[{"department":[{"_id":"GeKa"},{"_id":"GradSch"},{"_id":"JoFi"}],"language":[{"iso":"eng"}],"publication_status":"draft","month":"07","date_created":"2024-09-26T09:50:43Z","supplementarymaterial":"unclear","article_processing_charge":"No","related_material":{"record":[{"id":"18886","relation":"research_data","status":"public"},{"status":"public","id":"19401","relation":"later_version"},{"relation":"dissertation_contains","id":"18129","status":"public"}]},"project":[{"grant_number":"101069515","name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices","call_identifier":"FWF"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507"},{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"}],"corr_author":"1","author":[{"full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","orcid":"0009-0003-9037-8831","first_name":"Marian"},{"first_name":"Kevin Etienne Robert","full_name":"Roux, Kevin Etienne Robert","id":"53f93ea2-803f-11ed-ab7e-b283135794ef","last_name":"Roux"},{"full_name":"Borja Espinosa, Carla N","last_name":"Borja Espinosa","id":"18777c01-896a-11ed-bdf8-e4851dc07d16","first_name":"Carla N"},{"full_name":"Sagi, Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver"},{"full_name":"Baghdadi, Abdulhamid","id":"160D87FA-96B5-11E9-BF77-7626E6697425","last_name":"Baghdadi","first_name":"Abdulhamid"},{"first_name":"Thomas","last_name":"Adletzberger","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","full_name":"Adletzberger, Thomas"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"first_name":"Alba Garzón","full_name":"Manjón, Alba Garzón","last_name":"Manjón"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"first_name":"Ioan M.","full_name":"Pop, Ioan M.","last_name":"Pop"},{"first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"publication":"arXiv","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2407.03079"}],"doi":"10.48550/arXiv.2407.03079","type":"preprint","oa":1,"title":"Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors","article_number":"2407.03079","oa_version":"Preprint","_id":"18144","researchdata_availability":"yes","status":"public","acknowledgement":"We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue 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, the FWF Projects with DOI:10.55776/P32235, DOI:10.55776/I5060 and DOI:10.55776/P36507. IMP acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG – German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC’s\r\nQuantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors\r\nacknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development\r\nFund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM [60].","year":"2024","citation":{"ista":"Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T, Calcaterra S, Botifoll M, Manjón AG, Arbiol J, Chrastina D, Isella G, Pop IM, Katsaros G. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. arXiv, 2407.03079.","ama":"Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. arXiv. doi:10.48550/arXiv.2407.03079","ieee":"M. Janik et al., “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors,” arXiv. .","apa":"Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger, T., … Katsaros, G. (n.d.). Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. arXiv. https://doi.org/10.48550/arXiv.2407.03079","chicago":"Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.03079.","mla":"Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” ArXiv, 2407.03079, doi:10.48550/arXiv.2407.03079.","short":"M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger, S. Calcaterra, M. Botifoll, A.G. Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M. Pop, G. Katsaros, ArXiv (n.d.)."},"arxiv":1,"day":"03","das_tickbox":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"arxiv":["2407.03079"]},"date_updated":"2026-10-26T23:31:01Z","abstract":[{"text":"High kinetic inductance superconductors are gaining increasing interest for\r\nthe realisation of qubits, amplifiers and detectors. Moreover, thanks to their\r\nhigh impedance, quantum buses made of such materials enable large zero-point\r\nfluctuations of the voltage, boosting the coupling rates to spin and charge\r\nqubits. However, fully exploiting the potential of disordered or granular\r\nsuperconductors is challenging, as their inductance and, therefore, impedance\r\nat high values are difficult to control. Here we have integrated a granular\r\naluminium resonator, having a characteristic impedance exceeding the resistance\r\nquantum, with a germanium double quantum dot and demonstrate strong\r\ncharge-photon coupling with a rate of $g_\\text{c}/2\\pi= (566 \\pm 2)$ MHz. This\r\nwas achieved due to the realisation of a wireless ohmmeter, which allows\r\n\\emph{in situ} measurements during film deposition and, therefore, control of\r\nthe kinetic inductance of granular aluminium films. Reproducible fabrication of\r\ncircuits with impedances (inductances) exceeding 13 k$\\Omega$ (1 nH per square)\r\nis now possible. This broadly applicable method opens the path for novel qubits\r\nand high-fidelity, long-distance two-qubit gates.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.48550/arXiv.2407.03079","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-07-03T00:00:00Z","OA_place":"repository"},{"external_id":{"arxiv":["2403.07803"]},"oa_version":"Preprint","status":"public","_id":"20571","year":"2024","acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful\r\ncomments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, and Oliver Tse for pointing out the reference [15]. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.\r\n","citation":{"ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv. doi:10.48550/arXiv.2403.07803","ista":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv, 2403.07803.","ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” arXiv. .","apa":"Quattrocchi, F. (n.d.). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv. https://doi.org/10.48550/arXiv.2403.07803","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.07803.","short":"F. Quattrocchi, ArXiv (n.d.).","mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” ArXiv, 2403.07803, doi:10.48550/arXiv.2403.07803."},"arxiv":1,"day":"09","fulldoi":"https://doi.org/10.48550/arXiv.2403.07803","keyword":["gradient flows","Jordan–Kinderlehrer–Otto scheme","curves of maximal slope","optimal transport","Dirichlet boundary conditions","Fokker–Planck equation"],"OA_type":"green","date_published":"2024-04-09T00:00:00Z","OA_place":"repository","date_updated":"2026-10-26T23:31:03Z","abstract":[{"lang":"eng","text":"We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\\Omega \\Subset \\mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum. In the special case where $\\Omega$ is an interval in $\\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.