[{"publication_status":"published","author":[{"last_name":"Chen","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","first_name":"Huihuang"},{"last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","first_name":"Linlin"},{"first_name":"Minxia","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou"},{"first_name":"Mengting","full_name":"Lu, Mengting","id":"a8198a14-1ffe-11ee-8b67-d2bdff9d9178","last_name":"Lu"},{"first_name":"M","full_name":"Kwiatkowski, M","last_name":"Kwiatkowski"},{"full_name":"Pei, Yuanrong","first_name":"Yuanrong","last_name":"Pei","id":"98605edc-6ce7-11ee-95f3-cc16b866efcd"},{"first_name":"K","full_name":"Jaworski, K","last_name":"Jaworski"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"type":"journal_article","file_date_updated":"2025-08-05T12:29:35Z","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Chen, Huihuang, Linlin Qi, Minxia Zou, Mengting Lu, M Kwiatkowski, Yuanrong Pei, K Jaworski, and Jiří Friml. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08669-w\">https://doi.org/10.1038/s41586-025-08669-w</a>.","ama":"Chen H, Qi L, Zou M, et al. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. <i>Nature</i>. 2025;640:1011-1016. doi:<a href=\"https://doi.org/10.1038/s41586-025-08669-w\">10.1038/s41586-025-08669-w</a>","apa":"Chen, H., Qi, L., Zou, M., Lu, M., Kwiatkowski, M., Pei, Y., … Friml, J. (2025). TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08669-w\">https://doi.org/10.1038/s41586-025-08669-w</a>","ieee":"H. Chen <i>et al.</i>, “TIR1-produced cAMP as a second messenger in transcriptional auxin signalling,” <i>Nature</i>, vol. 640. Springer Nature, pp. 1011–1016, 2025.","short":"H. Chen, L. Qi, M. Zou, M. Lu, M. Kwiatkowski, Y. Pei, K. Jaworski, J. Friml, Nature 640 (2025) 1011–1016.","ista":"Chen H, Qi L, Zou M, Lu M, Kwiatkowski M, Pei Y, Jaworski K, Friml J. 2025. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. 640, 1011–1016.","mla":"Chen, Huihuang, et al. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” <i>Nature</i>, vol. 640, Springer Nature, 2025, pp. 1011–16, doi:<a href=\"https://doi.org/10.1038/s41586-025-08669-w\">10.1038/s41586-025-08669-w</a>."},"month":"04","file":[{"checksum":"f5f18081003e7a1b8e372ecb7da82e7d","content_type":"application/pdf","date_updated":"2025-08-05T12:29:35Z","date_created":"2025-08-05T12:29:35Z","relation":"main_file","file_name":"2025_Nature_Chen.pdf","creator":"dernst","success":1,"file_size":13549245,"access_level":"open_access","file_id":"20132"}],"date_created":"2025-03-19T09:44:39Z","date_updated":"2026-11-14T23:31:17Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"has_accepted_license":"1","status":"public","OA_place":"publisher","language":[{"iso":"eng"}],"ddc":["580"],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/updating-the-textbook/","description":"News on ISTA website"}],"record":[{"id":"19478","relation":"dissertation_contains","status":"public"}]},"isi":1,"title":"TIR1-produced cAMP as a second messenger in transcriptional auxin signalling","intvolume":"       640","date_published":"2025-04-24T00:00:00Z","article_type":"original","corr_author":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"oa":1,"department":[{"_id":"JiFr"}],"PlanS_conform":"1","_id":"19421","external_id":{"isi":["001437493900001"],"pmid":["40044868"]},"publication":"Nature","page":"1011-1016","publisher":"Springer Nature","pmid":1,"fulldoi":"https://doi.org/10.1038/s41586-025-08669-w","day":"24","OA_type":"hybrid","acknowledgement":"We are grateful to J. Callis and H.-Q. Yang for sharing materials and to M. Estelle and S. Kepinski for inspiring discussions. This research was supported by the Laboratory Support Facility, the Plant Facility and the Imaging and Optics Facility of the Institute of Science and Technology Austria. This project has received funding from the European Research Council (101142681 CYNIPS) and Austrian Science Fund (P 37051-B). L.Q. was supported by the National Natural Science Foundation of China (grant no. 32470327). M.Z. was supported by the Interdisciplinary Project Committee of the Institute of Science and Technology Austria, and Y.P. was supported by an EMBO Postdoctoral Fellowship (ALTF 38-2023). Open access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1038/s41586-025-08669-w","year":"2025","volume":640,"project":[{"grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"abstract":[{"text":"The phytohormone auxin (Aux) is a principal endogenous developmental signal in plants. It mediates transcriptional reprogramming by a well-established canonical signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin ligase complex; after auxin perception, they associate with Aux/IAA transcriptional repressors and ubiquitinate them for degradation, thus enabling the activation of auxin response factor (ARF) transcription factors1,2,3. Here we revise this paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming and auxin-regulated development, including shoot, root, root hair growth and lateral root formation. Transgenic plants show that local cAMP production in the vicinity of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin perception and is sufficient to induce ARF-mediated transcription. These discoveries revise the canonical model of auxin signalling and establish TIR1/AFB-produced cAMP as a second messenger essential for transcriptional reprograming.","lang":"eng"}]},{"file":[{"file_id":"20420","file_size":88706648,"embargo_to":"open_access","access_level":"closed","creator":"slee","file_name":"2025_Lee_Seungho_Thesis.docx","date_updated":"2026-10-03T22:30:02Z","date_created":"2025-10-03T12:29:43Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"fa6d5946feb37b678ee1c6dffb4fa167"},{"access_level":"open_access","file_size":14587276,"file_id":"20421","content_type":"application/pdf","embargo":"2026-10-03","checksum":"c5ba6d464113ad0c5812a9d24b539b86","creator":"slee","file_name":"2025_Lee_Seungho_Thesis__.pdf","date_updated":"2026-10-03T22:30:02Z","date_created":"2025-10-03T12:29:25Z","relation":"main_file"}],"date_updated":"2026-10-23T08:16:15Z","date_created":"2025-10-01T09:04:00Z","doi_confirm":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"OA_place":"publisher","related_material":{"record":[{"id":"12237","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"15357"}]},"ddc":["540"],"degree_awarded":"PhD","publication_status":"published","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"first_name":"Loredana","full_name":"Protesescu, Loredana","last_name":"Protesescu"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"}],"type":"dissertation","author":[{"full_name":"Lee, Seungho","first_name":"Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425"}],"file_date_updated":"2026-10-03T22:30:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","oa_version":"Published Version","citation":{"mla":"Lee, Seungho. <i>Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>.","ista":"Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria.","short":"S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025.","apa":"Lee, S. (2025). <i>Nanoparticle-based precursors toward advanced crystalline inorganic solids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>","ieee":"S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic solids,” Institute of Science and Technology Austria, 2025.","ama":"Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>","chicago":"Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>."