree_awarded":"PhD","citation":{"apa":"Zivadinovic, P. (2025). <i>Scale-free activity as a basis for spatial learning and memory in the brain</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>","ista":"Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria.","mla":"Zivadinovic, Predrag. <i>Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>.","chicago":"Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>.","short":"P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain, Institute of Science and Technology Austria, 2025.","ama":"Zivadinovic P. Scale-free activity as a basis for spatial learning and memory in the brain. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>","ieee":"P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory in the brain,” Institute of Science and Technology Austria, 2025."},"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"day":"11","oa_version":"Published Version","das_tickbox":"1","ddc":["570","539","571"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20777","alternative_title":["ISTA Thesis"],"acknowledgement":"My work has been funded through the project \"Functional Advantages of Critical Brain\r\nDynamics\" of the ISTA interdisciplinary fund and through the FWF.\r\n","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"A major challenge in neuroscience is deciphering how the brain orchestrates behavior in\r\nresponse to changes in environmental conditions. This process is characterized by several\r\nprocessing stages, from perception to the storage of important information. Information\r\nstorage is performed by a memory system implemented through complex networks of highly\r\ninterconnected neurons. The collective operational principles of neuronal networks that support\r\nformation and storage are the main topics of this thesis.\r\nTo investigate the collective dynamics of the hippocampus from the perspective of the brain\r\ncriticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches\r\n¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures\r\nderived from neuronal avalanches suggested that during wakefulness the hippocampus operated\r\nfurther away from criticality than during sleep/rest. In addition, neural activity propagated\r\ndifferently in these two brain states, as indicated by different collapses of the avalanche shapes.\r\nNext, the Phenomenological Renormalization Group approach also indicated conceptually\r\nsimilar differences, through the scaling exponent of activity variance α, which was higher during\r\nsleep/rest than during awake. These results confirmed that the activity of the hippocampus\r\nexhibits signatures of criticality and that these signatures change with the state of the brain.\r\nNext, I found that memory retention was predicted by the scaling exponent of activity variance\r\nα. The exponent α measured during the sleep/rest session that followed learning correlated\r\nwith memory retention during the subsequent unrewarded testing session. Moreover, α\r\npredicted performance even when controlled for reactivation that occurs in parallel. Second, α\r\nmeasured in the sleep/rest phase that preceded learning was correlated with the learning speed.\r\nI analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day\r\nvariability of these distributions, during sleep/rest that followed learning, correlated with the\r\nscaling exponent of activity variance α, as well as with memory retention. These findings\r\nconfirmed that variance scaling and functional heterogeneity provide behaviorally meaningful\r\nperspectives on hippocampal activity, as they are directly related to memory consolidation.\r\nI further investigated the process of memory acquisition and consolidation between the\r\nhippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards\r\nthe goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals\r\nduring sleep/rest that followed learning. This shift during sleep/rest was supported by the\r\nreactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and\r\nindependently of the hippocampal SWRs. Both types of reactivation predicted subsequent\r\nmemory retention, as well as the amount of goal-related remapping. Again, the day-to-day\r\nvariability of the distribution of the cell timescales correlated with the goal-related remapping,\r\nin CA1 during the learning session and in mEC during sleep/rest. These results suggest that\r\nin spatial navigation tasks, the functional responsibilities of CA1 and mEC change between\r\nlearning and sleep/rest and that their function benefits from increased functional heterogeneity\r\namong cells.