\r\nOur discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\\partial \\Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\\overline \\Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\\Omega$ is an interval in $\\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-10-28T13:12:56Z","article_processing_charge":"No","related_material":{"record":[{"id":"20865","relation":"later_version","status":"public"},{"status":"public","id":"20563","relation":"dissertation_contains"}]},"project":[{"_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Differential Systems","call_identifier":"FWF","grant_number":"F06504"}],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publication_status":"draft","month":"04","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2403.07803","open_access":"1"}],"doi":"10.48550/arXiv.2403.07803","type":"preprint","oa":1,"title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","article_number":"2403.07803","corr_author":"1","author":[{"first_name":"Filippo","orcid":"0009-0000-9773-1931","last_name":"Quattrocchi","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","full_name":"Quattrocchi, Filippo"}],"publication":"arXiv"},{"oa_version":"Preprint","_id":"20570","status":"public","acknowledgement":"The author is thankful to Nicolas Clozeau, Lorenzo Dello Schiavo, Jan Maas, Dejan Slepčev,\r\nand Dario Trevisan for many fruitful discussions and comments. The author gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","year":"2024","citation":{"chicago":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.12924.","short":"F. Quattrocchi, ArXiv (n.d.).","mla":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” ArXiv, 2408.12924, doi:10.48550/arXiv.2408.12924.","ama":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv. doi:10.48550/arXiv.2408.12924","ista":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924.","apa":"Quattrocchi, F. (n.d.). Asymptotics for optimal empirical quantization of measures. arXiv. https://doi.org/10.48550/arXiv.2408.12924","ieee":"F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” arXiv. ."},"day":"23","arxiv":1,"external_id":{"arxiv":["2408.12924"]},"date_updated":"2026-10-26T23:31:03Z","abstract":[{"text":"We investigate the minimal error in approximating a general probability\r\nmeasure $\\mu$ on $\\mathbb{R}^d$ by the uniform measure on a finite set with\r\nprescribed cardinality $n$. The error is measured in the $p$-Wasserstein\r\ndistance. In particular, when $1\\le pPRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.010327.","mla":"Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” PRX Quantum, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:10.1103/prxquantum.5.010327.","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024).","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 2024;5(1). doi:10.1103/prxquantum.5.010327","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.5.010327","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” PRX Quantum, vol. 5, no. 1. American Physical Society, 2024."},"publisher":"American Physical Society","arxiv":1,"das_tickbox":"0","day":"16","isi":1},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"file":[{"date_updated":"2025-05-05T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"nagudelo","relation":"source_file","checksum":"6d7c7725d040d8debc070dcb35ac965d","access_level":"closed","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","file_size":183077763,"date_created":"2024-10-26T22:29:06Z","file_id":"18475","embargo_to":"open_access"},{"file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","file_size":47027710,"date_created":"2024-10-26T23:13:33Z","embargo":"2025-05-05","file_id":"18476","date_updated":"2025-05-05T22:30:04Z","content_type":"application/pdf","creator":"nagudelo","relation":"main_file","access_level":"open_access","checksum":"52f9c0bf2bdafa3baf827b73814a53ff"}],"_id":"18471","researchdata_availability":"unclear","status":"public","oa_version":"Published Version","supervisor":[{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"day":"28","publisher":"Institute of Science and Technology Austria","citation":{"apa":"Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:10.15479/at:ista:18471","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","mla":"Agudelo Duenas, Nathalie. Visualizing the Neuronal Transcriptional Landscape with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471.","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471."},"year":"2024","date_published":"2024-10-28T00:00:00Z","has_accepted_license":"1","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/at:ista:18471","OA_place":"publisher","date_updated":"2026-10-02T11:26:48Z","alternative_title":["ISTA Thesis"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"abstract":[{"lang":"eng","text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. "}],"file_date_updated":"2025-05-05T22:30:04Z","article_processing_charge":"No","date_created":"2024-10-26T20:02:42Z","supplementarymaterial":"unclear","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"W1232","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"degree_awarded":"PhD","page":"97","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"language":[{"iso":"eng"}],"month":"10","title":"Visualizing the neuronal transcriptional landscape with tissue context","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-044-2"]},"type":"dissertation","doi":"10.15479/at:ista:18471","doi_confirm":"1","corr_author":"1","author":[{"first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"}]},{"file":[{"date_created":"2024-11-25T14:44:03Z","file_size":75512262,"file_name":"PhD Thesis - Divyansh Gupta.zip","file_id":"18589","embargo_to":"open_access","creator":"dgupta","date_updated":"2025-11-11T23:30:02Z","content_type":"application/zip","relation":"source_file","checksum":"ebb000d361c36b22ed6e639a931c6b7c","access_level":"closed"},{"checksum":"1282401eb71598bc311058b0fcefc6a1","access_level":"open_access","relation":"main_file","creator":"dgupta","content_type":"application/pdf","date_updated":"2025-11-11T23:30:02Z","file_id":"18591","date_created":"2024-11-26T11:43:19Z","file_size":6412619,"embargo":"2025-11-11","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"citation":{"chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18574.","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","mla":"Gupta, Divyansh. Visual Adaptations to Natural Statistics. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18574.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:10.15479/at:ista:18574","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","apa":"Gupta, D. (2024). Visual adaptations to natural statistics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18574"},"year":"2024","acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","publisher":"Institute of Science and Technology Austria","day":"22","supervisor":[{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"oa_version":"Published Version","_id":"18574","researchdata_availability":"unclear","status":"public","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/at:ista:18574","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"ddc":["573"],"has_accepted_license":"1","date_published":"2024-11-22T00:00:00Z","file_date_updated":"2025-11-11T23:30:02Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_embargo":"12","date_updated":"2026-10-02T11:33:52Z","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"12349","status":"public"},{"relation":"research_data","id":"12370","status":"public"}]},"project":[{"grant_number":"101086580","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention"}],"degree_awarded":"PhD","supplementarymaterial":"unclear","date_created":"2024-11-20T21:30:44Z","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"11","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publication_status":"published","page":"86","doi_confirm":"1","doi":"10.15479/at:ista:18574","type":"dissertation","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-050-3"]},"title":"Visual adaptations to natural statistics","oa":1,"author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Divyansh","orcid":"0000-0001-7400-6665","first_name":"Divyansh"}],"corr_author":"1"},{"abstract":[{"text":"Data analysis files for the manuscript \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\".