},"month":"10","publisher":"Institute of Science and Technology Austria","page":"144","day":"01","fulldoi":"https://doi.org/10.15479/AT-ISTA-20415","doi":"10.15479/AT-ISTA-20415","year":"2025","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"abstract":[{"lang":"eng","text":"Well-defined powder precursors are important for the rational design of crystalline inorganic \r\nmaterials with controlled defects and functional properties. Such powders can be prepared from \r\ndried nanoparticles synthesized using a surfactant-assisted/colloidal method that provides \r\nprecise control over size, shape, composition, and surface chemistry of nanoparticles. These \r\ntailored nanoparticles further act as building blocks for three-dimensional assemblies, \r\nexhibiting collective nanoscale properties and enabling tailored microstructures of crystalline \r\ninorganic materials. However, the programmable engineering of such materials using \r\nnanoparticle-based precursors remains limited, due to a lack of fundamental understanding of \r\nboth the synthesis of nanoparticles and their conversion into macroscopic solids. Furthermore, \r\nthe formation of three-dimensional assemblies often requires multi-step post-synthetic \r\ntreatments, which can limit reproducibility and the production of the bulk inorganic materials. \r\nIn this thesis, I demonstrate a key synthetic parameter governing the formation of desired \r\nnanostructures, especially metal/semiconductor core–shell nanoparticles which are potential \r\nprecursors for engineering composition, crystal structure, and defects of final materials. Then, \r\nI investigate their transformative pathways to unveil structural and chemical changes that occur \r\nduring heat treatment of the nanoparticle-based precursors. Building on understanding of \r\natomic-scale interactions during nanoparticle-based precursor formation, I further demonstrate \r\nthe possibility of synthesizing the nanoparticle assembly directly in the nanoparticle synthesis \r\nreaction and rationalize the process of in situ self-assembly of nanoparticles. Finally, the impact \r\nof NP-based precursors on the formation and properties of crystalline inorganic materials is \r\nevaluated, demonstrating the potential of employing NP-based precursors for the rational \r\ndesign of functional inorganic materials. "}],"title":"Nanoparticle-based precursors toward advanced crystalline inorganic solids","date_published":"2025-10-01T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"oa":1,"_id":"20415"},{"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version","citation":{"mla":"Rus, Stefanie. <i>Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>.","ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria.","short":"S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025.","ama":"Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>","ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025.","apa":"Rus, S. (2025). <i>Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>","chicago":"Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>."},"month":"05","alternative_title":["ISTA Thesis"],"publication_status":"published","supervisor":[{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"}],"author":[{"full_name":"Rus, Stefanie","first_name":"Stefanie","orcid":"0000-0001-8703-1093","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","file_date_updated":"2025-11-30T23:30:02Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"has_accepted_license":"1","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13136"},{"status":"public","id":"17148","relation":"part_of_dissertation"},{"id":"18807","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18601","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"ddc":["570"],"OA_place":"publisher","degree_awarded":"PhD","file":[{"file_id":"19764","access_level":"open_access","file_size":42879974,"file_name":"Thesis_Lehr_PDFA.pdf","creator":"cchlebak","relation":"main_file","date_created":"2025-05-30T09:10:22Z","date_updated":"2025-11-30T23:30:02Z","embargo":"2025-11-30","content_type":"application/pdf","checksum":"8cd7fe3ca990adbcafdece119aa0973d"},{"date_created":"2025-05-30T09:31:15Z","relation":"source_file","date_updated":"2025-11-30T23:30:02Z","file_name":"Thesis_Lehr_emptyPages.docx","creator":"cchlebak","checksum":"0c87dd5fc803450a47b20736b5f86a2f","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"19765","embargo_to":"open_access","file_size":18731094,"access_level":"closed"}],"date_updated":"2026-11-11T10:12:10Z","date_created":"2025-05-30T09:14:58Z","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"oa":1,"department":[{"_id":"AnKi"},{"_id":"GradSch"}],"_id":"19763","title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","date_published":"2025-05-29T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-19763","day":"29","acknowledgement":"My work would also not have been possible without the Imaging and Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has facilitated my research substantially. I\r\nalso want to thank the Graduate School Office for their never-ending support and their sincere\r\neffort to improve the PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank you for recognizing the importance of this project.","doi":"10.15479/AT-ISTA-19763","year":"2025","project":[{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011"}],"abstract":[{"lang":"eng","text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation."