[{"file":[{"date_updated":"2024-08-05T08:19:58Z","content_type":"application/pdf","file_name":"2024_JourApplPhysics_Lenton.pdf","file_size":2537502,"file_id":"17386","access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"date_created":"2024-08-05T08:19:58Z","checksum":"6141d05cd68d540a7446dce9490975db"}],"doi":"10.1063/5.0215151","researchdata_availability":"upon request","volume":136,"article_number":"045305","isi":1,"month":"07","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"publisher":"AIP Publishing","external_id":{"isi":["001281681100003"]},"corr_author":"1","oa":1,"day":"28","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"fulldoi":"https://doi.org/10.1063/5.0215151","das_tickbox":"1","article_processing_charge":"No","date_published":"2024-07-28T00:00:00Z","file_date_updated":"2024-08-05T08:19:58Z","has_accepted_license":"1","intvolume":"       136","year":"2024","quality_controlled":"1","publication_status":"published","ddc":["530"],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"ec_funded":1,"publication_identifier":{"issn":["0021-8979"],"eissn":["1089-7550"]},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank the contributions of the whole Waitukaitis Group for useful discussions and feedback.","issue":"4","scopus_import":"1","publication":"Journal of Applied Physics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"yes","date_updated":"2026-10-21T08:39:25Z","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120"}],"citation":{"ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” <i>Journal of Applied Physics</i>, vol. 136, no. 4. AIP Publishing, 2024.","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024).","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. 2024;136(4). doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>","mla":"Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>.","apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>."},"related_material":{"record":[{"status":"public","id":"22684","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results."}],"article_type":"original","type":"journal_article","oa_version":"Published Version","author":[{"full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","last_name":"Lenton","first_name":"Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb"},{"full_name":"Pertl, Felix","orcid":"0000-0003-0463-5794","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix","last_name":"Pertl"},{"orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B","first_name":"Lubuna B","last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_created":"2024-08-04T22:01:21Z","_id":"17373","title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging"},{"language":[{"iso":"eng"}],"publication":"STAR Protocols","scopus_import":"1","issue":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","ec_funded":1,"publication_identifier":{"issn":["2666-1667"]},"citation":{"short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024).","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>."},"project":[{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-10-21T08:40:15Z","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","_id":"14683","status":"public","date_created":"2023-12-13T11:48:05Z","author":[{"last_name":"Amberg","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer"}],"oa_version":"Published Version","type":"journal_article","article_type":"review","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"article_number":"102771","volume":5,"researchdata_availability":"not applicable","doi":"10.1016/j.xpro.2023.102771","file":[{"file_size":8871807,"file_name":"2024_STARProtoc_Amberg.pdf","date_updated":"2024-07-16T11:50:03Z","content_type":"application/pdf","file_id":"17260","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"3f0ee62e04bf5a44b45b035662826e95","date_created":"2024-07-16T11:50:03Z","success":1}],"dataavailabilitystatement":"No custom code or dataset was generated in this protocol.","day":"15","corr_author":"1","oa":1,"external_id":{"pmid":["38070137"]},"publisher":"Elsevier","month":"03","department":[{"_id":"SiHi"}],"has_accepted_license":"1","file_date_updated":"2024-07-16T11:50:03Z","date_published":"2024-03-15T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"das_tickbox":"1","fulldoi":"https://doi.org/10.1016/j.xpro.2023.102771","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","quality_controlled":"1","pmid":1,"year":"2024","intvolume":"         5"},{"acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","ec_funded":1,"publication_identifier":{"eissn":["2666-1667"]},"publication":"STAR Protocols","issue":"3","scopus_import":"1","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"gold","article_type":"original","type":"journal_article","oa_version":"Published Version","abstract":[{"text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1","lang":"eng"}],"_id":"17187","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","author":[{"last_name":"Cheung","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"status":"public","date_created":"2024-06-30T22:01:04Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T09:14:52Z","supplementarymaterial":"yes","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"citation":{"short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).","ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>."},"external_id":{"pmid":["38935508"]},"department":[{"_id":"SiHi"}],"month":"09","publisher":"Elsevier","dataavailabilitystatement":"No dataset was generated while composing this protocol. A FIJI macro script “3DSerialSectionAlignmentLineROI.ijm” and a Microsoft Excel template used in this protocol are provided as supplementary materials.","day":"20","oa":1,"corr_author":"1","volume":5,"file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"checksum":"d8a8cdba82a394e731aa699ace1ae433","date_created":"2025-01-09T12:12:40Z","date_updated":"2025-01-09T12:12:40Z","content_type":"application/pdf","file_name":"2024_STARProtoc_Cheung.pdf","file_size":5186071,"file_id":"18809"}],"researchdata_availability":"yes (supplementary data)","doi":"10.1016/j.xpro.2024.103157","article_number":"103157","year":"2024","quality_controlled":"1","pmid":1,"publication_status":"published","intvolume":"         5","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103157","das_tickbox":"1","APC_amount":"804 EUR","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_published":"2024-09-20T00:00:00Z","file_date_updated":"2025-01-09T12:12:40Z","has_accepted_license":"1","article_processing_charge":"Yes"},{"article_processing_charge":"Yes","date_published":"2024-09-20T00:00:00Z","file_date_updated":"2025-01-09T12:16:53Z","has_accepted_license":"1","APC_amount":"804 EUR","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","das_tickbox":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ddc":["570"],"intvolume":"         5","quality_controlled":"1","year":"2024","pmid":1,"publication_status":"published","article_number":"103168","file":[{"file_id":"18810","file_name":"2024_STARProtoc_Cheung2.pdf","content_type":"application/pdf","date_updated":"2025-01-09T12:16:53Z","file_size":6445556,"success":1,"date_created":"2025-01-09T12:16:53Z","checksum":"464f52ecc6ec92f509552823bb82bf79","access_level":"open_access","creator":"dernst","relation":"main_file"}],"doi":"10.1016/j.xpro.2024.103168","researchdata_availability":"not applicable","volume":5,"corr_author":"1","oa":1,"dataavailabilitystatement":"No dataset or new code was generated while composing this protocol.","day":"20","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"month":"09","publisher":"Elsevier","external_id":{"pmid":["38968076"]},"project":[{"_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"}],"citation":{"apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","date_updated":"2026-10-21T09:15:51Z","author":[{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian"},{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer"}],"status":"public","date_created":"2024-07-14T22:01:10Z","_id":"17232","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","abstract":[{"text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1","lang":"eng"}],"article_type":"original","type":"journal_article","oa_version":"Published Version","OA_type":"gold","OA_place":"publisher","language":[{"iso":"eng"}],"issue":"3","scopus_import":"1","publication":"STAR Protocols","publication_identifier":{"eissn":["2666-1667"]},"acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation)."},{"external_id":{"pmid":["38165800"]},"month":"03","department":[{"_id":"SiHi"}],"publisher":"Elsevier","day":"15","dataavailabilitystatement":"All scripts that were used to prepare data and figures for this manuscript are available via GitHub at http://github.com/hippenmeyerlab. GitHub DOI is listed in the key resources table. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","corr_author":"1","oa":1,"volume":5,"file":[{"file_id":"17264","file_size":3758943,"content_type":"application/pdf","date_updated":"2024-07-16T12:04:46Z","file_name":"2024_STARProtoc_Hansen.pdf","checksum":"4644d537451c5c114a9d7c7829b65bba","date_created":"2024-07-16T12:04:46Z","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access"}],"researchdata_availability":"yes","doi":"10.1016/j.xpro.2023.102795","article_number":"102795","year":"2024","quality_controlled":"1","pmid":1,"publication_status":"published","intvolume":"         5","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.xpro.2023.102795","das_tickbox":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_published":"2024-03-15T00:00:00Z","file_date_updated":"2024-07-16T12:04:46Z","has_accepted_license":"1","article_processing_charge":"Yes","acknowledgement":"We thank Florian Pauler for discussion and his expert technical support. This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging and Optics Facility (IOF) and Preclinical Facility (PCF). A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences.","publication_identifier":{"eissn":["2666-1667"]},"publication":"STAR Protocols","issue":"1","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"review","type":"journal_article","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3"}],"_id":"14794","title":"Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers","author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"date_created":"2024-01-14T23:00:56Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","date_updated":"2026-10-21T09:13:13Z","related_material":{"link":[{"relation":"software","url":"http://github.com/hippenmeyerlab"}]},"project":[{"name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"citation":{"apa":"Hansen, A. H., &#38; Hippenmeyer, S. (2024). Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>.","ieee":"A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","ista":"Hansen AH, Hippenmeyer S. 2024. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 5(1), 102795.","short":"A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024).","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 5, no. 1, 102795, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>.","ama":"Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>"}},{"publication":"Physical Review E","issue":"3","scopus_import":"1","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"language":[{"iso":"eng"}],"_id":"15322","title":"Multiple charge carrier species as a possible cause for triboelectric cycles","author":[{"full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A","last_name":"Sobarzo Ponce"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R"}],"status":"public","date_created":"2024-04-14T22:01:03Z","article_type":"letter_note","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The tendency of materials to order in triboelectric series has prompted suggestions that contact electrification might have a single, unified underlying description. However, the possibility of “triboelectric cycles,” i.e., series that loop back onto themselves, is seemingly at odds with such a coherent description. In this work, we propose that if multiple charge carrying species are at play, both triboelectric series and cycles are possible. We show how series arise naturally if only a single charge carrier species is involved and if the driving mechanism is approach toward thermodynamic equilibrium, and simultaneously, that cycles are forbidden under such conditions. Suspecting multiple carriers might relax the situation, we affirm this is the case by explicit construction of a cycle involving two carriers, and then extend this to show how more complex cycles emerge. Our work highlights the importance of series and cycles towards determining the underlying mechanism(s) and carrier(s) in contact electrification."}],"related_material":{"record":[{"status":"public","id":"20203","relation":"dissertation_contains"}]},"citation":{"chicago":"Sobarzo Ponce, Juan Carlos A, and Scott R Waitukaitis. “Multiple Charge Carrier Species as a Possible Cause for Triboelectric Cycles.” <i>Physical Review E</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">https://doi.org/10.1103/PhysRevE.109.L032108</a>.","apa":"Sobarzo Ponce, J. C. A., &#38; Waitukaitis, S. R. (2024). Multiple charge carrier species as a possible cause for triboelectric cycles. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">https://doi.org/10.1103/PhysRevE.109.L032108</a>","ama":"Sobarzo Ponce JCA, Waitukaitis SR. Multiple charge carrier species as a possible cause for triboelectric cycles. <i>Physical Review E</i>. 2024;109(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">10.1103/PhysRevE.109.L032108</a>","mla":"Sobarzo Ponce, Juan Carlos A., and Scott R. Waitukaitis. “Multiple Charge Carrier Species as a Possible Cause for Triboelectric Cycles.” <i>Physical Review E</i>, vol. 109, no. 3, L032108, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevE.109.L032108\">10.1103/PhysRevE.109.L032108</a>.","ieee":"J. C. A. Sobarzo Ponce and S. R. Waitukaitis, “Multiple charge carrier species as a possible cause for triboelectric cycles,” <i>Physical Review E</i>, vol. 109, no. 3. American Physical Society, 2024.","short":"J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review E 109 (2024).","ista":"Sobarzo Ponce JCA, Waitukaitis SR. 2024. Multiple charge carrier species as a possible cause for triboelectric cycles. Physical Review E. 109(3), L032108."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","date_updated":"2026-10-21T08:38:31Z","day":"29","corr_author":"1","external_id":{"isi":["001199745200004"],"pmid":["38632754"]},"month":"03","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","article_number":"L032108","isi":1,"volume":109,"researchdata_availability":"no","doi":"10.1103/PhysRevE.109.L032108","year":"2024","quality_controlled":"1","pmid":1,"publication_status":"published","intvolume":"       109","date_published":"2024-03-29T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1103/PhysRevE.109.L032108","das_tickbox":"0"},{"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"citation":{"ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(11). doi:<a href=\"https://doi.org/10.1073/pnas.2316284121\">10.1073/pnas.2316284121</a>","mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11, e2316284121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2316284121\">10.1073/pnas.2316284121</a>.","short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11. National Academy of Sciences, 2024.","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2316284121\">https://doi.org/10.1073/pnas.2316284121</a>.","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., &#38; Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2316284121\">https://doi.org/10.1073/pnas.2316284121</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T10:25:57Z","supplementarymaterial":"yes","date_created":"2023-10-31T13:30:00Z","author":[{"first_name":"Michael","last_name":"Habig","full_name":"Habig, Michael"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"full_name":"Müller, Judith","last_name":"Müller","first_name":"Judith"},{"last_name":"Stukenbrock","first_name":"Eva H.","full_name":"Stukenbrock, Eva H."},{"full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna","last_name":"Leitner"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"status":"public","_id":"14478","title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","abstract":[{"lang":"eng","text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungus<jats:italic>Metarhizium robertsii</jats:italic>during experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment between<jats:italic>M. robertsii</jats:italic>and another congeneric insect pathogen,<jats:italic>M. guizhouense</jats:italic>. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.</jats:p><jats:sec><jats:title>Significance Statement</jats:title><jats:p>The enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens."}],"article_type":"original","oa_version":"Published Version","type":"journal_article","OA_type":"hybrid","OA_place":"publisher","language":[{"iso":"eng"}],"issue":"11","scopus_import":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","ec_funded":1,"acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_processing_charge":"Yes (in subscription journal)","date_published":"2024-03-12T00:00:00Z","file_date_updated":"2024-03-19T09:02:57Z","has_accepted_license":"1","APC_amount":"3040,36 EUR","fulldoi":"https://doi.org/10.1073/pnas.2316284121","das_tickbox":"1","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"       121","quality_controlled":"1","year":"2024","pmid":1,"publication_status":"published","article_number":"e2316284121","isi":1,"file":[{"file_id":"15124","file_size":5750361,"date_updated":"2024-03-19T09:02:57Z","content_type":"application/pdf","file_name":"2024_PNAS_Habig.pdf","checksum":"f5e871db617b682edc71fcd08670dc81","date_created":"2024-03-19T09:02:57Z","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access"}],"doi":"10.1073/pnas.2316284121","researchdata_availability":"yes","volume":121,"corr_author":"1","oa":1,"dataavailabilitystatement":"Sequencing reads have been deposited in the Sequence Read Archive and are available under the BioProject PRJNA1017668 (67). The Nanopore-based assemblies and Gene annotations were deposited at NCBI under the BioProjects PRJNA1015426 (68), PRJNA1015429 (69), and PRJNA1015431 (70). All source data for the figures are given in Datasets S3–S14. Note that of the total of 2,626 spore-clones shown in Fig. 2, 872 had been produced, analyzed for strain identity and previously published in Stock et al. (35). The production and strain-identification of the remaining 1,754 spore-derived clones, as well as the presence/absence characterization of chrA within all 883 R3 spore-clones were performed in this study.","day":"12","month":"03","department":[{"_id":"SyCr"}],"publisher":"National Academy of Sciences","external_id":{"isi":["001207630200005"],"pmid":["38442176"]}},{"intvolume":"       112","pmid":1,"quality_controlled":"1","year":"2024","publication_status":"published","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"fulldoi":"https://doi.org/10.1016/j.neuron.2023.11.009","das_tickbox":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-02-06T13:56:15Z","date_published":"2024-01-17T00:00:00Z","has_accepted_license":"1","department":[{"_id":"SiHi"},{"_id":"RySh"}],"month":"01","publisher":"Elsevier","external_id":{"pmid":["38096816"],"isi":["001163937900001"]},"oa":1,"corr_author":"1","dataavailabilitystatement":"All data generated and analyzed in this study are included in the paper and/or supplementary materials. Raw sequencing data has been deposited at Gene Expression Omnibus (GEO). All scripts that were used to prepare data and figures for this manuscript are available via GitHub at https://github.com/fpauler. Accession numbers and github DOI are listed in the key resources table. Files for 3D printing of acute slice recovery chamber (3D model 361319) are deposited to https://www.printables.com.","day":"17","file":[{"creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2024-02-06T13:56:15Z","checksum":"32b3788f7085cf44a84108d8faaff3ce","success":1,"file_size":5942467,"content_type":"application/pdf","date_updated":"2024-02-06T13:56:15Z","file_name":"2024_Neuron_Cheung.pdf","file_id":"14944"}],"doi":"10.1016/j.neuron.2023.11.009","researchdata_availability":"yes","volume":112,"isi":1,"abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"article_type":"original","oa_version":"Published Version","type":"journal_article","date_created":"2023-04-27T09:41:48Z","author":[{"orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"last_name":"Koppensteiner","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"first_name":"Thomas","last_name":"Krausgruber","full_name":"Krausgruber, Thomas"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","first_name":"Martin","last_name":"Schrammel","full_name":"Schrammel, Martin"},{"id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","first_name":"Natalie Y","last_name":"Özgen","full_name":"Özgen, Natalie Y"},{"full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","last_name":"Ivec","first_name":"Alexis"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"status":"public","_id":"12875","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"yes","date_updated":"2026-10-21T09:51:58Z","project":[{"_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"}],"citation":{"apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.","ieee":"G. T. Cheung <i>et al.</i>, “Multipotent progenitors instruct ontogeny of the superior colliculus,” <i>Neuron</i>, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. 2024;112(2):230-246.e11. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>","mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>."},"page":"230-246.e11","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/"}]},"acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","publication_identifier":{"issn":["0896-6273"]},"issue":"2","scopus_import":"1","publication":"Neuron","language":[{"iso":"eng"}]},{"keyword":["Electrical and Electronic Engineering","Materials Chemistry","Electrochemistry","Energy Engineering and Power Technology","Chemical Engineering (miscellaneous)"],"article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-07-16T11:59:24Z","date_published":"2024-01-22T00:00:00Z","has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.1021/acsaem.3c02223","open_access":"1"}],"fulldoi":"https://doi.org/10.1021/acsaem.3c02223","das_tickbox":"0","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["540"],"intvolume":"         7","pmid":1,"quality_controlled":"1","year":"2024","publication_status":"published","isi":1,"file":[{"file_size":5607177,"file_name":"2024_ACSAppElecMaterials_Jethwa.pdf","date_updated":"2024-07-16T11:59:24Z","content_type":"application/pdf","file_id":"17262","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"2841e86a041d249ac0df2531b7f9aec1","date_created":"2024-07-16T11:59:24Z","success":1}],"researchdata_availability":"no","doi":"10.1021/acsaem.3c02223","volume":7,"oa":1,"day":"22","month":"01","department":[{"_id":"StFr"}],"publisher":"American Chemical Society","external_id":{"isi":["001146733200001"],"pmid":["38273966"]},"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"page":"414-426","citation":{"ama":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. Exploring the landscape of heterocyclic quinones for redox flow batteries. <i>ACS Applied Energy Materials</i>. 2024;7(2):414-426. doi:<a href=\"https://doi.org/10.1021/acsaem.3c02223\">10.1021/acsaem.3c02223</a>","mla":"Jethwa, Rajesh B., et al. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” <i>ACS Applied Energy Materials</i>, vol. 7, no. 2, American Chemical Society, 2024, pp. 414–26, doi:<a href=\"https://doi.org/10.1021/acsaem.3c02223\">10.1021/acsaem.3c02223</a>.","ista":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. 2024. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. 7(2), 414–426.","short":"R.B. Jethwa, D. Hey, R.N. Kerber, A.D. Bond, D.S. Wright, C.P. Grey, ACS Applied Energy Materials 7 (2024) 414–426.","ieee":"R. B. Jethwa, D. Hey, R. N. Kerber, A. D. Bond, D. S. Wright, and C. P. Grey, “Exploring the landscape of heterocyclic quinones for redox flow batteries,” <i>ACS Applied Energy Materials</i>, vol. 7, no. 2. American Chemical Society, pp. 414–426, 2024.","chicago":"Jethwa, Rajesh B, Dominic Hey, Rachel N. Kerber, Andrew D. Bond, Dominic S. Wright, and Clare P. Grey. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” <i>ACS Applied Energy Materials</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsaem.3c02223\">https://doi.org/10.1021/acsaem.3c02223</a>.","apa":"Jethwa, R. B., Hey, D., Kerber, R. N., Bond, A. D., Wright, D. S., &#38; Grey, C. P. (2024). Exploring the landscape of heterocyclic quinones for redox flow batteries. <i>ACS Applied Energy Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsaem.3c02223\">https://doi.org/10.1021/acsaem.3c02223</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T09:53:30Z","supplementarymaterial":"yes","status":"public","author":[{"full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","first_name":"Rajesh B","last_name":"Jethwa"},{"last_name":"Hey","first_name":"Dominic","full_name":"Hey, Dominic"},{"last_name":"Kerber","first_name":"Rachel N.","full_name":"Kerber, Rachel N."},{"last_name":"Bond","first_name":"Andrew D.","full_name":"Bond, Andrew D."},{"last_name":"Wright","first_name":"Dominic S.","full_name":"Wright, Dominic S."},{"first_name":"Clare P.","last_name":"Grey","full_name":"Grey, Clare P."}],"date_created":"2024-01-05T09:20:48Z","_id":"14733","title":"Exploring the landscape of heterocyclic quinones for redox flow batteries","abstract":[{"text":"Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy.","lang":"eng"}],"article_type":"original","type":"journal_article","oa_version":"Published Version","language":[{"iso":"eng"}],"issue":"2","scopus_import":"1","publication":"ACS Applied Energy Materials","ec_funded":1,"publication_identifier":{"eissn":["2574-0962"]}},{"has_accepted_license":"1","date_published":"2024-07-08T00:00:00Z","file_date_updated":"2024-07-16T11:54:46Z","article_processing_charge":"Yes (via OA deal)","keyword":["General Chemistry","Catalysis"],"das_tickbox":"0","fulldoi":"https://doi.org/10.1002/anie.202316476","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ddc":["540"],"publication_status":"published","quality_controlled":"1","year":"2024","pmid":1,"intvolume":"        63","isi":1,"article_number":"e202316476","volume":63,"doi":"10.1002/anie.202316476","researchdata_availability":"no","file":[{"success":1,"checksum":"fe2c23454279eb9d76ed6ca9970c21c7","date_created":"2024-07-16T11:54:46Z","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"17261","content_type":"application/pdf","date_updated":"2024-07-16T11:54:46Z","file_name":"2024_AngChemieInt_Jethwa.pdf","file_size":4766445}],"day":"08","oa":1,"corr_author":"1","external_id":{"pmid":["38095355"],"isi":["001241932700001"]},"publisher":"Wiley","month":"07","department":[{"_id":"StFr"},{"_id":"GradSch"}],"related_material":{"record":[{"id":"20607","relation":"dissertation_contains","status":"public"}]},"citation":{"ieee":"R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28. Wiley, 2024.","ista":"Jethwa RB, Mondal S, Pant B, Freunberger SA. 2024. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 63(28), e202316476.","short":"R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition 63 (2024).","ama":"Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. 2024;63(28). doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>","mla":"Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28, e202316476, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>.","apa":"Jethwa, R. B., Mondal, S., Pant, B., &#38; Freunberger, S. A. (2024). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>","chicago":"Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>."},"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"date_updated":"2026-10-21T10:25:05Z","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","_id":"14687","author":[{"orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B","last_name":"Jethwa","first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","first_name":"Soumyadip","full_name":"Mondal, Soumyadip"},{"full_name":"Pant, Bhargavi","first_name":"Bhargavi","last_name":"Pant","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"}],"status":"public","date_created":"2023-12-15T16:10:13Z","oa_version":"Published Version","type":"journal_article","article_type":"review","abstract":[{"lang":"eng","text":"The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity."}],"language":[{"iso":"eng"}],"publication":"Angewandte Chemie International Edition","scopus_import":"1","issue":"28","acknowledgement":"S.A.F. is indebted to ISTA for support. R.B.J. thanks the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 for funding. B.P. thanks Alistore ERI for providing a PhD scholarship.","ec_funded":1,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]}},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"scopus_import":"1","publication":"Faraday Discussions","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T10:24:27Z","supplementarymaterial":"yes","citation":{"apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., &#38; Freunberger, S. A. (2024). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>","chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>.","ista":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2024. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. 248, 175–189.","ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” <i>Faraday Discussions</i>, vol. 248. Royal Society of Chemistry, pp. 175–189, 2024.","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions 248 (2024) 175–189.","mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>, vol. 248, Royal Society of Chemistry, 2024, pp. 175–89, doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>.","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. 2024;248:175-189. doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>"},"page":"175-189","related_material":{"record":[{"status":"public","id":"20607","relation":"dissertation_contains"}]},"license":"https://creativecommons.org/licenses/by-nc/3.0/","abstract":[{"lang":"eng","text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation."}],"article_type":"original","type":"journal_article","oa_version":"Published Version","status":"public","author":[{"full_name":"Mondal, Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip","last_name":"Mondal"},{"full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356","last_name":"Jethwa","first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f"},{"first_name":"Bhargavi","last_name":"Pant","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","full_name":"Pant, Bhargavi"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"date_created":"2023-05-22T06:53:34Z","_id":"13044","title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","file":[{"checksum":"6515a227ed3e8942496fe6a1feeffd18","date_created":"2024-07-16T07:46:39Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"17249","file_size":1303733,"content_type":"application/pdf","date_updated":"2024-07-16T07:46:39Z","file_name":"2024_FaradayDiscussions_Mondal.pdf"}],"doi":"10.1039/d3fd00088e","researchdata_availability":"no","volume":248,"isi":1,"department":[{"_id":"StFr"},{"_id":"Bio"}],"month":"01","publisher":"Royal Society of Chemistry","external_id":{"pmid":["37750344"],"isi":["001070423500001"]},"corr_author":"1","oa":1,"day":"01","fulldoi":"https://doi.org/10.1039/d3fd00088e","das_tickbox":"0","keyword":["Physical and Theoretical Chemistry"],"article_processing_charge":"Yes (via OA deal)","date_published":"2024-01-01T00:00:00Z","file_date_updated":"2024-07-16T07:46:39Z","has_accepted_license":"1","intvolume":"       248","pmid":1,"year":"2024","quality_controlled":"1","publication_status":"published","ddc":["540"],"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"}},{"fulldoi":"https://doi.org/10.1039/d3fd90062b","das_tickbox":"0","keyword":["Physical and Theoretical Chemistry"],"article_processing_charge":"No","date_published":"2024-01-29T00:00:00Z","intvolume":"       248","year":"2024","pmid":1,"quality_controlled":"1","publication_status":"published","doi":"10.1039/d3fd90062b","researchdata_availability":"no","volume":248,"isi":1,"department":[{"_id":"StFr"}],"month":"01","publisher":"Royal Society of Chemistry","external_id":{"pmid":["38112202"],"isi":["001130090400001"]},"day":"29","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","date_updated":"2026-10-21T09:52:47Z","citation":{"mla":"Archer, Lynden A., et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” <i>Faraday Discussions</i>, vol. 248, Royal Society of Chemistry, 2024, pp. 392–411, doi:<a href=\"https://doi.org/10.1039/d3fd90062b\">10.1039/d3fd90062b</a>.","ama":"Archer LA, Bruce PG, Calvo EJ, et al. Towards practical metal–oxygen batteries: General discussion. <i>Faraday Discussions</i>. 2024;248:392-411. doi:<a href=\"https://doi.org/10.1039/d3fd90062b\">10.1039/d3fd90062b</a>","short":"L.A. Archer, P.G. Bruce, E.J. Calvo, D. Dewar, J.H.J. Ellison, S.A. Freunberger, X. Gao, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Menkin, S. Mondal, Q. Qiu, T. Samarakoon, I. Temprano, K. Uosaki, G. Vailaya, E.D. Wachsman, Y. Wu, S. Ye, Faraday Discussions 248 (2024) 392–411.","ista":"Archer LA, Bruce PG, Calvo EJ, Dewar D, Ellison JHJ, Freunberger SA, Gao X, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Menkin S, Mondal S, Qiu Q, Samarakoon T, Temprano I, Uosaki K, Vailaya G, Wachsman ED, Wu Y, Ye S. 2024. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. 248, 392–411.","ieee":"L. A. Archer <i>et al.</i>, “Towards practical metal–oxygen batteries: General discussion,” <i>Faraday Discussions</i>, vol. 248. Royal Society of Chemistry, pp. 392–411, 2024.","chicago":"Archer, Lynden A., Peter G. Bruce, Ernesto J. Calvo, Daniel Dewar, James H. J. Ellison, Stefan Alexander Freunberger, Xiangwen Gao, et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d3fd90062b\">https://doi.org/10.1039/d3fd90062b</a>.","apa":"Archer, L. A., Bruce, P. G., Calvo, E. J., Dewar, D., Ellison, J. H. J., Freunberger, S. A., … Ye, S. (2024). Towards practical metal–oxygen batteries: General discussion. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3fd90062b\">https://doi.org/10.1039/d3fd90062b</a>"},"page":"392-411","article_type":"letter_note","oa_version":"None","type":"journal_article","author":[{"last_name":"Archer","first_name":"Lynden A.","full_name":"Archer, Lynden A."},{"full_name":"Bruce, Peter G.","first_name":"Peter G.","last_name":"Bruce"},{"first_name":"Ernesto J.","last_name":"Calvo","full_name":"Calvo, Ernesto J."},{"first_name":"Daniel","last_name":"Dewar","full_name":"Dewar, Daniel"},{"first_name":"James H. J.","last_name":"Ellison","full_name":"Ellison, James H. J."},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"},{"first_name":"Xiangwen","last_name":"Gao","full_name":"Gao, Xiangwen"},{"last_name":"Hardwick","first_name":"Laurence J.","full_name":"Hardwick, Laurence J."},{"first_name":"Gabriela","last_name":"Horwitz","full_name":"Horwitz, Gabriela"},{"last_name":"Janek","first_name":"Jürgen","full_name":"Janek, Jürgen"},{"first_name":"Lee R.","last_name":"Johnson","full_name":"Johnson, Lee R."},{"full_name":"Jordan, Jack W.","first_name":"Jack W.","last_name":"Jordan"},{"full_name":"Matsuda, Shoichi","first_name":"Shoichi","last_name":"Matsuda"},{"last_name":"Menkin","first_name":"Svetlana","full_name":"Menkin, Svetlana"},{"full_name":"Mondal, Soumyadip","last_name":"Mondal","first_name":"Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"full_name":"Qiu, Qianyuan","last_name":"Qiu","first_name":"Qianyuan"},{"first_name":"Thukshan","last_name":"Samarakoon","full_name":"Samarakoon, Thukshan"},{"full_name":"Temprano, Israel","first_name":"Israel","last_name":"Temprano"},{"first_name":"Kohei","last_name":"Uosaki","full_name":"Uosaki, Kohei"},{"full_name":"Vailaya, Ganesh","first_name":"Ganesh","last_name":"Vailaya"},{"last_name":"Wachsman","first_name":"Eric D.","full_name":"Wachsman, Eric D."