\r\n"}],"doi":"10.15479/AT-ISTA-20777","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"project":[{"name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"}],"year":"2025","type":"dissertation","corr_author":"1","oa":1,"OA_place":"publisher","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"104","file_date_updated":"2026-06-11T22:30:02Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","article_processing_charge":"No","date_updated":"2026-07-24T08:14:37Z","month":"12","date_created":"2025-12-10T19:37:41Z","title":"Scale-free activity as a basis for spatial learning and memory in the brain","_id":"20777","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"pzivadin","embargo":"2026-06-11","file_name":"2025_Zivadinovic_Predrag_PhD_thesis.pdf","checksum":"aae9d1ed53f7b67f75e289c26a02b72f","relation":"main_file","date_updated":"2026-06-11T22:30:02Z","file_id":"20778","file_size":8105379,"date_created":"2025-12-10T19:28:20Z"},{"date_created":"2025-12-10T19:28:10Z","file_size":8512240,"file_id":"20779","date_updated":"2026-06-11T22:30:02Z","relation":"source_file","checksum":"8a08a3804ce7d9d625fdf1631113da8c","file_name":"2025_Zivadinovic_Predrag_PhD_thesis_source.zip","creator":"pzivadin","embargo_to":"open_access","content_type":"application/zip","access_level":"closed"}],"author":[{"first_name":"Predrag","last_name":"Zivadinovic","full_name":"Zivadinovic, Predrag","id":"68AA0E5A-AFDA-11E9-9994-141DE6697425"}],"date_published":"2025-12-11T00:00:00Z"},{"pmid":1,"project":[{"name":"Integrated Germanium Quantum Technology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"OA_type":"gold","department":[{"_id":"GeKa"}],"corr_author":"1","type":"journal_article","scopus_import":"1","year":"2025","file_date_updated":"2025-05-05T07:08:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","OA_place":"publisher","oa":1,"article_number":"3862","quality_controlled":"1","date_created":"2025-03-19T13:28:12Z","arxiv":1,"article_type":"original","title":"Exchange anisotropies in microwave-driven singlet-triplet qubits","article_processing_charge":"Yes","month":"04","date_updated":"2026-11-07T23:30:49Z","publication":"Nature Communications","APC_amount":"7068 EUR","file":[{"file_size":1548756,"date_created":"2025-05-05T07:08:23Z","success":1,"file_id":"19645","date_updated":"2025-05-05T07:08:23Z","checksum":"13fe84cddc9d4e47213bf17acdac70d7","relation":"main_file","creator":"dernst","file_name":"2025_NatureComm_SaezMollejo.pdf","content_type":"application/pdf","access_level":"open_access"}],"date_published":"2025-04-24T00:00:00Z","author":[{"full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo"},{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"last_name":"Schell","first_name":"Yona A","id":"fe39122d-06bb-11ec-a33b-9e22b40e40a5","full_name":"Schell, Yona A"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip"},{"first_name":"Stefano","last_name":"Calcaterra","full_name":"Calcaterra, Stefano"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Rimbach-Russ, Maximilian","first_name":"Maximilian","last_name":"Rimbach-Russ"},{"full_name":"Bosco, Stefano","last_name":"Bosco","first_name":"Stefano"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios"}],"_id":"19424","status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"24","DOAJ_listed":"1","oa_version":"Published Version","external_id":{"isi":["001475587400022"],"arxiv":["2408.03224"],"pmid":["40274808"]},"citation":{"short":"J. Saez Mollejo, D. Jirovec, Y.A. Schell, J. Kukucka, S. Calcaterra, D. Chrastina, G. Isella, M. Rimbach-Russ, S. Bosco, G. Katsaros, Nature Communications 16 (2025).","chicago":"Saez Mollejo, Jaime, Daniel Jirovec, Yona A Schell, Josip Kukucka, Stefano Calcaterra, Daniel Chrastina, Giovanni Isella, Maximilian Rimbach-Russ, Stefano Bosco, and Georgios Katsaros. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-58969-y\">https://doi.org/10.1038/s41467-025-58969-y</a>.","ama":"Saez Mollejo J, Jirovec D, Schell YA, et al. Exchange anisotropies in microwave-driven singlet-triplet qubits. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-58969-y\">10.1038/s41467-025-58969-y</a>","ieee":"J. Saez Mollejo <i>et al.</i>, “Exchange anisotropies in microwave-driven singlet-triplet qubits,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","mla":"Saez Mollejo, Jaime, et al. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” <i>Nature Communications</i>, vol. 16, 3862, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-58969-y\">10.1038/s41467-025-58969-y</a>.","ista":"Saez Mollejo J, Jirovec D, Schell YA, Kukucka J, Calcaterra S, Chrastina D, Isella G, Rimbach-Russ M, Bosco S, Katsaros G. 2025. Exchange anisotropies in microwave-driven singlet-triplet qubits. Nature Communications. 16, 3862.","apa":"Saez Mollejo, J., Jirovec, D., Schell, Y. A., Kukucka, J., Calcaterra, S., Chrastina, D., … Katsaros, G. (2025). Exchange anisotropies in microwave-driven singlet-triplet qubits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-58969-y\">https://doi.org/10.1038/s41467-025-58969-y</a>"},"related_material":{"record":[{"status":"public","relation":"research_data","id":"19409"},{"status":"public","relation":"dissertation_contains","id":"19836"}],"link":[{"relation":"research_data","description":"News on ISTA website","url":"https://ista.ac.at/en/news/the-shadow-of-an-electron/"}]},"fulldoi":"https://doi.org/10.1038/s41467-025-58969-y","acknowledgement":"We thank A. Crippa for helpful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project and the FWF Projects with DOI:10.55776/F86 and DOI:10.55776/I5060. M.R.-R. acknowledges support from the Netherlands Organization of Scientific Research (NWO) under Veni grant VI.Veni.212.223. The\r\nResearch of S.B. and M.R.