}],"page":"129","publisher":"Institute of Science and Technology Austria"},{"researchdata_availability":"yes","intvolume":"        60","title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","scopus_import":"1","article_type":"original","date_published":"2025-02-24T00:00:00Z","publication_identifier":{"issn":["1534-5807"]},"corr_author":"1","oa":1,"department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"_id":"18807","publisher":"Cell Press","page":"567-580","publication":"Developmental Cell","supplementarymaterial":"yes","external_id":{"pmid":["39603235"],"isi":["001434279000001"]},"pmid":1,"acknowledgement":"We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","day":"24","OA_type":"hybrid","fulldoi":"https://doi.org/10.1016/j.devcel.2024.10.024","doi":"10.1016/j.devcel.2024.10.024","year":"2025","das_tickbox":"1","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"},{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"volume":60,"abstract":[{"text":"Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues.","lang":"eng"}],"publication_status":"published","type":"journal_article","dataavailabilitystatement":"RNA-seq data has been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. Code for the quantification of fluorescence intensity (FI) profiles in differentiated cells on stencils, as well as for model simulations, is available on GitHub (https://github.com/dbrueckner/NeuralTubeColonies, https://doi.org/10.5281/zenodo.13335390","author":[{"full_name":"Rus, Stefanie","first_name":"Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David"},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","first_name":"Thomas","full_name":"Minchington, Thomas"},{"last_name":"Greunz","id":"48A59534-F248-11E8-B48F-1D18A9856A87","full_name":"Greunz, Martina","first_name":"Martina"},{"first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"}],"file_date_updated":"2025-04-16T10:54:07Z","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>","ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Cell Press, pp. 567–580, 2025.","ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>","chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Cell Press, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>.","ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580."},"oa_version":"Published Version","month":"02","file":[{"relation":"main_file","date_updated":"2025-04-16T10:54:07Z","date_created":"2025-04-16T10:54:07Z","file_name":"2025_DevelopmentalCell_Lehr.pdf","creator":"dernst","success":1,"checksum":"bb58db4a908a1f4aabe4004706154541","content_type":"application/pdf","file_id":"19584","file_size":6994499,"access_level":"open_access"}],"date_updated":"2026-11-14T23:31:20Z","date_created":"2025-01-09T11:25:47Z","status":"public","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"ddc":["570"],"related_material":{"record":[{"relation":"dissertation_contains","id":"19763","status":"public"}]},"issue":"4","isi":1},{"corr_author":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-068-8"]},"department":[{"_id":"GradSch"},{"_id":"MaDe"}],"oa":1,"_id":"20485","title":"Dissecting gap junction biology using the C. elegans nervous system","date_published":"2025-10-23T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20485","day":"23","acknowledgement":"I would also like to acknowledge the funding that I received from the European Union’s\r\nHorizon 2020 research and Innovation programme under the Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been possible without the contribution and support of people\r\nbehind the scientific service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit. I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC) Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. ","year":"2025","doi":"10.15479/AT-ISTA-20485","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"abstract":[{"lang":"eng","text":"Neurons communicate with each other via chemical and electrical synapses. While \r\nmuch attention has been devoted to understanding the molecular players involved in \r\nchemical neurotransmission, the biology of gap junctions mediating electrical \r\ncommunication is understudied. This imbalance is not for their lack of significance – \r\nelectrical synapses make up about 20% of neuronal connections in different species \r\nfrom invertebrates to vertebrates, but rather reflects technical constraints and \r\ninvestigator bias. Many regard electrical synapses as simple channels, and much of \r\nwhat is known about them comes from studies on cell culture models. Insights into \r\ntheir in vivo biology are just starting to emerge.  \r\nThe channels of electrical synapses in most animals are formed by innexins. \r\nChordates are an exception: their electrical synapses consist of connexins. Even \r\nthough at the level of primary sequence innexins and connexins appear to be \r\nunrelated, structurally and functionally they have much in common. The nematode \r\nCaenorhabditis elegans is a promising model to study the biology of electrical \r\nsynapses. This animal offers a powerful toolbox to study neuron function at the \r\nmolecular, cell biological and physiological levels. It also offers a detailed connectome \r\nmap of all of its 302 neurons. The implications from studies of molecular pathways in \r\nC. elegans go beyond this organism, since ~80% of the nematode’s proteins have \r\nhuman homologs.  \r\nThis work aims to enhance our understanding of the in vivo biology of gap junctions \r\nusing C. elegans as a model. Using a proximity labelling approach, we profiled the \r\ninteractomes of two innexins that are expressed predominantly in neurons: UNC-7 and \r\nUNC-9. We identified scores of proteins that may have important roles for these \r\ninnexins and their electrical synapses. Using localization and functional assays to \r\nvalidate and further probe our findings, both at the whole-organism and the single-cell \r\nlevel, we found that gap junctions have heterogeneous protein compositions. Our \r\nfindings imply that electrical synapses are sophisticated, molecularly diverse \r\nstructures.  "}],"ec_funded":1,"page":"155","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","citation":{"mla":"Misova, Michaela. <i>Dissecting Gap Junction Biology Using the C. Elegans Nervous System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>.","ista":"Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria.","short":"M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System, Institute of Science and Technology Austria, 2025.","ama":"Misova M. Dissecting gap junction biology using the C. elegans nervous system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>","apa":"Misova, M. (2025). <i>Dissecting gap junction biology using the C. elegans nervous system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>","ieee":"M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,” Institute of Science and Technology Austria, 2025.","chicago":"Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans Nervous System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>."