\r\n\r\nThis contains the raw data and the data analysis files for generating the figures in the manuscript.\r\n\r\n Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.\r\n Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file\r\n Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.\r\nFigure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included. ","lang":"eng"}],"author":[{"last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","orcid":"0000-0001-7641-8348","first_name":"Riya"},{"first_name":"Farid","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan","full_name":"Phan, Duc T","first_name":"Duc T"},{"first_name":"Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"first_name":"Andras","last_name":"Vukics","full_name":"Vukics, Andras"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","date_updated":"2026-10-26T23:31:03Z","OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.10518320"}],"fulldoi":"https://doi.org/10.5281/ZENODO.10518320","doi":"10.5281/ZENODO.10518320","type":"research_data_reference","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"OA_type":"gold","title":"Data Analysis files for \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\"","date_published":"2024-01-16T00:00:00Z","has_accepted_license":"1","oa":1,"year":"2024","citation":{"short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024).","mla":"Sett, Riya, et al. Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo, 2024, doi:10.5281/ZENODO.10518320.","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Data Analysis Files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10518320.","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. https://doi.org/10.5281/ZENODO.10518320","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024.","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit’, Zenodo, 10.5281/ZENODO.10518320.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” 2024. doi:10.5281/ZENODO.10518320"},"publisher":"Zenodo","day":"16","month":"01","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"oa_version":"Published Version","status":"public","_id":"18978","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17183"},{"id":"19533","relation":"used_in_publication","status":"public"}]},"date_created":"2025-01-30T08:30:03Z","article_processing_charge":"No"},{"file":[{"date_created":"2024-07-26T13:14:24Z","file_size":24639084,"embargo":"2025-01-26","file_name":"Thesis_Kristina_Lukic.pdf","file_id":"17320","creator":"cchlebak","date_updated":"2025-01-26T23:30:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"95517e697ea6a87e267e649cad560989"},{"relation":"source_file","checksum":"74325746a9a05078fb9935dbf2aef752","access_level":"closed","date_updated":"2025-01-26T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","file_id":"17321","embargo_to":"open_access","file_name":"Thesis_Kristina_Lukic.docx","file_size":96334272,"date_created":"2024-07-26T13:14:50Z"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"supervisor":[{"orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"das_tickbox":"0","day":"26","publisher":"Institute of Science and Technology Austria","year":"2024","citation":{"chicago":"Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17319.","mla":"Lukic, Kristina. Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17319.","short":"K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.","ista":"Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.","ama":"Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:10.15479/at:ista:17319","ieee":"K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.","apa":"Lukic, K. (2024). Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17319"},"researchdata_availability":"no","_id":"17319","status":"public","oa_version":"Published Version","OA_place":"publisher","has_accepted_license":"1","date_published":"2024-07-26T00:00:00Z","ddc":["580"],"fulldoi":"https://doi.org/10.15479/at:ista:17319","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-01-26T23:30:04Z","abstract":[{"lang":"eng","text":"This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor."}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-16T08:50:36Z","degree_awarded":"PhD","article_processing_charge":"No","supplementarymaterial":"no","date_created":"2024-07-26T09:05:55Z","month":"07","page":"224","publication_status":"published","department":[{"_id":"LeSa"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"doi_confirm":"1","oa":1,"title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/at:ista:17319","author":[{"orcid":"0000-0003-1581-881X","first_name":"Kristina","full_name":"Lukic, Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","last_name":"Lukic"}],"corr_author":"1"},{"ddc":["570"],"date_published":"2024-09-04T00:00:00Z","has_accepted_license":"1","article_type":"original","fulldoi":"https://doi.org/10.1038/s42003-024-06747-9","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-10-26T23:31:05Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-09-17T09:44:29Z","abstract":[{"lang":"eng","text":"The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters."}],"dataavailabilitystatement":"The RNA-seq data for this study are available online at the NCBI Sequence Read Archive (accession number: PRJNA1116831). Uncropped images of the DNA gels are provided in the Supplementary Figs. 21 to 22. The source data used to generate the plots are provided in the Supplementary Data 2.","external_id":{"pmid":["39232040"],"isi":["001306499600002"]},"file":[{"file_name":"2024_CommBiology_Peng.pdf","file_size":7718758,"date_created":"2024-09-17T09:44:29Z","file_id":"18084","success":1,"date_updated":"2024-09-17T09:44:29Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"7d66af41c90e73d1b8a375eb652a9561"}],"intvolume":" 7","_id":"18063","researchdata_availability":"yes (supplementary data)","status":"public","oa_version":"Published Version","das_tickbox":"1","day":"04","isi":1,"year":"2024","acknowledgement":"We thank Drs. Erika Isono (University of Constance), Grégory Vert (University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong) for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University), and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported by grants to S.T. from the National Natural Science Foundation of China (32321001), the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, the Division of Life Sciences and Medicine, the University of Science and Technology of China (QYPY20220012), the Fundamental Research Funds for the Central Universities (WK9100000021), and start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026, KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science Fund (FWF; projects I6123 and P37051-B).","citation":{"chicago":"Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology. Springer Nature, 2024. https://doi.org/10.1038/s42003-024-06747-9.","mla":"Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology, vol. 7, 1085, Springer Nature, 2024, doi:10.1038/s42003-024-06747-9.","short":"Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková, J. Friml, S. Tan, Communications Biology 7 (2024).","ama":"Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 2024;7. doi:10.1038/s42003-024-06747-9","ista":"Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085.","ieee":"Y. Peng et al., “Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis,” Communications Biology, vol. 7. Springer Nature, 2024.","apa":"Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024). Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-024-06747-9"},"publisher":"Springer Nature","pmid":1,"publication_identifier":{"eissn":["2399-3642"]},"title":"Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis","oa":1,"doi":"10.1038/s42003-024-06747-9","type":"journal_article","article_number":"1085","scopus_import":"1","publication":"Communications Biology","author":[{"last_name":"Peng","full_name":"Peng, Yakun","first_name":"Yakun"},{"full_name":"Ji, Kangkang","last_name":"Ji","first_name":"Kangkang"},{"first_name":"Yanbo","last_name":"Mao","full_name":"Mao, Yanbo"},{"first_name":"Yiqun","last_name":"Wang","id":"82F537F2-B517-11E9-84D7-6433E6697425","full_name":"Wang, Yiqun"},{"full_name":"Korbei, Barbara","last_name":"Korbei","first_name":"Barbara"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"last_name":"Shen","full_name":"Shen, Jinbo","first_name":"Jinbo"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285"}],"date_created":"2024-09-15T22:01:38Z","supplementarymaterial":"yes","article_processing_charge":"Yes","project":[{"grant_number":"I06123","name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"}],"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"20117","relation":"dissertation_contains"}]},"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"language":[{"iso":"eng"}],"volume":7,"publication_status":"published","month":"09"},{"acknowledged_ssus":[{"_id":"Bio"}],"intvolume":" 2831","external_id":{"pmid":["39134857"]},"oa_version":"None","editor":[{"full_name":"Toyooka, Kazuhito","last_name":"Toyooka","first_name":"Kazuhito"}],"_id":"17425","status":"public","researchdata_availability":"no","publisher":"Springer Nature","citation":{"ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in Neuronal Morphogenesis, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","apa":"Miranda, O., Cheung, G. T., & Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), Neuronal Morphogenesis (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-3969-6_19","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. Neuronal Morphogenesis. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:10.1007/978-1-0716-3969-6_19","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:10.1007/978-1-0716-3969-6_19.","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3969-6_19."},"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","year":"2024","das_tickbox":"0","day":"13","fulldoi":"https://doi.org/10.1007/978-1-0716-3969-6_19","date_published":"2024-08-13T00:00:00Z","alternative_title":["Methods in Molecular Biology"],"date_updated":"2026-10-26T23:31:05Z","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","date_created":"2024-08-13T12:16:41Z","supplementarymaterial":"yes","quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20212"}]},"place":"New York, NY","project":[{"name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"volume":2831,"language":[{"iso":"eng"}],"series_title":"MIMB","page":"283-299","month":"08","type":"book_chapter","doi":"10.1007/978-1-0716-3969-6_19","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"eisbn":["9781071639696"],"isbn":["9781071639689"]},"pmid":1,"scopus_import":"1","edition":"1","corr_author":"1","author":[{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Miranda","full_name":"Miranda, Osvaldo","first_name":"Osvaldo","orcid":"0000-0001-6618-6889"},{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","orcid":"0000-0001-8457-2572","first_name":"Giselle T"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"publication":"Neuronal Morphogenesis"},{"related_material":{"link":[{"url":"https://doi.org/10.1038/s41594-025-01721-3","relation":"erratum"}]},"quality_controlled":"1","project":[{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","grant_number":"101020697"}],"article_processing_charge":"No","supplementarymaterial":"yes","date_created":"2024-04-14T22:01:03Z","month":"07","publication_status":"published","department":[{"_id":"LeSa"}],"volume":31,"language":[{"iso":"eng"}],"page":"1061-1071","type":"journal_article","doi":"10.1038/s41594-024-01255-0","oa":1,"title":"SCAF1 drives the compositional diversity of mammalian respirasomes","pmid":1,"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"author":[{"first_name":"Irene","orcid":"0000-0001-5618-3449","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","full_name":"Vercellino, Irene"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"publication":"Nature Structural and Molecular Biology","scopus_import":"1","corr_author":"1","intvolume":" 31","file":[{"file_name":"megacomplex_submit_NSMB_withFigures.pdf","date_created":"2024-05-14T11:57:56Z","file_size":24424729,"embargo":"2025-01-01","file_id":"15392","date_updated":"2025-01-01T23:30:03Z","content_type":"application/pdf","creator":"lsazanov","relation":"main_file","checksum":"21f05d188762acd7f49a97f3d09c8d9f","access_level":"open_access"}],"external_id":{"pmid":["38575788"],"isi":["001196897300001"]},"dataavailabilitystatement":"Structures of the three SCs were deposited in PDB (accessions 8PW5, 8PW6 and 8PW7) with corresponding cryo-EM density maps in EMDB (IDs 17989, 17990 and 17991). As the models were built on composite maps, the consensus and focused maps for all components of the three SCs have also been deposited on EMDB (18023, 18022, 18025, 18024, 18027, 18026, 18017, 18018, 18019, 18021, 18020, 18015, 18011, 18012, 18013 and 18014). Similarly, structures of complex I were deposited in PDB (accessions 8RGR, 8RGQ, 8RGP and 8RGT) with corresponding composite cryo-EM density maps (19147, 19146, 19145 and 19148) and consensus/focused maps (19085, 19086, 19087, 19091, 19092, 19093, 19088, 19089, 19090, 19105, 19106 and 19107) in EMDB. The following previously deposited models (PDB codes) have been used in the manuscript: 5gup, 5xth, 5iy5, 1ooc, 5z62, 3cx5, 7o3c, 5j4z, 5j7y, 7o37 and 6g2j. Uncropped gels and western blot, as well as the raw data for the activity assays summarized in Extended Data Fig. 8h, have been provided as Source data in this publication. Source data are provided with this paper.","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"ScienComp"}],"publisher":"Springer Nature","year":"2024","citation":{"apa":"Vercellino, I., & Sazanov, L. A. (2024). SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01255-0","ieee":"I. Vercellino and L. A. Sazanov, “SCAF1 drives the compositional diversity of mammalian respirasomes,” Nature Structural and Molecular Biology, vol. 31. Springer Nature, pp. 1061–1071, 2024.","ama":"Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 2024;31:1061-1071. doi:10.1038/s41594-024-01255-0","ista":"Vercellino I, Sazanov LA. 2024. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 31, 1061–1071.","short":"I. Vercellino, L.A. Sazanov, Nature Structural and Molecular Biology 31 (2024) 1061–1071.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” Nature Structural and Molecular Biology, vol. 31, Springer Nature, 2024, pp. 1061–71, doi:10.1038/s41594-024-01255-0.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” Nature Structural and Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-024-01255-0."},"acknowledgement":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.","isi":1,"das_tickbox":"1","day":"01","oa_version":"Submitted Version","_id":"15323","status":"public","researchdata_availability":"yes","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1038/s41594-024-01255-0","has_accepted_license":"1","date_published":"2024-07-01T00:00:00Z","ddc":["572"],"file_date_updated":"2025-01-01T23:30:03Z","abstract":[{"text":"Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.","lang":"eng"}],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-16T08:43:37Z"},{"publisher":"Public Library of Science","year":"2024","citation":{"short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","mla":"Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” PLoS Computational Biology, vol. 20, e1012508, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1012508.","chicago":"Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” PLoS Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1012508.","ieee":"R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” PLoS Computational Biology, vol. 20. Public Library of Science, 2024.","apa":"Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., & Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012508","ama":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 2024;20. doi:10.1371/journal.pcbi.1012508","ista":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508."},"acknowledgement":"We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","isi":1,"das_tickbox":"1","day":"14","oa_version":"Published Version","_id":"18481","researchdata_availability":"yes","status":"public","intvolume":" 20","file":[{"access_level":"open_access","checksum":"42fa714459943cb3961b40fab8fd82c8","relation":"main_file","creator":"dernst","date_updated":"2024-10-29T11:59:09Z","content_type":"application/pdf","success":1,"file_id":"18487","file_size":3732443,"date_created":"2024-10-29T11:59:09Z","file_name":"2024_PloSComBio_Ho.pdf"}],"external_id":{"pmid":["39401260"],"isi":["001331700300003"]},"dataavailabilitystatement":"Custom software in C++ used to run the computational screen is available as S1 Simulation code. Custom script in Python used to analyze Shh profiles is available as S1 Script code. All data are in the manuscript and/or supporting information files","file_date_updated":"2024-10-29T11:59:09Z","abstract":[{"text":"A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-26T23:31:07Z","DOAJ_listed":"1","OA_place":"publisher","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1371/journal.pcbi.1012508","article_type":"original","OA_type":"gold","has_accepted_license":"1","date_published":"2024-10-14T00:00:00Z","ddc":["570"],"month":"10","publication_status":"published","language":[{"iso":"eng"}],"volume":20,"department":[{"_id":"AnKi"}],"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"20393","relation":"dissertation_contains"}]},"project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"}],"APC_amount":"3197,23 EUR","article_processing_charge":"No","supplementarymaterial":"yes","date_created":"2024-10-27T23:01:45Z","author":[{"last_name":"Ho","full_name":"Ho, Richard D.J.G.","first_name":"Richard D.J.G."},{"orcid":"0000-0001-6060-4795","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","full_name":"Kishi, Kasumi"},{"first_name":"Maciej","last_name":"Majka","full_name":"Majka, Maciej"},{"first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","full_name":"Zagórski, Marcin P","first_name":"Marcin P","orcid":"0000-0001-7896-7762"}],"publication":"PLoS Computational Biology","scopus_import":"1","corr_author":"1","article_number":"e1012508","type":"journal_article","doi":"10.1371/journal.pcbi.1012508","title":"Dynamics of morphogen source formation in a growing tissue","oa":1,"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"pmid":1},{"scopus_import":"1","author":[{"last_name":"Krammer","full_name":"Krammer, Teresa","first_name":"Teresa"},{"full_name":"Stuart, Hannah T.","last_name":"Stuart","first_name":"Hannah T."},{"last_name":"Gromberg","full_name":"Gromberg, Elena","first_name":"Elena"},{"full_name":"Ishihara, Keisuke","last_name":"Ishihara","first_name":"Keisuke"},{"last_name":"Cislo","full_name":"Cislo, Dillon","first_name":"Dillon"},{"full_name":"Melchionda, Manuela","last_name":"Melchionda","first_name":"Manuela"},{"last_name":"Becerril Perez","full_name":"Becerril Perez, Fernando","first_name":"Fernando"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"full_name":"Costantini, Elena","last_name":"Costantini","first_name":"Elena"},{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093","first_name":"Stefanie"},{"first_name":"Laura","full_name":"Arbanas, Laura","last_name":"Arbanas"},{"first_name":"Alexandra","full_name":"Hörmann, Alexandra","last_name":"Hörmann"},{"first_name":"Ralph A.","last_name":"Neumüller","full_name":"Neumüller, Ralph A."},{"first_name":"Nicola","last_name":"Elvassore","full_name":"Elvassore, Nicola"},{"first_name":"Eric","last_name":"Siggia","full_name":"Siggia, Eric"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"last_name":"Tanaka","full_name":"Tanaka, Elly M.","first_name":"Elly M."}],"publication":"Developmental Cell","doi":"10.1016/j.devcel.2024.04.021","type":"journal_article","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"pmid":1,"oa":1,"title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","language":[{"iso":"eng"}],"volume":59,"department":[{"_id":"AnKi"}],"publication_status":"published","page":"1940-1953.e10","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"08","supplementarymaterial":"yes","date_created":"2024-06-16T22:01:07Z","article_processing_charge":"Yes (in subscription journal)","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19763"}]},"quality_controlled":"1","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011"}],"date_updated":"2026-10-26T23:31:09Z","file_date_updated":"2025-01-13T10:59:12Z","abstract":[{"lang":"eng","text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1016/j.devcel.2024.04.021","article_type":"original","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"],"date_published":"2024-08-01T00:00:00Z","OA_type":"hybrid","has_accepted_license":"1","OA_place":"publisher","oa_version":"Published Version","researchdata_availability":"yes","_id":"17148","status":"public","year":"2024","acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","citation":{"ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 2024;59(15):1940-1953.e10. doi:10.1016/j.devcel.2024.04.021","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.04.021","ieee":"T. Krammer et al., “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” Developmental Cell, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.04.021.","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10.","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:10.1016/j.devcel.2024.04.021."