},{"first_name":"Yiying","last_name":"Wu","full_name":"Wu, Yiying"},{"full_name":"Ye, Shen","last_name":"Ye","first_name":"Shen"}],"date_created":"2023-12-20T10:48:09Z","status":"public","_id":"14701","title":"Towards practical metal–oxygen batteries: General discussion","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"scopus_import":"1","publication":"Faraday Discussions"},{"language":[{"iso":"eng"}],"scopus_import":"1","publication":"Faraday Discussions","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"citation":{"mla":"Attard, Gary A., et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” <i>Faraday Discussions</i>, vol. 248, Royal Society of Chemistry, 2024, pp. 75–88, doi:<a href=\"https://doi.org/10.1039/d3fd90059b\">10.1039/d3fd90059b</a>.","ama":"Attard GA, Calvo EJ, Curtiss LA, et al. Materials for stable metal–oxygen battery cathodes: general discussion. <i>Faraday Discussions</i>. 2024;248:75-88. doi:<a href=\"https://doi.org/10.1039/d3fd90059b\">10.1039/d3fd90059b</a>","short":"G.A. Attard, E.J. Calvo, L.A. Curtiss, D. Dewar, J.H.J. Ellison, X. Gao, C.P. Grey, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Mondal, A.R. Neale, N. Ortiz-Vitoriano, I. Temprano, G. Vailaya, E.D. Wachsman, H.-H. Wang, Y. Wu, S. Ye, Faraday Discussions 248 (2024) 75–88.","ieee":"G. A. Attard <i>et al.</i>, “Materials for stable metal–oxygen battery cathodes: general discussion,” <i>Faraday Discussions</i>, vol. 248. Royal Society of Chemistry, pp. 75–88, 2024.","ista":"Attard GA, Calvo EJ, Curtiss LA, Dewar D, Ellison JHJ, Gao X, Grey CP, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Mondal S, Neale AR, Ortiz-Vitoriano N, Temprano I, Vailaya G, Wachsman ED, Wang H-H, Wu Y, Ye S. 2024. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. 248, 75–88.","chicago":"Attard, Gary A., Ernesto J. Calvo, Larry A. Curtiss, Daniel Dewar, James H. J. Ellison, Xiangwen Gao, Clare P. Grey, et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d3fd90059b\">https://doi.org/10.1039/d3fd90059b</a>.","apa":"Attard, G. A., Calvo, E. J., Curtiss, L. A., Dewar, D., Ellison, J. H. J., Gao, X., … Ye, S. (2024). Materials for stable metal–oxygen battery cathodes: general discussion. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3fd90059b\">https://doi.org/10.1039/d3fd90059b</a>"},"page":"75-88","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T09:53:09Z","supplementarymaterial":"no","date_created":"2023-12-20T10:49:43Z","status":"public","author":[{"full_name":"Attard, Gary A.","first_name":"Gary A.","last_name":"Attard"},{"first_name":"Ernesto J.","last_name":"Calvo","full_name":"Calvo, Ernesto J."},{"last_name":"Curtiss","first_name":"Larry A.","full_name":"Curtiss, Larry A."},{"first_name":"Daniel","last_name":"Dewar","full_name":"Dewar, Daniel"},{"full_name":"Ellison, James H. J.","first_name":"James H. J.","last_name":"Ellison"},{"full_name":"Gao, Xiangwen","first_name":"Xiangwen","last_name":"Gao"},{"last_name":"Grey","first_name":"Clare P.","full_name":"Grey, Clare P."},{"first_name":"Laurence J.","last_name":"Hardwick","full_name":"Hardwick, Laurence J."},{"full_name":"Horwitz, Gabriela","first_name":"Gabriela","last_name":"Horwitz"},{"last_name":"Janek","first_name":"Juergen","full_name":"Janek, Juergen"},{"first_name":"Lee R.","last_name":"Johnson","full_name":"Johnson, Lee R."},{"full_name":"Jordan, Jack W.","first_name":"Jack W.","last_name":"Jordan"},{"full_name":"Matsuda, Shoichi","last_name":"Matsuda","first_name":"Shoichi"},{"full_name":"Mondal, Soumyadip","last_name":"Mondal","first_name":"Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"last_name":"Neale","first_name":"Alex R.","full_name":"Neale, Alex R."},{"full_name":"Ortiz-Vitoriano, Nagore","first_name":"Nagore","last_name":"Ortiz-Vitoriano"},{"first_name":"Israel","last_name":"Temprano","full_name":"Temprano, Israel"},{"full_name":"Vailaya, Ganesh","first_name":"Ganesh","last_name":"Vailaya"},{"first_name":"Eric D.","last_name":"Wachsman","full_name":"Wachsman, Eric D."},{"full_name":"Wang, Hsien-Hau","last_name":"Wang","first_name":"Hsien-Hau"},{"full_name":"Wu, Yiying","first_name":"Yiying","last_name":"Wu"},{"full_name":"Ye, Shen","first_name":"Shen","last_name":"Ye"}],"_id":"14702","title":"Materials for stable metal–oxygen battery cathodes: general discussion","article_type":"letter_note","type":"journal_article","oa_version":"None","isi":1,"researchdata_availability":"no","doi":"10.1039/d3fd90059b","volume":248,"day":"29","department":[{"_id":"StFr"}],"month":"01","publisher":"Royal Society of Chemistry","external_id":{"pmid":["38109098"],"isi":["001130029600001"]},"keyword":["Physical and Theoretical Chemistry"],"article_processing_charge":"No","date_published":"2024-01-29T00:00:00Z","fulldoi":"https://doi.org/10.1039/d3fd90059b","das_tickbox":"0","intvolume":"       248","quality_controlled":"1","year":"2024","pmid":1,"publication_status":"published"},{"doi":"10.1038/s41929-024-01184-7","researchdata_availability":"no","volume":7,"isi":1,"department":[{"_id":"StFr"}],"month":"07","publisher":"Springer Nature","external_id":{"isi":["001278986700012"]},"corr_author":"1","day":"26","fulldoi":"https://doi.org/10.1038/s41929-024-01184-7","das_tickbox":"0","article_processing_charge":"No","date_published":"2024-07-26T00:00:00Z","intvolume":"         7","quality_controlled":"1","year":"2024","publication_status":"published","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2520-1158"]},"issue":"7","scopus_import":"1","publication":"Nature Catalysis","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-21T09:52:22Z","supplementarymaterial":"no","page":"759-760","citation":{"apa":"Mondal, S., &#38; Freunberger, S. A. (2024). Catalysing rate and capacity. <i>Nature Catalysis</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41929-024-01184-7\">https://doi.org/10.1038/s41929-024-01184-7</a>","chicago":"Mondal, Soumyadip, and Stefan Alexander Freunberger. “Catalysing Rate and Capacity.” <i>Nature Catalysis</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41929-024-01184-7\">https://doi.org/10.1038/s41929-024-01184-7</a>.","short":"S. Mondal, S.A. Freunberger, Nature Catalysis 7 (2024) 759–760.","ieee":"S. Mondal and S. A. Freunberger, “Catalysing rate and capacity,” <i>Nature Catalysis</i>, vol. 7, no. 7. Springer Nature, pp. 759–760, 2024.","ista":"Mondal S, Freunberger SA. 2024. Catalysing rate and capacity. Nature Catalysis. 7(7), 759–760.","ama":"Mondal S, Freunberger SA. Catalysing rate and capacity. <i>Nature Catalysis</i>. 2024;7(7):759-760. doi:<a href=\"https://doi.org/10.1038/s41929-024-01184-7\">10.1038/s41929-024-01184-7</a>","mla":"Mondal, Soumyadip, and Stefan Alexander Freunberger. “Catalysing Rate and Capacity.” <i>Nature Catalysis</i>, vol. 7, no. 7, Springer Nature, 2024, pp. 759–60, doi:<a href=\"https://doi.org/10.1038/s41929-024-01184-7\">10.1038/s41929-024-01184-7</a>."},"abstract":[{"text":"Aqueous zinc-ion batteries are attractive due to their low cost, environmental friendliness, and exceptional performance, but the latter remains poorly understood. Now, a fast catalytic step involved in oxygen redox catalysis is shown to contribute to capacity at a high rate.","lang":"eng"}],"article_type":"letter_note","type":"journal_article","oa_version":"None","status":"public","author":[{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip","last_name":"Mondal","full_name":"Mondal, Soumyadip"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"}],"date_created":"2024-07-29T07:05:33Z","_id":"17333","title":"Catalysing rate and capacity"},{"oa_version":"Published Version","type":"conference","abstract":[{"lang":"eng","text":"Machine Learning and AI have the potential to transform data-driven\r\nscientific discovery, enabling accurate predictions for several scientific\r\nphenomena. As many scientific questions are inherently causal, this paper looks\r\nat the causal inference task of treatment effect estimation, where the outcome\r\nof interest is recorded in high-dimensional observations in a Randomized\r\nControlled Trial (RCT). Despite being the simplest possible causal setting and\r\na perfect fit for deep learning, we theoretically find that many common choices\r\nin the literature may lead to biased estimates. To test the practical impact of\r\nthese considerations, we recorded ISTAnt, the first real-world benchmark for\r\ncausal inference downstream tasks on high-dimensional observations as an RCT\r\nstudying how garden ants (Lasius neglectus) respond to microparticles applied\r\nonto their colony members by hygienic grooming. Comparing 6 480 models\r\nfine-tuned from state-of-the-art visual backbones, we find that the sampling\r\nand modeling choices significantly affect the accuracy of the causal estimate,\r\nand that classification accuracy is not a proxy thereof. We further validated\r\nthe analysis, repeating it on a synthetically generated visual data set\r\ncontrolling the causal model. Our results suggest that future benchmarks should\r\ncarefully consider real downstream scientific questions, especially causal\r\nones. Further, we highlight guidelines for representation learning methods to\r\nhelp answer causal questions in the sciences."