},"month":"10","publication_status":"published","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario"}],"author":[{"last_name":"Misova","id":"495A3C32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2427-6856","full_name":"Misova, Michaela","first_name":"Michaela"}],"type":"dissertation","file_date_updated":"2026-10-23T22:30:02Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"has_accepted_license":"1","status":"public","OA_place":"publisher","ddc":["570"],"language":[{"iso":"eng"}],"degree_awarded":"PhD","file":[{"date_updated":"2026-10-23T22:30:02Z","relation":"source_file","date_created":"2025-10-23T08:22:35Z","file_name":"2025-Misova-Michaela-Thesis.docx","creator":"mmisova","checksum":"e042ea314e7e13fce76c6c95e126779a","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20518","access_level":"closed","file_size":75070995,"embargo_to":"open_access"},{"checksum":"fcd8973d6a025256eb0eb1a82c02172c","embargo":"2026-10-23","content_type":"application/pdf","date_updated":"2026-10-23T22:30:02Z","date_created":"2025-10-23T08:21:21Z","relation":"main_file","creator":"mmisova","file_name":"2025-Misova-Michaela-Thesis.pdf","file_size":10974630,"access_level":"open_access","file_id":"20519"}],"date_created":"2025-10-17T16:15:09Z","date_updated":"2026-11-13T09:57:29Z","doi_confirm":"1"},{"abstract":[{"lang":"eng","text":"During vertebrate development, the morphogen Sonic Hedgehog (Shh) plays a key role in \r\npatterning the tissues of the extending body. This requires precise coordination between the \r\nsize of the source of Shh production and the embryo body. Shh is produced by the notochord, \r\nas well as floorplate of the neural tube. In this thesis, we investigated how the sizes of the \r\nnotochord and floorplate are regulated and how they impact the developing mouse embryo.  \r\nTo measure the size and shape of the developing mouse notochord and the cell behaviours \r\nwithin this organ, we performed high-resolution measurements in cleared embryos between \r\nE8.5 and E10.5 of development. Strikingly, our data revealed that the notochord maintains a \r\nconstant cross-sectional area throughout the trunk over time as it lengthens by cell \r\nproliferation. We show that this is achieved by a feedback between the notochord cell \r\nproliferation rate and both the cross-sectional area of the trunk notochord and elongation of \r\nthe embryo. Using live imaging, we further show that notochord cells undergo posteriorly\r\ndirected active cell migration and that this cell migration contributes to maintaining the \r\nstructural integrity of the notochord. Our results show a complex coordination of cell \r\nbehaviours that allow for robust notochord morphogenesis during mouse development and \r\nthe maintenance of a defined Shh source size.  \r\nShh produced by the notochord induces a secondary Shh-producing domain, the floor plate. \r\nHow the notochord and floor plate contribute to the formation of the Shh gradient in the \r\nneural tube and to the regulation of the floor plate size is poorly understood. Our theoretical \r\nand experimental analysis indicates that only the initial levels of notochord-derived Shh \r\ninfluence the size of the floor plate, and the floor plate is insensitive to its own production of \r\nShh. After its initial establishment, the floor plate expands by tissue growth, leading to scaling \r\nof the Shh gradient amplitude with tissue size.   \r\nAltogether, we show that the mechanisms regulating the sizes of the notochord and \r\nfloorplate in mouse development help to achieve size robustness of these tissues. Our data \r\ndemonstrate that the initial establishment of the Shh gradient in the neural tube is strongly \r\ndependent on the notochord and suggest that the robustness of notochord morphogenesis \r\nis essential for pattern formation. Later in development, the floor plate size and the Shh \r\ngradient are coupled to neural tube growth. Our findings provide new insights on how pattern \r\nformation, tissue growth and morphogenesis interact to ensure reproducible developmental \r\noutcomes. "}],"doi":"10.15479/AT-ISTA-20393","year":"2025","day":"24","fulldoi":"https://doi.org/10.15479/AT-ISTA-20393","publisher":"Institute of Science and Technology Austria","page":"102","_id":"20393","department":[{"_id":"GradSch"},{"_id":"AnKi"},{"_id":"EdHa"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","date_published":"2025-09-24T00:00:00Z","title":"Regulation of notochord and floor plate size during mouse development","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"18481","relation":"part_of_dissertation"}]},"OA_place":"publisher","language":[{"iso":"eng"}],"ddc":["570"],"status":"public","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"doi_confirm":"1","date_updated":"2026-11-11T10:11:08Z","date_created":"2025-09-25T10:08:10Z","file":[{"checksum":"6bb5a7ce318dc3f7bd165f2523e77b89","content_type":"application/x-zip-compressed","relation":"source_file","date_updated":"2026-09-30T22:30:04Z","date_created":"2025-09-30T14:33:17Z","file_name":"2025-Kishi-Kasumi-Thesis.zip","creator":"kkishi","file_size":41847994,"embargo_to":"open_access","access_level":"closed","file_id":"20413"},{"file_size":55747072,"access_level":"open_access","file_id":"20414","content_type":"application/pdf","embargo":"2026-09-30","checksum":"88349b9177e1dcbe1242cd3884b36fdb","file_name":"2025-Kishi-Kasumi-Thesis.pdf","creator":"kkishi","date_created":"2025-09-30T14:33:22Z","date_updated":"2026-09-30T22:30:04Z","relation":"main_file"}],"month":"09","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"citation":{"apa":"Kishi, K. (2025). <i>Regulation of notochord and floor plate size during mouse development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>","ieee":"K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025.","ama":"Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>","chicago":"Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>.","mla":"Kishi, Kasumi. <i>Regulation of Notochord and Floor Plate Size during Mouse Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>.","short":"K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025.","ista":"Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria."},"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","file_date_updated":"2026-09-30T22:30:04Z","type":"dissertation","author":[{"full_name":"Kishi, Kasumi","first_name":"Kasumi","last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6060-4795"}],"supervisor":[{"full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"publication_status":"published","alternative_title":["ISTA Thesis"]},{"file":[{"checksum":"50290a8604edb0a720387f01e9d59fe4","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_created":"2025-04-15T08:43:36Z","date_updated":"2026-10-15T22:30:02Z","creator":"lschwarz","file_name":"Schwarz_Thesis_2025_FINAL.docx","access_level":"closed","embargo_to":"open_access","file_size":21783427,"file_id":"19561"},{"file_size":11432175,"access_level":"open_access","file_id":"19562","checksum":"ed028488180ac4901e018ef1c330cf01","embargo":"2026-10-15","content_type":"application/pdf","relation":"main_file","date_created":"2025-04-15T08:43:42Z","date_updated":"2026-10-15T22:30:02Z","file_name":"Schwarz_Thesis_2025_FINALpdfa.pdf","creator":"lschwarz"}],"doi_confirm":"1","date_updated":"2026-11-13T12:31:10Z","date_created":"2025-04-14T06:59:06Z","status":"public","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"ScienComp"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"12802","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9429"}]},"ddc":["570"],"language":[{"iso":"eng"}],"OA_place":"publisher","type":"dissertation","author":[{"first_name":"Lena