-R. was sponsored in part by the Army Research Office and was accomplished under Award Number: W911NF-23-1-0110. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein.","intvolume":"        16","volume":16,"ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41467-025-58969-y","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Hole spin qubits are rapidly emerging as the workhorse of semiconducting quantum processors because of their large spin-orbit interaction, enabling fast all-electric operations at low power. However, spin-orbit interaction also causes non-uniformities in devices, resulting in locally varying qubit energies and site-dependent anisotropies. While these anisotropies can be used to drive single-spins, if not properly harnessed, they can hinder the path toward large-scale quantum processors. Here, we report on microwave-driven singlet-triplet qubits in planar germanium and use them to investigate the anisotropy of two spins in a double quantum dot. We show two distinct operating regimes depending on the magnetic field direction. For in-plane fields, the two spins are largely anisotropic, and electrically tunable, which enables to measure all the available transitions; coherence times exceeding 3 $\\mu$s are extracted. For out-of-plane fields, they have an isotropic response but preserve the substantial energy difference required to address the singlet-triplet qubit. Even in this field direction, where the qubit lifetime\r\nis strongly affected by nuclear spins, we find 400 ns coherence times. Our work adds a valuable tool to investigate and harness the anisotropy of spin qubits and can be implemented in any large-scale NxN device, facilitating the path towards scalable quantum processors."}],"isi":1},{"author":[{"full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo"}],"date_published":"2025-06-13T00:00:00Z","file":[{"file_name":"istaustriathesis-master - Copy.zip","creator":"jsaezmol","checksum":"643bfddead59857536cce4d57c775b32","relation":"source_file","embargo_to":"open_access","access_level":"closed","content_type":"application/x-zip-compressed","date_created":"2025-06-16T09:38:49Z","file_size":59892829,"file_id":"19849","date_updated":"2026-04-01T22:30:07Z"},{"date_updated":"2026-04-01T22:30:07Z","file_id":"19851","file_size":22382376,"date_created":"2025-06-18T08:50:16Z","access_level":"open_access","content_type":"application/pdf","creator":"jsaezmol","embargo":"2026-04-01","file_name":"SaezMollejo_PhDFinal_pdfa-1b.pdf","relation":"main_file","checksum":"e3dcb767fcc2b1787a455fdda991cefb"}],"_id":"19836","title":"Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ","date_created":"2025-06-13T09:01:50Z","month":"06","date_updated":"2026-07-29T12:55:59Z","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"175","file_date_updated":"2026-04-01T22:30:07Z","oa":1,"OA_place":"publisher","type":"dissertation","year":"2025","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"project":[{"name":"Integrated Germanium Quantum Technology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT-ISTA-19836","abstract":[{"text":"Over the past century, researchers have been fascinated by the quantum nature of the\r\nphysical world, initially striving to understand its fundamental principles and consequences, and\r\neventually progressing toward engineering systems that can control and manipulate quantum\r\nproperties. Today, we stand at the dawn of the quantum technology era. While some quantum\r\ntechnologies follow well-defined roadmaps, others are still in the exciting and uncertain early\r\nstages of development. In the fields of quantum computing and quantum simulation, research\r\nis being conducted across a wide variety of platforms. Each of these demonstrates control over\r\nquantum properties but also faces challenges in scaling up to the level of a mature technology.\r\nThis thesis explores some of the fundamental properties of hole spin qubits in planar germanium.\r\nSemiconductor spin qubits are considered strong candidates for the realization of quantum\r\nprocessors, owing to their long relaxation and coherence times, as well as their compatibility\r\nwith existing semiconductor industry infrastructure. Among these, hole spin qubits in planar\r\ngermanium are particularly promising. Their advantages include a large effective mass, which\r\neases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit\r\ninteraction, which enables fast and purely electrical control. However, spin-orbit coupling also\r\nintroduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip\r\ntunneling, which might cause that the quantization axes are not aligned. In this thesis, we\r\ninvestigate the tilt between the quantization axes of two hole spins hosted in a double quantum\r\ndot as a function of both the magnetic field direction and various electrostatic configurations,\r\ndemonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove\r\nto be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the\r\nphysics governing spin qubit behavior.