},"publisher":"Elsevier","das_tickbox":"1","day":"01","isi":1,"dataavailabilitystatement":"RNA-seq data generated in this study have been deposited at GEO under accession codes GSE221187 (FOXA2+ versus FOXA2- cells at Day 5, Figure 3), GSE236543 (FOXA2+ versus FOXA2- cells after BMP perturbations, Figure 4), and GSE260579 (RNA-seq of FOXA2- versus FOXA2+ low, medium, high cells, Figure S4) and RNA-seq analyses are provided in Table S2.","file":[{"file_size":6249076,"date_created":"2025-01-13T10:59:12Z","file_name":"2024_DevelopmentalCell_Krammer.pdf","file_id":"18841","success":1,"creator":"dernst","date_updated":"2025-01-13T10:59:12Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"fefdea9c02862b4bb74de49b65ce638a"}],"intvolume":" 59","external_id":{"pmid":["38776925"],"isi":["001289684800001"]},"issue":"15"},{"oa_version":"Published Version","status":"public","_id":"18642","researchdata_availability":"unclear","publisher":"Institute of Science and Technology Austria","year":"2024","citation":{"apa":"Machnik, N. N. (2024). Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18642","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:10.15479/at:ista:18642","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","mla":"Machnik, Nick N. Algorithms for Causal Learning and Comparative Analysis for Genomic Data. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18642.","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024.","chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18642."},"acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","supervisor":[{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"day":"11","file":[{"date_created":"2024-12-11T11:59:54Z","file_size":12845009,"embargo":"2025-06-12","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","file_id":"18649","creator":"nmachnik","date_updated":"2025-06-12T22:30:02Z","content_type":"application/pdf","checksum":"d45e4d170f9a70a1f69b44b99bd058e4","access_level":"open_access","relation":"main_file"},{"file_id":"18650","embargo_to":"open_access","file_name":"thesis.zip","date_created":"2024-12-11T11:59:34Z","file_size":14189810,"relation":"source_file","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","access_level":"closed","date_updated":"2025-06-12T22:30:02Z","content_type":"application/zip","creator":"nmachnik"}],"date_updated":"2026-10-16T11:01:16Z","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"This thesis consists of two pieces of work in the broader field of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefficient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fine-map genetic effects, find the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal effect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe effects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specific genetic effects, and how the error rates of this recovery are influenced\r\nby missing data due to different censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size differences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand finally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n"}],"file_date_updated":"2025-06-12T22:30:02Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.15479/at:ista:18642","has_accepted_license":"1","date_published":"2024-12-11T00:00:00Z","ddc":["576"],"OA_place":"publisher","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"page":"138","month":"12","article_processing_charge":"No","date_created":"2024-12-10T13:49:15Z","supplementarymaterial":"unclear","related_material":{"record":[{"status":"public","id":"8707","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18648","status":"public"}]},"project":[{"name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181"}],"degree_awarded":"PhD","corr_author":"1","author":[{"full_name":"Machnik, Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik","first_name":"Nick N","orcid":"0000-0001-6617-9742"}],"type":"dissertation","doi":"10.15479/at:ista:18642","title":"Algorithms for causal learning and comparative analysis for genomic data","oa":1,"publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1"},{"month":"12","publication_status":"published","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"volume":5,"language":[{"iso":"eng"}],"project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"APC_amount":"804 EUR","article_processing_charge":"Yes","date_created":"2024-12-01T23:01:53Z","supplementarymaterial":"no","publication":"STAR Protocols","author":[{"orcid":"0000-0001-8703-1093","first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","full_name":"Rus, Stefanie"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"Kulig, Monika Aleksandra","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","last_name":"Kulig","first_name":"Monika Aleksandra"},{"first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","full_name":"Minchington, Thomas"},{"first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"}],"corr_author":"1","scopus_import":"1","article_number":"103187","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","oa":1,"publication_identifier":{"eissn":["2666-1667"]},"pmid":1,"type":"journal_article","doi":"10.1016/j.xpro.2024.103187","day":"20","das_tickbox":"1","publisher":"Elsevier","year":"2024","citation":{"mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols, vol. 5, no. 4, 103187, Elsevier, 2024, doi:10.1016/j.xpro.2024.103187.","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103187.","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., & Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103187","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” STAR Protocols, vol. 5, no. 4. Elsevier, 2024.","ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 2024;5(4). doi:10.1016/j.xpro.2024.103187"},"acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","_id":"18601","researchdata_availability":"no","status":"public","oa_version":"Published Version","issue":"4","external_id":{"pmid":["39602310"]},"intvolume":" 5","file":[{"file_name":"2024_STARProtoc_Lehr.pdf","date_created":"2024-12-03T10:53:23Z","file_size":4989169,"file_id":"18610","success":1,"date_updated":"2024-12-03T10:53:23Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"0c61a6f9978608a103865905e06f4581"}],"dataavailabilitystatement":"This study did not generate