A","full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz"}],"supervisor":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"file_date_updated":"2026-10-15T22:30:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","month":"04","citation":{"ieee":"L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025.","apa":"Schwarz, L. A. (2025). <i>Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>","ama":"Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>","chicago":"Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>.","mla":"Schwarz, Lena A. <i>Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>.","ista":"Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria.","short":"L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","page":"124","year":"2025","doi":"10.15479/AT-ISTA-19557","day":"14","acknowledgement":"The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses.","fulldoi":"https://doi.org/10.15479/AT-ISTA-19557","abstract":[{"lang":"eng","text":"Numerous studies have revealed a wide range of genes associated with autism \r\nspectrum disorder (ASD), raising critical questions about how mutations across \r\ndifferent genes lead to similar clinical presentations. Yet, specific molecular \r\nmechanisms underlying most ASD cases remain elusive. Notably, ASD is diagnosed \r\nfour times more frequently in males than in females, highlighting a substantial sex \r\ndisparity. This male predominance is among the most recognized but least understood \r\ncharacteristics of the disorder. Thus, uncovering molecular mechanisms involved is \r\ncrucial for exploring both shared and distinct aspects of ASD.  \r\nWe utilized single-nucleus multi-omics sequencing to explore these unresolved \r\nquestions, enabling us to investigate changes in gene expression and chromatin \r\naccessibility concurrently. In the present work, we analyzed and compared 251 \r\nsamples collected from eleven different monogenic mouse models of ASD, \r\nincorporating both sexes and two brain regions. Samples span three primary \r\ndevelopmental stages, which include prenatal, early postnatal, and juvenile brain \r\ndevelopment. This comprehensive dataset allowed us to map functional mechanisms \r\nspecific to cell states, sex, and developmental periods. \r\nWe discovered that ASD mutations commonly delay the progression of radial glial \r\ncells, temporarily affecting the neural lineage specification. The most notable gene \r\nexpression changes occurred perinatally, mainly affecting excitatory and inhibitory \r\nneurons. These alterations involved a downregulation of genes related to synapses \r\nand ion channels, indicating possible homeostatic adaptations. While there were \r\nseveral common molecular changes across all models, each mutant also displayed \r\nunique states.  \r\nThroughout the perinatal phase, numerous processes of cortical regulation and \r\nrefinement take place. At this stage, several ASD risk genes exhibit a common set of \r\ndifferentially expressed genes, converging on a subclass of dysregulated \r\nmechanisms. However, as cortical development progresses, these shared processes \r\nstart to diverge. This suggests that the period around P4 represents a critical time \r\nwindow for many converging molecular processes, marking it as the most impacted \r\nstage. \r\nImportantly, our study highlighted sex-specific gene expression alterations, with \r\nfemales often showing broader dysregulations and larger effect sizes compared to \r\nmales.  \r\nIn contrast to the cerebral cortex, the cerebellum showed fewer gene expression \r\nchanges across most ASD mutant models, with the exception of one mutant that \r\nshowed consistent alterations in both brain regions.  \r\nOverall, our findings provide a thorough view of the cellular and molecular dynamics \r\nin different ASD models, highlighting both common and unique features across \r\ndifferent genetic backgrounds. By exploring multiple genetic forms of ASD, we could \r\ndemonstrate the dynamic nature of ASD-related changes in the brain and emphasize \r\nthe importance of accounting for sex-dependent factors. In conclusion, this work \r\nserves as a valuable multi-omics resource, providing a foundation for future \r\ninvestigations. "}],"project":[{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964"},{"grant_number":"101044865","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders"},{"call_identifier":"FWF","grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"title":"Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution","date_published":"2025-04-14T00:00:00Z","oa":1,"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","_id":"19557"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","DOAJ_listed":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"mla":"Labbe, Ivo, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 &#60; z &#60; 7 with JWST and ALMA.” <i>The Astrophysical Journal</i>, vol. 978, 92, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad3551\">10.3847/1538-4357/ad3551</a>.","ista":"Labbe I, Greene JE, Bezanson R, Fujimoto S, Furtak LJ, Goulding AD, Matthee JJ, Naidu RP, Oesch PA, Atek H, Brammer G, Chemerynska I, Coe D, Cutler SE, Dayal P, Feldmann R, Franx M, Glazebrook K, Leja J, Maseda M, Marchesini D, Nanayakkara T, Nelson EJ, Pan R, Papovich C, Price SH, Suess KA, Wang B冰洁, Weaver JR, Whitaker KE, Williams CC, Zitrin A. 2024. UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA. The Astrophysical Journal. 978, 92.","short":"I. Labbe, J.E. Greene, R. Bezanson, S. Fujimoto, L.J. Furtak, A.D. Goulding, J.J. Matthee, R.P. Naidu, P.A. Oesch, H. Atek, G. Brammer, I. Chemerynska, D. Coe, S.E. Cutler, P. Dayal, R. Feldmann, M. Franx, K. Glazebrook, J. Leja, M. Maseda, D. Marchesini, T. Nanayakkara, E.J. Nelson, R. Pan, C. Papovich, S.H. Price, K.A. Suess, B.冰洁 Wang, J.R. Weaver, K.E. Whitaker, C.C. Williams, A. Zitrin, The Astrophysical Journal 978 (2024).","ama":"Labbe I, Greene JE, Bezanson R, et al. UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA. <i>The Astrophysical Journal</i>. 2024;978. doi:<a href=\"https://doi.org/10.3847/1538-4357/ad3551\">10.3847/1538-4357/ad3551</a>","ieee":"I. Labbe <i>et al.</i>, “UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA,” <i>The Astrophysical Journal</i>, vol. 978. IOP Publishing, 2024.","apa":"Labbe, I., Greene, J. E., Bezanson, R., Fujimoto, S., Furtak, L. J., Goulding, A. D., … Zitrin, A. (2024). UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad3551\">https://doi.org/10.3847/1538-4357/ad3551</a>","chicago":"Labbe, Ivo, Jenny E. Greene, Rachel Bezanson, Seiji Fujimoto, Lukas J. Furtak, Andy D. Goulding, Jorryt J Matthee, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 &#60; z &#60; 7 with JWST and ALMA.” <i>The Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad3551\">https://doi.org/10.3847/1538-4357/ad3551</a>."