}],"title":"Smoke and mirrors in causal downstream tasks","_id":"18847","status":"public","date_created":"2025-01-14T07:27:26Z","author":[{"full_name":"Cadei, Riccardo","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b","first_name":"Riccardo","last_name":"Cadei"},{"id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","first_name":"Lukas","last_name":"Lindorfer","full_name":"Lindorfer, Lukas"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmid, Cordelia","last_name":"Schmid","first_name":"Cordelia"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"}],"supplementarymaterial":"yes","date_updated":"2026-10-21T10:52:44Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"status":"public","relation":"research_data","id":"18895"},{"status":"public","id":"19509","relation":"later_version"}],"link":[{"relation":"software","url":"https://github.com/CausalLearningAI/ISTAnt"}]},"citation":{"chicago":"Cadei, Riccardo, Lukas Lindorfer, Sylvia Cremer, Cordelia Schmid, and Francesco Locatello. “Smoke and Mirrors in Causal Downstream Tasks.” In <i>ICML 2024 Workshop AI4Science</i>, Vol. 38. Curran Associates, 2024.","apa":"Cadei, R., Lindorfer, L., Cremer, S., Schmid, C., &#38; Locatello, F. (2024). Smoke and mirrors in causal downstream tasks. In <i>ICML 2024 Workshop AI4Science</i> (Vol. 38). Curran Associates.","mla":"Cadei, Riccardo, et al. “Smoke and Mirrors in Causal Downstream Tasks.” <i>ICML 2024 Workshop AI4Science</i>, vol. 38, Curran Associates, 2024.","ama":"Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. Smoke and mirrors in causal downstream tasks. In: <i>ICML 2024 Workshop AI4Science</i>. Vol 38. Curran Associates; 2024.","ieee":"R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, and F. Locatello, “Smoke and mirrors in causal downstream tasks,” in <i>ICML 2024 Workshop AI4Science</i>, 2024, vol. 38.","ista":"Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. 2024. Smoke and mirrors in causal downstream tasks. ICML 2024 Workshop AI4Science. ICML: International Conference on Machine Learning vol. 38.","short":"R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, F. Locatello, in:, ICML 2024 Workshop AI4Science, Curran Associates, 2024."},"acknowledgement":"We thank Piersilvio De Bartolomeis, and the full Causal Learning and Artificial Intelligence (CLAI) group at ISTA for the extremely helpful discussions. Riccardo Cadei was supported by a Google Research Scholar Award and a Google Initiated Gift to Francesco Locatello. We thank the Social Immunity team at ISTA particularly Michaela Hönigsberger and Wilfrid Jean Louis, for supporting the ecological experiment and Farnaz Beikzadeh Abbasi, Luisa Fiebig and Martin Estermann for annotating ant behavior in ISTAnt.","publication":"ICML 2024 Workshop AI4Science","scopus_import":"1","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"gold","publication_status":"published","quality_controlled":"1","year":"2024","intvolume":"        38","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["000","570"],"das_tickbox":"0","arxiv":1,"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2024-07-26","start_date":"2024-07-26"},"has_accepted_license":"1","date_published":"2024-09-25T00:00:00Z","file_date_updated":"2025-01-27T11:42:24Z","article_processing_charge":"No","external_id":{"arxiv":["2405.17151"]},"publisher":"Curran Associates","month":"09","department":[{"_id":"SyCr"},{"_id":"FrLo"},{"_id":"GradSch"}],"day":"25","oa":1,"corr_author":"1","volume":38,"researchdata_availability":"yes","file":[{"file_id":"18896","file_size":4453014,"file_name":"2024_ICML_Cadei.pdf","content_type":"application/pdf","date_updated":"2025-01-27T11:42:24Z","date_created":"2025-01-27T11:42:24Z","checksum":"beedf05388bbdb7ddda81ec3d5ec7026","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access"}]},{"researchdata_availability":"yes","doi":"10.52202/079017-0820","volume":37,"oa":1,"day":"20","dataavailabilitystatement":"Code: https://github.com/CausalLearningAI/ISTAnt\r\nData: https://doi.org/10.6084/m9.figshare.26484934.v2","department":[{"_id":"SyCr"},{"_id":"FrLo"}],"month":"12","publisher":"Neural Information Processing Systems Foundation","external_id":{"arxiv":["2405.17151"]},"article_processing_charge":"No","date_published":"2024-12-20T00:00:00Z","alternative_title":["Advances in Neural Information Processing Systems"],"conference":{"location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems","end_date":"2024-12-15","start_date":"2024-12-09"},"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.17151"}],"fulldoi":"https://doi.org/10.52202/079017-0820","das_tickbox":"1","intvolume":"        37","year":"2024","quality_controlled":"1","publication_status":"published","OA_type":"green","OA_place":"repository","language":[{"iso":"eng"}],"scopus_import":"1","publication":"38th Conference on Neural Information Processing Systems","publication_identifier":{"eissn":["1049-5258"]},"acknowledgement":"We thank Piersilvio De Bartolomeis, and the full Causal Learning and Artificial Intelligence (CLAI) group at ISTA for the extremely helpful discussions. Riccardo Cadei was supported by a Google Research Scholar Award and a Google Initiated Gift to Francesco Locatello. We thank the Social Immunity team at ISTA, particularly Michaela Hönigsberger and Wilfrid Jean Louis, for supporting the ecological experiment and Farnaz Beikzadeh Abbasi, Luisa Fiebig and Martin Estermann for annotating ant behavior in ISTAnt.","citation":{"ama":"Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. Smoke and mirrors in causal downstream tasks. In: <i>38th Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024. doi:<a href=\"https://doi.org/10.52202/079017-0820\">10.52202/079017-0820</a>","mla":"Cadei, Riccardo, et al. “Smoke and Mirrors in Causal Downstream Tasks.” <i>38th Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024, doi:<a href=\"https://doi.org/10.52202/079017-0820\">10.52202/079017-0820</a>.","short":"R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, F. Locatello, in:, 38th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ista":"Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. 2024. Smoke and mirrors in causal downstream tasks. 38th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","ieee":"R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, and F. Locatello, “Smoke and mirrors in causal downstream tasks,” in <i>38th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","chicago":"Cadei, Riccardo, Lukas Lindorfer, Sylvia Cremer, Cordelia Schmid, and Francesco Locatello. “Smoke and Mirrors in Causal Downstream Tasks.” In <i>38th Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024. <a href=\"https://doi.org/10.52202/079017-0820\">https://doi.org/10.52202/079017-0820</a>.","apa":"Cadei, R., Lindorfer, L., Cremer, S., Schmid, C., &#38; Locatello, F. (2024). Smoke and mirrors in causal downstream tasks. In <i>38th Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation. <a href=\"https://doi.org/10.52202/079017-0820\">https://doi.org/10.52202/079017-0820</a>"},"related_material":{"link":[{"url":"https://github.com/CausalLearningAI/ISTAnt","relation":"software"}],"record":[{"relation":"earlier_version","id":"18847","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-21T10:52:44Z","supplementarymaterial":"yes","date_created":"2025-04-06T22:01:32Z","author":[{"full_name":"Cadei, Riccardo","first_name":"Riccardo","last_name":"Cadei","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b"},{"id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","first_name":"Lukas","last_name":"Lindorfer","full_name":"Lindorfer, Lukas"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmid","first_name":"Cordelia","full_name":"Schmid, Cordelia"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"status":"public","_id":"19509","title":"Smoke and mirrors in causal downstream tasks","abstract":[{"text":"Machine Learning and AI have the potential to transform data-driven scientific discovery,\r\nenabling accurate predictions for several scientific phenomena. As many scientific questions\r\nare inherently causal, this paper looks at the causal inference task of treatment effect\r\nestimation, where the outcome of interest is recorded in high-dimensional observations\r\nin a Randomized Controlled Trial (RCT). Despite being the simplest possible causal setting\r\nand a perfect fit for deep learning, we theoretically find that many common choices in the\r\nliterature may lead to biased estimates. To test the practical impact of these considerations,\r\nwe recorded ISTAnt, the first real-world benchmark for causal inference downstream tasks\r\non high-dimensional observations as an RCT studying how garden ants (Lasius neglectus)\r\nrespond to microparticles applied onto their colony members by hygienic grooming.