\r\n","lang":"eng"}],"language":[{"iso":"eng"}],"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided\r\nby the MIBA Machine Shop and the Nanofabrication facility. We acknowledge the support from\r\nthe European Commission with the project Integrated Germanium Quantum Technology (with\r\nDOI:10.3030/101069515), the NOMIS Foundation, the HORIZON-RIA 101069515 project and\r\nthe FWF Projects Center for Correlated Quantum Materials and Solid State Quantum Systems:\r\nConventional and unconventional topological superconductors (with DOI:10.55776/F86) and\r\nHigh impedance circuit quantum electrodynamics with hole spins (with DOI:10.55776/I5060).\r\n","fulldoi":"https://doi.org/10.15479/AT-ISTA-19836","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"19424","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"ddc":["530","539"],"oa_version":"Published Version","day":"13","supervisor":[{"first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Saez Mollejo, Jaime. <i>Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>.","ieee":"J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025.","ama":"Saez Mollejo J. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>","chicago":"Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>.","short":"J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025.","apa":"Saez Mollejo, J. (2025). <i>Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>","ista":"Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria."},"degree_awarded":"PhD","doi_confirm":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1"},{"ec_funded":1,"_id":"19906","file":[{"file_name":"Thesis_v9_PDFA2b.pdf","embargo":"2025-12-27","creator":"cchlebak","relation":"main_file","checksum":"302a07605a9e64ac247c2036d5f5b1cd","access_level":"open_access","content_type":"application/pdf","file_size":6504571,"date_created":"2025-06-26T08:40:53Z","date_updated":"2025-12-27T23:30:02Z","file_id":"19907"},{"date_created":"2025-06-26T08:41:24Z","file_size":59092991,"date_updated":"2025-12-27T23:30:02Z","file_id":"19908","creator":"cchlebak","file_name":"Thesis Template - ISTA [istaustriathesis].zip","relation":"source_file","checksum":"5d69d10bdacc24c27f02924379405bd9","access_level":"closed","content_type":"application/x-zip-compressed","embargo_to":"open_access"}],"date_published":"2025-06-26T00:00:00Z","author":[{"full_name":"Suresh, Sarath S","id":"3D126CC4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarath S","last_name":"Suresh"}],"article_processing_charge":"No","month":"06","date_updated":"2026-07-29T12:55:31Z","date_created":"2025-06-26T08:39:08Z","title":"Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote","OA_place":"publisher","oa":1,"file_date_updated":"2025-12-27T23:30:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"82","publication_status":"published","publisher":"Institute of Science and Technology Austria","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"corr_author":"1","type":"dissertation","year":"2025","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Flows of ordinary fluids such as water or air transition from laminar to turbulent\r\nmotion as the velocity increases. This simple dependence of the flow state\r\nsolely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here\r\nvarious different instabilities and turbulent states can arise at low and even\r\nvanishing inertia, while high inertia turbulence counterintuitively is suppressed\r\nand its drag strongly reduced. We here show in experiments of a viscoelastic\r\nmodel fluid that the phenomena observed at low and high inertia have a\r\ncommon origin and that the same dynamical state, elasto-inertial turbulence,\r\npersists across four orders of magnitude in Reynolds number, ranging from\r\nvery low inertia, all the way to high inertia Maximum drag reduction (MDR)\r\nasymptote. We also explore the transitions from Newtonian turbulence to\r\nMDR, and specific cases of flow at high polymer concentrations, exploring the\r\nrelationship between flow at these wide range of control parameters.\r\n"}],"doi":"10.15479/AT-ISTA-19906","publication_identifier":{"issn":["2663-337X"]},"ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10299","status":"public"}]},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19906","alternative_title":["ISTA Thesis"],"acknowledgement":"This work was partially funded by the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie grant agreement\r\nNo. 665385.","supervisor":[{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"citation":{"mla":"Suresh, Sarath S. <i>Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>.","short":"S.S. Suresh, Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote, Institute of Science and Technology Austria, 2025.","ama":"Suresh SS. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>","chicago":"Suresh, Sarath S. “Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>.","ieee":"S. S. Suresh, “Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote,” Institute of Science and Technology Austria, 2025.","apa":"Suresh, S. S. (2025). <i>Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>","ista":"Suresh SS. 2025. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute of Science and Technology Austria."},"day":"26","oa_version":"Published Version","has_accepted_license":"1","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"doi_confirm":"1","degree_awarded":"PhD"}]