},"month":"12","publication_status":"published","type":"journal_article","author":[{"full_name":"Labbe, Ivo","first_name":"Ivo","last_name":"Labbe"},{"first_name":"Jenny E.","full_name":"Greene, Jenny E.","last_name":"Greene"},{"last_name":"Bezanson","full_name":"Bezanson, Rachel","first_name":"Rachel"},{"last_name":"Fujimoto","full_name":"Fujimoto, Seiji","first_name":"Seiji"},{"last_name":"Furtak","first_name":"Lukas J.","full_name":"Furtak, Lukas J."},{"last_name":"Goulding","full_name":"Goulding, Andy D.","first_name":"Andy D."},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"last_name":"Oesch","first_name":"Pascal A.","full_name":"Oesch, Pascal A."},{"first_name":"Hakim","full_name":"Atek, Hakim","last_name":"Atek"},{"last_name":"Brammer","full_name":"Brammer, Gabriel","first_name":"Gabriel"},{"last_name":"Chemerynska","first_name":"Iryna","full_name":"Chemerynska, Iryna"},{"full_name":"Coe, Dan","first_name":"Dan","last_name":"Coe"},{"last_name":"Cutler","full_name":"Cutler, Sam E.","first_name":"Sam E."},{"last_name":"Dayal","full_name":"Dayal, Pratika","first_name":"Pratika"},{"full_name":"Feldmann, Robert","first_name":"Robert","last_name":"Feldmann"},{"first_name":"Marijn","full_name":"Franx, Marijn","last_name":"Franx"},{"last_name":"Glazebrook","full_name":"Glazebrook, Karl","first_name":"Karl"},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"last_name":"Maseda","full_name":"Maseda, Michael","first_name":"Michael"},{"last_name":"Marchesini","first_name":"Danilo","full_name":"Marchesini, Danilo"},{"first_name":"Themiya","full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara"},{"last_name":"Nelson","first_name":"Erica J.","full_name":"Nelson, Erica J."},{"last_name":"Pan","full_name":"Pan, Richard","first_name":"Richard"},{"last_name":"Papovich","first_name":"Casey","full_name":"Papovich, Casey"},{"full_name":"Price, Sedona H.","first_name":"Sedona H.","last_name":"Price"},{"full_name":"Suess, Katherine A.","first_name":"Katherine A.","last_name":"Suess"},{"last_name":"Wang","full_name":"Wang, Bingjie 冰洁","first_name":"Bingjie 冰洁"},{"full_name":"Weaver, John R.","first_name":"John R.","last_name":"Weaver"},{"first_name":"Katherine E.","full_name":"Whitaker, Katherine E.","last_name":"Whitaker"},{"last_name":"Williams","first_name":"Christina C.","full_name":"Williams, Christina C."},{"last_name":"Zitrin","first_name":"Adi","full_name":"Zitrin, Adi"}],"file_date_updated":"2026-02-10T06:44:24Z","quality_controlled":"1","status":"public","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"ddc":["520"],"file":[{"access_level":"open_access","file_size":5041924,"file_id":"21201","checksum":"825c35ebd26e292c8a5c2bffac327854","content_type":"application/pdf","relation":"main_file","date_created":"2026-02-10T06:44:24Z","date_updated":"2026-02-10T06:44:24Z","success":1,"file_name":"2024_AstrophysicalJourn_Labbe.pdf","creator":"dernst"}],"date_created":"2026-01-28T15:26:12Z","date_updated":"2026-02-10T06:49:49Z","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"oa":1,"PlanS_conform":"1","department":[{"_id":"JoMa"}],"_id":"21064","article_number":"92","intvolume":"       978","scopus_import":"1","title":"UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA","article_type":"original","date_published":"2024-12-26T00:00:00Z","OA_type":"gold","day":"26","acknowledgement":"I.L. acknowledges support from Australian Research Council Future Fellowship FT220100798. J.E.G. and A.D.G acknowledge support from NSF/AAG grant #1007094, and J.E.G. also acknowledges support from NSF/AAG grant #1007052. L.J.F. and A.Z. acknowledge support by Grant No. 2020750 from the United States–Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (“ODIN”) and from the European Commission’s and University of Groningen’s CO-FUND Rosalind Franklin program. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. This paper makes use of the ALMA data: ADS/JAO. ALMA #2022.1.00073.S, 2018.1.00035.L, and 2013.1.00999.S. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation.","fulldoi":"https://doi.org/10.3847/1538-4357/ad3551","year":"2024","doi":"10.3847/1538-4357/ad3551","volume":978,"abstract":[{"text":"The James Webb Space Telescope (JWST) is revolutionizing our knowledge of z > 5 galaxies and their actively accreting black holes. Using the JWST Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam Observations before the Epoch of Reionization (UNCOVER) in the lensing field A2744, we report the identification of a sample of little red dots at 3 < zphot < 7 that likely contain highly reddened accreting supermassive black holes. Using a NIRCam-only selection to F444W < 27.7 mag, we find 26 sources over the ∼45 arcmin^2 field that are blue in F115W − F200W ∼ 0 (or βUV ∼ –2.0 for fλ ∝ λ^β), red in F200W − F444W = 1−4 (βopt ∼ +2.0), and are dominated by a point-source-like central component. Of the 20 sources with deep Atacama Large Millimeter/submillimeter Array (ALMA) 1.2 mm coverage, none are detected individually or in a stack. For the majority of the sample, spectral energy distribution fits to the JWST+ALMA observations prefer models with hot dust rather than obscured star formation to reproduce the red NIRCam colors and ALMA 1.2 mm nondetections. While compact dusty star formation cannot be ruled out, the combination of extremely small sizes (〈re〉 ≈ 50 pc after correction for magnification), red rest-frame optical slopes, and hot dust can be explained by reddened broad-line active galactic nuclei (AGNs). Our targets have faint M1450 ≈ −14 to −18 mag but inferred bolometric luminosities of Lbol = 10^43–10^46 erg s^−1, reflecting their obscured nature. If the candidates are confirmed as AGNs with upcoming UNCOVER spectroscopy, then we have found an abundant population of reddened luminous AGNs that are at least ten times more numerous than UV-luminous AGNs at the same intrinsic bolometric luminosity.","lang":"eng"}],"arxiv":1,"publisher":"IOP Publishing","publication":"The Astrophysical Journal","external_id":{"arxiv":["2306.07320"]}},{"publisher":"Zenodo","date_updated":"2026-02-23T11:49:05Z","date_created":"2026-02-17T12:52:26Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.13934991"}],"abstract":[{"lang":"eng","text":"No description provided."}],"related_material":{"record":[{"relation":"used_for_analysis_in","id":"21251","status":"public"}]},"OA_place":"repository","status":"public","doi":"10.5281/ZENODO.13934991","year":"2024","has_accepted_license":"1","OA_type":"green","day":"15","fulldoi":"https://doi.org/10.5281/ZENODO.13934991","date_published":"2024-10-15T00:00:00Z","type":"research_data_reference","author":[{"first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","last_name":"Santana de Freitas Amaral"}],"title":"archaeal_membranes : code and examples","month":"10","_id":"21304","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","citation":{"ama":"Santana de Freitas Amaral M. archaeal_membranes : code and examples. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>","apa":"Santana de Freitas Amaral, M. (2024). archaeal_membranes : code and examples. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>","ieee":"M. Santana de Freitas Amaral, “archaeal_membranes : code and examples.” Zenodo, 2024.