datasets or code.","acknowledged_ssus":[{"_id":"NanoFab"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1","lang":"eng"}],"file_date_updated":"2024-12-03T10:53:23Z","date_updated":"2026-10-26T23:31:09Z","DOAJ_listed":"1","OA_place":"publisher","OA_type":"gold","date_published":"2024-12-20T00:00:00Z","has_accepted_license":"1","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103187"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n","lang":"eng"}],"date_updated":"2026-10-26T23:31:09Z","OA_place":"repository","OA_type":"free access","date_published":"2024-08-10T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"fulldoi":"https://doi.org/10.1101/2023.12.06.570392","day":"10","das_tickbox":"0","citation":{"chicago":"Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024. https://doi.org/10.1101/2023.12.06.570392.","mla":"Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024, doi:10.1101/2023.12.06.570392.","short":"N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024).","ista":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, 10.1101/2023.12.06.570392.","ama":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. 2024. doi:10.1101/2023.12.06.570392","ieee":"N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” bioRxiv. 2024.","apa":"Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., & Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. https://doi.org/10.1101/2023.12.06.570392"},"year":"2024","acknowledgement":"We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). ","status":"public","_id":"18648","researchdata_availability":"not applicable","oa_version":"Preprint","acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"bioRxiv","author":[{"last_name":"Machnik","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","full_name":"Machnik, Nick N","first_name":"Nick N","orcid":"0000-0001-6617-9742"},{"id":"b9f6d5ef-7774-11eb-a47f-df2c75c02ee7","last_name":"Mahmoudi","full_name":"Mahmoudi, Seyed Mahdi","first_name":"Seyed Mahdi"},{"last_name":"Borczyk","full_name":"Borczyk, Malgorzata","first_name":"Malgorzata"},{"orcid":"0000-0002-5636-9259","first_name":"Ilse","last_name":"Krätschmer","id":"30d4014e-7753-11eb-b44b-db6d61112e73","full_name":"Krätschmer, Ilse"},{"first_name":"Markus J.","last_name":"Bauer","full_name":"Bauer, Markus J."},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"corr_author":"1","title":"Causal inference for multiple risk factors and diseases from genomics data","oa":1,"type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2023.12.06.570392","open_access":"1"}],"doi":"10.1101/2023.12.06.570392","month":"08","publication_status":"published","department":[{"_id":"MaRo"}],"language":[{"iso":"eng"}],"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181"},{"grant_number":"590359","_id":"bd936e6f-d553-11ed-ba76-a82299f63e8c","name":"Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation"}],"related_material":{"record":[{"status":"public","id":"23043","relation":"later_version"},{"id":"18642","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","date_created":"2024-12-11T10:42:59Z","supplementarymaterial":"yes"},{"corr_author":"1","scopus_import":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","author":[{"last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","first_name":"Peter"},{"first_name":"Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","last_name":"Önal","full_name":"Önal, Hüseyin C","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011"},{"last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina","first_name":"Carolina","orcid":"0000-0003-0005-401X"},{"first_name":"Elodie","last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie"},{"first_name":"Utsa","full_name":"Roy, Utsa","last_name":"Roy","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"first_name":"Yukihiro","full_name":"Nakamura, Yukihiro","last_name":"Nakamura"},{"first_name":"Tetsushi","last_name":"Sadakata","full_name":"Sadakata, Tetsushi"},{"last_name":"Sanbo","full_name":"Sanbo, Makoto","first_name":"Makoto"},{"full_name":"Hirabayashi, Masumi","last_name":"Hirabayashi","first_name":"Masumi"},{"first_name":"JeongSeop","full_name":"Rhee, JeongSeop","last_name":"Rhee"},{"last_name":"Brose","full_name":"Brose, Nils","first_name":"Nils"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"pmid":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","oa":1,"doi":"10.1073/pnas.2301449121","type":"journal_article","article_number":"e2301449121","language":[{"iso":"eng"}],"volume":121,"department":[{"_id":"RySh"},{"_id":"PeJo"}],"publication_status":"published","month":"02","supplementarymaterial":"yes","date_created":"2024-03-05T09:23:55Z","APC_amount":"5887,8 EUR","article_processing_charge":"Yes (in subscription journal)","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","related_material":{"record":[{"id":"13173","relation":"research_data","status":"public"},{"id":"19271","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","description":"News on ISTA Website","relation":"press_release"}]},"date_updated":"2026-10-26T23:31:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-03-12T13:42:42Z","ec_funded":1,"abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"ddc":["570"],"date_published":"2024-02-20T00:00:00Z","OA_type":"hybrid","has_accepted_license":"1","fulldoi":"https://doi.org/10.1073/pnas.2301449121","article_type":"original","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"OA_place":"publisher","_id":"15084","researchdata_availability":"yes","status":"public","oa_version":"Published Version","das_tickbox":"1","day":"20","isi":1,"year":"2024","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","citation":{"short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8. National Academy of Sciences, 2024.","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(8). doi:10.1073/pnas.2301449121"},"publisher":"National Academy of Sciences","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"external_id":{"pmid":["38346189"],"isi":["001208567300006"]},"issue":"8","file":[{"file_id":"15110","success":1,"file_name":"2024_PNAS_Koppensteiner.pdf","date_created":"2024-03-12T13:42:42Z","file_size":13648221,"relation":"main_file","access_level":"open_access","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","date_updated":"2024-03-12T13:42:42Z","content_type":"application/pdf","creator":"dernst"}],"intvolume":" 121"},{"alternative_title":["ISTA Master's Thesis"],"date_updated":"2026-10-21T08:37:37Z","file_date_updated":"2025-05-02T22:30:04Z","abstract":[{"lang":"eng","text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. "}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.15479/at:ista:15352","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"date_published":"2024-05-02T00:00:00Z","has_accepted_license":"1","OA_place":"publisher","oa_version":"Published Version","_id":"15352","status":"public","researchdata_availability":"unclear","citation":{"mla":"Murmann, Julie Stefanie. Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15352.","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15352.","apa":"Murmann, J. S. (2024). Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15352","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:10.15479/at:ista:15352"},"year":"2024","publisher":"Institute of Science and Technology Austria","day":"02","supervisor":[{"orcid":"0000-0001-8635-0877","first_name":"Sandra","full_name":"Siegert, Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"file":[{"embargo":"2025-05-02","file_size":5936142,"date_created":"2024-05-02T12:26:13Z","file_name":"Murmann_Thesis_final_2024_2.pdf","file_id":"15354","creator":"cchlebak","content_type":"application/pdf","date_updated":"2025-05-02T22:30:04Z","relation":"main_file","access_level":"open_access","checksum":"095817a6c944954ac3f277e547031a33"},{"file_id":"15355","embargo_to":"open_access","file_name":"Murmann_Thesis_final_2024.zip","file_size":20645510,"date_created":"2024-05-02T12:37:56Z","relation":"source_file","access_level":"closed","checksum":"43b632255372973a437ac87739cfd4db","date_updated":"2025-05-02T22:30:04Z","content_type":"application/x-zip-compressed","creator":"cchlebak"}],"corr_author":"1","author":[{"id":"1d390868-f128-11eb-9611-a0ca5f7833b5","last_name":"Murmann","full_name":"Murmann, Julie Stefanie","first_name":"Julie Stefanie"}],"doi":"10.15479/at:ista:15352","type":"dissertation","publication_identifier":{"issn":["2791-4585"]},"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","oa":1,"doi_confirm":"1","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"54","month":"05","supplementarymaterial":"unclear","date_created":"2024-05-02T08:31:38Z","article_processing_charge":"No","degree_awarded":"MS"},{"type":"journal_article","doi":"10.1126/science.adi2982","main_file_link":[{"open_access":"1","url":"https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241"}],"oa":1,"title":"The genetic basis of a recent transition to live-bearing in marine snails","publication_identifier":{"eissn":["1095-9203"]},"pmid":1,"author":[{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"last_name":"Garlovsky","full_name":"Garlovsky, Martin D.","first_name":"Martin D."},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","first_name":"Arka"},{"orcid":"0000-0002-1145-9226","first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"first_name":"Diego Fernando","last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","full_name":"Garcia Castillo, Diego Fernando"},{"first_name":"Hila","last_name":"Lifchitz","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","full_name":"Lifchitz, Hila"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"first_name":"Erica","full_name":"Leder, Erica","last_name":"Leder"},{"first_name":"James","full_name":"Reeve, James","last_name":"Reeve"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"publication":"Science","scopus_import":"1","corr_author":"1","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"14812","relation":"research_data"},{"id":"20694","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/"}]},"article_processing_charge":"No","date_created":"2024-01-14T23:00:56Z","supplementarymaterial":"yes","month":"01","publication_status":"published","language":[{"iso":"eng"}],"volume":383,"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"page":"114-119","OA_place":"repository","fulldoi":"https://doi.org/10.1126/science.adi2982","article_type":"original","date_published":"2024-01-05T00:00:00Z","OA_type":"green","abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-26T23:31:10Z","intvolume":" 383","issue":"6678","external_id":{"isi":["001138156400003"],"pmid":["38175895"]},"dataavailabilitystatement":"Raw sequence data are available on the short-read archive (SRA) under bioproject PRJNA626520. VCF files have been archived on Zenodo (31). All analysis scripts have been archived on Zenodo (31) and are available on Github at https://github.com/seanstankowski/Littorina_reproductive_mode.","publisher":"American Association for the Advancement of Science","year":"2024","citation":{"ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119."},"acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","isi":1,"day":"05","das_tickbox":"1","oa_version":"Submitted Version","_id":"14796","status":"public","researchdata_availability":"yes"},{"corr_author":"1","author":[{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","last_name":"Puglia","full_name":"Puglia, Denise","first_name":"Denise","orcid":"0000-0003-1144-2763"}],"publication_identifier":{"issn":["2663-337X"]},"oa":1,"title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","doi":"10.15479/at:ista:18104","type":"dissertation","doi_confirm":"1","page":"63","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"09","supplementarymaterial":"unclear","date_created":"2024-09-20T12:13:30Z","article_processing_charge":"No","project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18143"}]},"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-21T14:08:09Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-05-20T22:30:05Z","abstract":[{"text":"We introduce a new all-electric platform, that strong couples light to mechanical motion\r\nby ensuring that the external environmental coupling dominates over internal mechanical\r\ndissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped on top of the device under test. This everyday\r\nelectromechanical device can be operated at low or room temperature and has 10000× lower\r\ninsertion loss than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion. The spatial properties of higher order mechanical modes are a promising feature for\r\nreconstructing unknown charge distributions.\r\n","lang":"eng"}],"ddc":["530"],"date_published":"2024-09-20T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/at:ista:18104","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"OA_place":"publisher","status":"public","_id":"18104","researchdata_availability":"unclear","oa_version":"Published Version","day":"20","supervisor":[{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"}],"citation":{"ama":"Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:10.15479/at:ista:18104","ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.","ieee":"D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.","apa":"Puglia, D. (2024). Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18104","chicago":"Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18104.","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024.","mla":"Puglia, Denise. Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18104."},"year":"2024","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"file":[{"creator":"cchlebak","date_updated":"2025-05-20T22:30:05Z","content_type":"application/pdf","relation":"main_file","checksum":"7969263451b2356bfa0924725aa9de10","access_level":"open_access","date_created":"2024-09-20T12:07:48Z","file_size":10778238,"embargo":"2025-05-20","file_name":"PhD_DPuglia_Final.pdf","file_id":"18105"},{"access_level":"closed","checksum":"98dfe7675775e30efffa03f7ff7c091b","relation":"source_file","date_updated":"2025-05-20T22:30:05Z","content_type":"application/x-zip-compressed","creator":"cchlebak","embargo_to":"open_access","file_id":"18106","file_name":"PhD_DPuglia_Thesis.zip","file_size":385419748,"date_created":"2024-09-20T12:13:09Z"}]}]