\r\nComparing 6 480 models fine-tuned from state-of-the-art visual backbones, we find that\r\nthe sampling and modeling choices significantly affect the accuracy of the causal estimate,\r\nand that classification accuracy is not a proxy thereof. We further validated the analysis,\r\nrepeating it on a synthetically generated visual data set controlling the causal model. Our\r\nresults suggest that future benchmarks should carefully consider real downstream scientific\r\nquestions, especially causal ones. Further, we highlight guidelines for representation\r\nlearning methods to help answer causal questions in the sciences.\r\nCode: https://github.com/CausalLearningAI/ISTAnt\r\nData: https://doi.org/10.6084/m9.figshare.26484934.v2","lang":"eng"}],"type":"conference","oa_version":"Preprint"},{"date_created":"2024-08-25T22:01:08Z","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","last_name":"Pull","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"}],"status":"public","title":"Unconditional versus condition-dependent social immunity","_id":"17461","abstract":[{"text":"Socially living animals can counteract disease through cooperative defences, leading to social immunity that collectively exceeds the sum of individual defences. In superorganismal colonies of social insects with permanent caste separation between reproductive queen(s) and nonreproducing workers, workers are obligate altruists and thus engage in unconditional social immunity, including highly specialised and self-sacrificial hygiene behaviours. Contrastingly, cooperation is facultative in cooperatively breeding families, where all members are reproductively totipotent but offspring transiently forgo reproduction to help their parents rear more siblings. Here, helpers should either express condition-dependent social immunity or disperse to pursue independent reproduction. We advocate inclusive fitness theory as a framework to predict when and how indirect fitness gains may outweigh direct fitness costs, thus favouring conditional social immunity.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","article_type":"original","page":"780-787","citation":{"apa":"Cremer, S., &#38; Pull, C. (2024). Unconditional versus condition-dependent social immunity. <i>Trends in Parasitology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">https://doi.org/10.1016/j.pt.2024.07.014</a>","chicago":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” <i>Trends in Parasitology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">https://doi.org/10.1016/j.pt.2024.07.014</a>.","ista":"Cremer S, Pull C. 2024. Unconditional versus condition-dependent social immunity. Trends in Parasitology. 40(9), 780–787.","ieee":"S. Cremer and C. Pull, “Unconditional versus condition-dependent social immunity,” <i>Trends in Parasitology</i>, vol. 40, no. 9. Elsevier, pp. 780–787, 2024.","short":"S. Cremer, C. Pull, Trends in Parasitology 40 (2024) 780–787.","ama":"Cremer S, Pull C. Unconditional versus condition-dependent social immunity. <i>Trends in Parasitology</i>. 2024;40(9):780-787. doi:<a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">10.1016/j.pt.2024.07.014</a>","mla":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” <i>Trends in Parasitology</i>, vol. 40, no. 9, Elsevier, 2024, pp. 780–87, doi:<a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">10.1016/j.pt.2024.07.014</a>."},"date_updated":"2026-10-21T10:27:15Z","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","issue":"9","publication":"Trends in Parasitology","acknowledgement":"We thank Koos Boomsma and two anonymous reviewers for their constructive comments on the manuscript.","publication_identifier":{"eissn":["1471-5007"],"issn":["1471-4922"]},"OA_type":"hybrid","OA_place":"publisher","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"intvolume":"        40","publication_status":"published","quality_controlled":"1","year":"2024","pmid":1,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","date_published":"2024-09-01T00:00:00Z","file_date_updated":"2025-01-09T13:46:05Z","das_tickbox":"0","fulldoi":"https://doi.org/10.1016/j.pt.2024.07.014","corr_author":"1","oa":1,"day":"01","publisher":"Elsevier","department":[{"_id":"SyCr"}],"month":"09","external_id":{"isi":["001307815700001"],"pmid":["39152078"]},"isi":1,"researchdata_availability":"no","doi":"10.1016/j.pt.2024.07.014","file":[{"file_id":"18816","file_name":"2024_TrendsParasitology_Cremer.pdf","content_type":"application/pdf","date_updated":"2025-01-09T13:46:05Z","file_size":1068464,"success":1,"checksum":"362fc994e5df66caf3025b7dc437b647","date_created":"2025-01-09T13:46:05Z","access_level":"open_access","relation":"main_file","creator":"dernst"}],"volume":40},{"volume":34,"researchdata_availability":"unclear","doi":"10.1016/j.cub.2024.01.017","isi":1,"external_id":{"pmid":["38307022"],"isi":["001195884300001"]},"publisher":"Elsevier","month":"02","department":[{"_id":"SyCr"}],"dataavailabilitystatement":"All data generated in this paper will be made publicly available upon acceptance.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","day":"26","oa":1,"das_tickbox":"1","fulldoi":"https://doi.org/10.1016/j.cub.2024.01.017","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.26.564092"}],"date_published":"2024-02-26T00:00:00Z","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","year":"2024","pmid":1,"intvolume":"        34","language":[{"iso":"eng"}],"acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"publication":"Current Biology","scopus_import":"1","issue":"4","supplementarymaterial":"yes","date_updated":"2026-10-21T10:26:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>.","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. 2024;34(4):902-909.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ieee":"E. Csata <i>et al.</i>, “Fungal infection alters collective nutritional intake of ant colonies,” <i>Current Biology</i>, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>"},"page":"902-909.e6","type":"journal_article","oa_version":"Preprint","article_type":"original","abstract":[{"text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.","lang":"eng"}],"title":"Fungal infection alters collective nutritional intake of ant colonies","_id":"14479","date_created":"2023-10-31T13:30:20Z","status":"public","author":[{"first_name":"Eniko","last_name":"Csata","full_name":"Csata, Eniko"},{"full_name":"Perez-Escudero, Alfonso","last_name":"Perez-Escudero","first_name":"Alfonso"},{"full_name":"Laury, Emmanuel","first_name":"Emmanuel","last_name":"Laury"},{"full_name":"Leitner, Hanna","last_name":"Leitner","first_name":"Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7"},{"last_name":"Latil","first_name":"Gerard","full_name":"Latil, Gerard"},{"full_name":"Heinze, Juerge","last_name":"Heinze","first_name":"Juerge"},{"full_name":"Simpson, Stephen","last_name":"Simpson","first_name":"Stephen"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"},{"full_name":"Dussutour, Audrey","first_name":"Audrey","last_name":"Dussutour"}]},{"main_file_link":[{"url":"https://10.6084/M9.FIGSHARE.26484934.V2","open_access":"1"}],"date_updated":"2026-10-21T10:52:44Z","fulldoi":"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cadei, Riccardo, et al. <i>ISTAnt</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","ama":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. ISTAnt. 2024. doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>","ista":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. 2024. ISTAnt, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","ieee":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, and C. Schmid, “ISTAnt.” Institute of Science and Technology Austria, 2024.","short":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, C. Schmid, (2024).","chicago":"Cadei, Riccardo, Francesco Locatello, Sylvia Cremer, Lukas Lindorfer, and Cordelia Schmid. “ISTAnt.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>.","apa":"Cadei, R., Locatello, F., Cremer, S., Lindorfer, L., &#38; Schmid, C. (2024). ISTAnt. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>"},"article_processing_charge":"No","related_material":{"record":[{"id":"18847","relation":"used_in_publication","status":"public"}]},"date_published":"2024-10-23T00:00:00Z","abstract":[{"text":"ISTAnt is a new ecological dataset for social immunity and represents the first real-world benchmark for causal inference downstream tasks on high-dimensional observations. It analyzes grooming behavior in the ant Lasius neglectus in groups of three worker ants. The workers for the experiment were obtained from their laboratory stock colony, which had been collected from the field in 2022 in the Botanical Garden Jena, Germany. Ant collection and all experimental work were performed in compliance with international, national and institutional regulations and ethical guidelines. For the experiment, the body surface of one of the three ants was treated with a suspension of either of two microparticle types (diameter ~5 µm) to induce grooming by the two nestmates, which were individually color-coded by application of a dot of blue or orange paint, respectively. The three ants were housed in small plastic containers (diameter 28mm, height 30mm) with moistened, plastered ground and the interior walls covered with PTFE (polytetrafluoroethane) to hamper climbing by the ants. Filming occurred in a temperature- and humidity-controlled room at 23°C within a custom-made filming box with controlled lighting and ventilation conditions. We set up nine ant groups at a time (always containing both treatments) and placed them randomly on positions 1-9 marked on the floor in a 3x3 grid, about 3mm from each other. The experiment was performed on two consecutive days. Videos were acquired using a USB camera (FLIR blackfly S BFS-U3-120S4C, Teledyne FLIR) with a high-performance lens (HP Series 25mm Focal Length, Edmund optics 86-572) in OBS studio 29.0.0 \\citep{bailey2017obs} at a framerate of 30 FPS and a resolution of 2500x2500 pixels. From each original video (105x105 mm), we generated nine individual videos .mkv (each ~32x32 mm, 770x770 pixels) by determining exact coordinates per container from one frame in GIMP 2.10.36 and cropping of the videos with FFmpeg 6.1.1. Annotation was performed over two consecutive days by three observers who had not been involved in the experimental setup or recording and were unaware of the treatment assignments to ensure bias-free behavioral annotation. They annotated the behavior of the ants during video observations, using custom-made software that saves the start and end frames of behaviors marked in a .csv file (see 'annotations' folder). In one of the videos, one of the nestmates' legs got inadvertently stuck to its body surface during the color-coding, interfering with its behavior, so the video was discarded. This left 44 videos from 5 independent setups (n=24 of treatment 1 and n=20 of treatment 2) of 10 minutes each for a total of 792 000 annotated frames (see 'video' folder). For each video, we provide the following information: the number of the set to which it belongs (1-5); the number of the position within the set reflecting the position of the ant group under the camera (1-9), for which we also provide ‘coordinates’ in the 3x3 grid (taking values -1/0/1 for both X and Y axis); treatment (1 or 2); the hour of the day when the recording was started (in 24h CEST); experimental day (A or B); the top left coordinate of the cropping square from the original video (CropX/CropY); the person annotating the video (given as A, B, C); the date of annotation (1: first day, 2: second day) and in which order the videos were annotated by each person, both reflecting a possible training effect of the person (see 'experiments_settings.csv' file).","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","year":"2024","ddc":["570"],"status":"public","date_created":"2025-01-27T11:45:43Z","author":[{"full_name":"Cadei, Riccardo","first_name":"Riccardo","last_name":"Cadei","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M"},{"last_name":"Lindorfer","first_name":"Lukas","id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","full_name":"Lindorfer, Lukas"},{"first_name":"Cordelia","last_name":"Schmid","full_name":"Schmid, Cordelia"}],"title":"ISTAnt","_id":"18895","doi":"10.6084/M9.FIGSHARE.26484934.V2","OA_place":"repository","OA_type":"gold","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SyCr"},{"_id":"FrLo"},{"_id":"GradSch"}],"month":"10","corr_author":"1","oa":1,"day":"23"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"yes","date_updated":"2026-10-21T10:43:21Z","related_material":{"record":[{"id":"23180","relation":"research_data","status":"public"}]},"citation":{"short":"A. Basu, A. Singh, S. Sehgal, T. Madaan, N.G. Prasad, Journal of Invertebrate Pathology 207 (2024).","ista":"Basu A, Singh A, Sehgal S, Madaan T, Prasad NG. 2024. Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females. Journal of Invertebrate Pathology. 207(11), 108209.","ieee":"A. Basu, A. Singh, S. Sehgal, T. Madaan, and N. G. Prasad, “Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females,” <i>Journal of Invertebrate Pathology</i>, vol. 207, no. 11. Elsevier, 2024.","mla":"Basu, Aabeer, et al. “Starvation Increases Susceptibility to Bacterial Infection and Promotes Systemic Pathogen Proliferation in Drosophila Melanogaster Females.” <i>Journal of Invertebrate Pathology</i>, vol. 207, no. 11, 108209, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jip.2024.108209\">10.1016/j.jip.2024.108209</a>.","ama":"Basu A, Singh A, Sehgal S, Madaan T, Prasad NG. Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females. <i>Journal of Invertebrate Pathology</i>. 2024;207(11). doi:<a href=\"https://doi.org/10.1016/j.jip.2024.108209\">10.1016/j.jip.2024.108209</a>","apa":"Basu, A., Singh, A., Sehgal, S., Madaan, T., &#38; Prasad, N. G. (2024). Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females. <i>Journal of Invertebrate Pathology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jip.2024.108209\">https://doi.org/10.1016/j.jip.2024.108209</a>","chicago":"Basu, Aabeer, Aparajita Singh, Suhaas Sehgal, Tanvi Madaan, and Nagaraj Guru Prasad. “Starvation Increases Susceptibility to Bacterial Infection and Promotes Systemic Pathogen Proliferation in Drosophila Melanogaster Females.” <i>Journal of Invertebrate Pathology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jip.2024.108209\">https://doi.org/10.1016/j.jip.2024.108209</a>."},"article_type":"original","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Defense against pathogens and parasites requires substantial investment of energy and resources on part of the host. This makes the host immune function dependent on availability and accessibility of resources. A resource deprived host is therefore expected to be more susceptible to infections, although empirical results do not always align with this prediction. Limiting host access to resources can additionally impact within-host pathogen numbers, either directly by altering the amount of resources available to the pathogens for proliferation or indirectly by altering the efficiency of the host immune system. We tested for the effects of host starvation (complete deprivation of resources) on susceptibility to bacterial pathogens, and within-host pathogen proliferation, in Drosophila melanogaster females. Our results show that starvation increases post-infection mortality of the host, but in a pathogen-specific manner. This increase in mortality is always accompanied by increased within-host pathogen proliferation. We therefore propose that starvation compromises host resistance to bacterial infections in Drosophila melanogaster females thereby increasing susceptibility to infections."}],"_id":"18171","title":"Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females","status":"public","author":[{"full_name":"Basu, Aabeer","first_name":"Aabeer","last_name":"Basu"},{"first_name":"Aparajita","last_name":"Singh","full_name":"Singh, Aparajita"},{"last_name":"Sehgal","first_name":"Suhaas","full_name":"Sehgal, Suhaas"},{"full_name":"Madaan, Tanvi","id":"419917ac-5355-11ee-ae5a-c952babcaad9","first_name":"Tanvi","last_name":"Madaan"},{"full_name":"Prasad, Nagaraj Guru","last_name":"Prasad","first_name":"Nagaraj Guru"}],"date_created":"2024-10-06T22:01:11Z","language":[{"iso":"eng"}],"OA_type":"closed access","acknowledgement":"The authors thank Tejashwini Hegde for logistical support during execution of the experiments reported here. The authors thank Prof. P. Cornelis (Vrije Universiteit Brussel, Belgium) for providing the Pseudomonas entomophila isolate, Dr. Elio Sucena and Tania Paulo (Instituto Gulbenkian Ciencia, Portugal) for providing the Erwinia c. carotovora, and Prof. Brian Lazzaro (Cornell University, USA) for providing the Enterococcus faecalis and Providencia rettgeri isolates, and Dr. Karan Singh (IISER Mohali, India) for isolating the Staphylococcus succinus isolate used in the experiments. The authors also thank Dr. Manas Geeta Arun for maintenance of the LH fly populations used in this study.\r\nThe study was funded by intra-mural funding from IISER Mohali, India, to NGP. AB was supported by Senior Research Fellowship for PhD students from CSIR, Govt. of India. AS was supported by Senior Research Fellowship for PhD students from UGC, Govt. of India. SS and TM were supported by KVPY fellowships for undergraduate studies from DST, Govt. of India.","publication_identifier":{"eissn":["1096-0805"],"issn":["0022-2011"]},"publication":"Journal of Invertebrate Pathology","issue":"11","scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.jip.2024.108209","das_tickbox":"1","date_published":"2024-11-01T00:00:00Z","article_processing_charge":"No","year":"2024","pmid":1,"quality_controlled":"1","publication_status":"published","intvolume":"       207","volume":207,"researchdata_availability":"yes","doi":"10.1016/j.jip.2024.108209","article_number":"108209","isi":1,"external_id":{"pmid":["39322010"],"isi":["001327816900001"]},"month":"11","department":[{"_id":"SyCr"}],"publisher":"Elsevier","day":"01","dataavailabilitystatement":"The data associated with this article are available in the Dryad Digital Repository at https://doi.org/10.5061/dryad.pvmcvdnp8","corr_author":"1"}]