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal_membranes : Code and Examples.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>.","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal_membranes : Code and Examples</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>.","short":"M. Santana de Freitas Amaral, (2024).","ista":"Santana de Freitas Amaral M. 2024. archaeal_membranes : code and examples, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>."},"department":[{"_id":"AnSa"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"21918","status":"public"}]},"status":"public","date_updated":"2026-06-12T12:43:34Z","date_created":"2026-06-09T12:14:08Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Preprint","citation":{"ista":"Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>.","short":"K. Khudiakova, F. Boenkost, J.N. Tourniaire, BioRxiv (n.d.).","mla":"Khudiakova, Kseniia, et al. “Genealogies under Purifying Selection.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>.","chicago":"Khudiakova, Kseniia, Florin Boenkost, and Julie N Tourniaire. “Genealogies under Purifying Selection.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.15.618444\">https://doi.org/10.1101/2024.10.15.618444</a>.","ama":"Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>","ieee":"K. Khudiakova, F. Boenkost, and J. N. Tourniaire, “Genealogies under purifying selection,” <i>bioRxiv</i>. .","apa":"Khudiakova, K., Boenkost, F., &#38; Tourniaire, J. N. (n.d.). Genealogies under purifying selection. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.15.618444\">https://doi.org/10.1101/2024.10.15.618444</a>"},"month":"10","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"draft","author":[{"orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia"},{"last_name":"Boenkost","first_name":"Florin","full_name":"Boenkost, Florin"},{"full_name":"Tourniaire, Julie N","first_name":"Julie N","last_name":"Tourniaire","id":"5dc06dd8-8e51-11ec-9170-8d9c450cc216"}],"type":"preprint","project":[{"grant_number":"26293","name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8"},{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"abstract":[{"text":"Selection against deleterious mutations, called purifying selection, plays a central role in evolution and acts in all populations. It is known that the genetic patterns observed in genomic regions undergoing purifying selection differ from those resulting from neutral evolution. However, a comprehensive understanding of the underlying mechanisms shaping those patterns is still lacking.\r\n\r\nIn the present work, we use simulations combined with a genealogical approach to identify the effect of purifying selection on the ancestry and thus on the genetic diversity. Our analysis relies on the postulate that the genealogy belongs to the universality class of Beta-coalescents. Under this assumption, we derive statistics measuring the distortion of the genealogy. This approach allows us to consider a wide range of regimes (i.e. arbitrary selection and mutation strengths) and uncover a rich phase diagram. We find that, for strong selection, the limiting genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple mergers in the genealogical structures. Our results show that while multiple-merger coalescents are often interpreted as the signature of selective sweeps in rapidly adapting populations, these structures can also appear in the context of Muller’s ratchet.","lang":"eng"}],"ec_funded":1,"fulldoi":"https://doi.org/10.1101/2024.10.15.618444","acknowledgement":"This work was supported by the Austrian Academy of Science, DOC fellowship No 26293 (K.K.) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 (J.T.). Simulations were performed on the ISTA High-performance Computing Cluster.","OA_type":"green","day":"18","year":"2024","doi":"10.1101/2024.10.15.618444","publication":"bioRxiv","main_file_link":[{"url":"https://doi.org/10.1101/2024.10.15.618444","open_access":"1"}],"_id":"21967","corr_author":"1","oa":1,"department":[{"_id":"NiBa"},{"_id":"JaMa"}],"date_published":"2024-10-18T00:00:00Z","title":"Genealogies under purifying selection"},{"issue":"4","ddc":["570"],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","date_created":"2023-11-16T12:36:51Z","date_updated":"2024-07-16T08:23:24Z","file":[{"success":1,"creator":"dernst","file_name":"2024_Brain_Kaiyrzhanov.pdf","relation":"main_file","date_updated":"2024-07-16T08:22:13Z","date_created":"2024-07-16T08:22:13Z","content_type":"application/pdf","checksum":"0ee7a8ab9300225d60968f7a3e3cfa0d","file_id":"17254","access_level":"open_access","file_size":2641456}],"month":"04","oa_version":"Submitted Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ista":"Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2024. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 147(4), 1436–1456.","short":"R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain 147 (2024) 1436–1456.","mla":"Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” <i>Brain</i>, vol. 147, no. 4, Oxford University Press, 2024, pp. 1436–56, doi:<a href=\"https://doi.org/10.1093/brain/awad380\">10.1093/brain/awad380</a>.","chicago":"Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” <i>Brain</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/brain/awad380\">https://doi.org/10.1093/brain/awad380</a>.","ama":"Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. <i>Brain</i>. 2024;147(4):1436-1456. doi:<a href=\"https://doi.org/10.1093/brain/awad380\">10.1093/brain/awad380</a>","apa":"Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2024). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. <i>Brain</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awad380\">https://doi.org/10.1093/brain/awad380</a>","ieee":"R. Kaiyrzhanov <i>et al.</i>, “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” <i>Brain</i>, vol. 147, no. 4. Oxford University Press, pp. 1436–1456, 2024."},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","extern":"1","file_date_updated":"2024-07-16T08:22:13Z","author":[{"last_name":"Kaiyrzhanov","full_name":"Kaiyrzhanov, Rauan","first_name":"Rauan"},{"full_name":"Rad, Aboulfazl","first_name":"Aboulfazl","last_name":"Rad"},{"first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia","last_name":"Lin"},{"full_name":"Bertoli-Avella, Aida","first_name":"Aida","last_name":"Bertoli-Avella"},{"last_name":"Kallemeijn","first_name":"Wouter W","full_name":"Kallemeijn, Wouter W"},{"full_name":"Godwin, Annie","first_name":"Annie","last_name":"Godwin"},{"last_name":"Zaki","full_name":"Zaki, Maha S","first_name":"Maha S"},{"last_name":"Huang","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin","first_name":"Kevin"},{"full_name":"Lau, Tracy","first_name":"Tracy","last_name":"Lau"},{"full_name":"Petree, Cassidy","first_name":"Cassidy","last_name":"Petree"},{"last_name":"Efthymiou","full_name":"Efthymiou, Stephanie","first_name":"Stephanie"},{"last_name":"Ghayoor Karimiani","full_name":"Ghayoor Karimiani, Ehsan","first_name":"Ehsan"},{"last_name":"Hempel","first_name":"Maja","full_name":"Hempel, Maja"},{"last_name":"Normand","full_name":"Normand, Elizabeth A","first_name":"Elizabeth A"},{"first_name":"Sabine","full_name":"Rudnik-Schöneborn, Sabine","last_name":"Rudnik-Schöneborn"},{"last_name":"Schatz","first_name":"Ulrich A","full_name":"Schatz, Ulrich A"},{"first_name":"Marc P","full_name":"Baggelaar, Marc P","last_name":"Baggelaar"},{"last_name":"Ilyas","full_name":"Ilyas, Muhammad","first_name":"Muhammad"},{"full_name":"Sultan, Tipu","first_name":"Tipu","last_name":"Sultan"},{"first_name":"Javeria Raza","full_name":"Alvi, Javeria Raza","last_name":"Alvi"},{"last_name":"Ganieva","full_name":"Ganieva, Manizha","first_name":"Manizha"},{"full_name":"Fowler, Ben","first_name":"Ben","last_name":"Fowler"},{"last_name":"Aanicai","first_name":"Ruxandra","full_name":"Aanicai, Ruxandra"},{"first_name":"Gulsen","full_name":"Akay Tayfun, Gulsen","last_name":"Akay Tayfun"},{"first_name":"Abdulaziz","full_name":"Al Saman, Abdulaziz","last_name":"Al Saman"},{"last_name":"Alswaid","full_name":"Alswaid, Abdulrahman","first_name":"Abdulrahman"},{"first_name":"Nafise","full_name":"Amiri, Nafise","last_name":"Amiri"},{"last_name":"Asilova","first_name":"Nilufar","full_name":"Asilova, Nilufar"},{"full_name":"Shotelersuk, Vorasuk","first_name":"Vorasuk","last_name":"Shotelersuk"},{"last_name":"Yeetong","full_name":"Yeetong, Patra","first_name":"Patra"},{"full_name":"Azam, Matloob","first_name":"Matloob","last_name":"Azam"},{"last_name":"Babaei","full_name":"Babaei, Meisam","first_name":"Meisam"},{"first_name":"Gholamreza","full_name":"Bahrami Monajemi, Gholamreza","last_name":"Bahrami Monajemi"},{"last_name":"Mohammadi","first_name":"Pouria","full_name":"Mohammadi, Pouria"},{"last_name":"Samie","first_name":"Saeed","full_name":"Samie, Saeed"},{"last_name":"Banu","first_name":"Selina Husna","full_name":"Banu, Selina Husna"},{"last_name":"Basto","full_name":"Basto, Jorge Pinto","first_name":"Jorge Pinto"},{"last_name":"Kortüm","first_name":"Fanny","full_name":"Kortüm, Fanny"},{"last_name":"Bauer","full_name":"Bauer, Mislen","first_name":"Mislen"},{"last_name":"Bauer","first_name":"Peter","full_name":"Bauer, Peter"},{"first_name":"Christian","full_name":"Beetz, Christian","last_name":"Beetz"},{"first_name":"Masoud","full_name":"Garshasbi, Masoud","last_name":"Garshasbi"},{"first_name":"Awatif","full_name":"Hameed Issa, Awatif","last_name":"Hameed Issa"},{"first_name":"Wafaa","full_name":"Eyaid, Wafaa","last_name":"Eyaid"},{"full_name":"Ahmed, Hind","first_name":"Hind","last_name":"Ahmed"},{"full_name":"Hashemi, Narges","first_name":"Narges","last_name":"Hashemi"},{"first_name":"Kazem","full_name":"Hassanpour, Kazem","last_name":"Hassanpour"},{"last_name":"Herman","full_name":"Herman, Isabella","first_name":"Isabella"},{"last_name":"Ibrohimov","full_name":"Ibrohimov, Sherozjon","first_name":"Sherozjon"},{"last_name":"Abdul-Majeed","first_name":"Ban A","full_name":"Abdul-Majeed, Ban A"},{"first_name":"Maria","full_name":"Imdad, Maria","last_name":"Imdad"},{"full_name":"Isrofilov, Maksudjon","first_name":"Maksudjon","last_name":"Isrofilov"},{"last_name":"Kaiyal","full_name":"Kaiyal, Qassem","first_name":"Qassem"},{"full_name":"Khan, Suliman","first_name":"Suliman","last_name":"Khan"},{"full_name":"Kirmse, Brian","first_name":"Brian","last_name":"Kirmse"},{"full_name":"Koster, Janet","first_name":"Janet","last_name":"Koster"},{"full_name":"Lourenço, Charles Marques","first_name":"Charles Marques","last_name":"Lourenço"},{"full_name":"Mitani, Tadahiro","first_name":"Tadahiro","last_name":"Mitani"},{"last_name":"Moldovan","first_name":"Oana","full_name":"Moldovan, Oana"},{"last_name":"Murphy","first_name":"David","full_name":"Murphy, David"},{"first_name":"Maryam","full_name":"Najafi, Maryam","last_name":"Najafi"},{"full_name":"Pehlivan, Davut","first_name":"Davut","last_name":"Pehlivan"},{"last_name":"Rocha","first_name":"Maria Eugenia","full_name":"Rocha, Maria Eugenia"},{"last_name":"Salpietro","first_name":"Vincenzo","full_name":"Salpietro, Vincenzo"},{"last_name":"Schmidts","first_name":"Miriam","full_name":"Schmidts, Miriam"},{"full_name":"Shalata, Adel","first_name":"Adel","last_name":"Shalata"},{"first_name":"Mohammad","full_name":"Mahroum, Mohammad","last_name":"Mahroum"},{"last_name":"Talbeya","first_name":"Jawabreh Kassem","full_name":"Talbeya, Jawabreh Kassem"},{"last_name":"Taylor","first_name":"Robert W","full_name":"Taylor, Robert W"},{"last_name":"Vazquez","first_name":"Dayana","full_name":"Vazquez, Dayana"},{"last_name":"Vetro","full_name":"Vetro, Annalisa","first_name":"Annalisa"},{"full_name":"Waterham, Hans R","first_name":"Hans R","last_name":"Waterham"},{"first_name":"Mashaya","full_name":"Zaman, Mashaya","last_name":"Zaman"},{"first_name":"Tina A","full_name":"Schrader, Tina A","last_name":"Schrader"},{"full_name":"Chung, Wendy K","first_name":"Wendy K","last_name":"Chung"},{"first_name":"Renzo","full_name":"Guerrini, Renzo","last_name":"Guerrini"},{"last_name":"Lupski","full_name":"Lupski, James R","first_name":"James R"},{"last_name":"Gleeson","full_name":"Gleeson, Joseph","first_name":"Joseph"},{"last_name":"Suri","first_name":"Mohnish","full_name":"Suri, Mohnish"},{"last_name":"Jamshidi","full_name":"Jamshidi, Yalda","first_name":"Yalda"},{"last_name":"Bhatia","full_name":"Bhatia, Kailash P","first_name":"Kailash P"},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"full_name":"Schrader, Michael","first_name":"Michael","last_name":"Schrader"},{"full_name":"Severino, Mariasavina","first_name":"Mariasavina","last_name":"Severino"},{"last_name":"Guille","full_name":"Guille, Matthew","first_name":"Matthew"},{"last_name":"Tate","full_name":"Tate, Edward W","first_name":"Edward W"},{"full_name":"Varshney, Gaurav K","first_name":"Gaurav K","last_name":"Varshney"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"}],"type":"journal_article","publication_status":"published","abstract":[{"text":"The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.","lang":"eng"}],"volume":147,"year":"2024","doi":"10.1093/brain/awad380","fulldoi":"https://doi.org/10.1093/brain/awad380","keyword":["Neurology (clinical)"],"day":"01","pmid":1,"publication":"Brain","external_id":{"pmid":["37951597"]},"page":"1436-1456","publisher":"Oxford University Press","_id":"14543","oa":1,"department":[{"_id":"GradSch"}],"publication_identifier":{"issn":["0006-8950"],"eissn":["1460-2156"]},"date_published":"2024-04-01T00:00:00Z","article_type":"original","title":"Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders","scopus_import":"1","intvolume":"       147"},{"_id":"15379","department":[{"_id":"PeJo"}],"oa":1,"publication_identifier":{"eissn":["1521-1878"],"issn":["0265-9247"]},"article_type":"review","date_published":"2024-07-01T00:00:00Z","article_number":" 2400006","intvolume":"        46","title":"Tuning synaptic strength by regulation of AMPA glutamate receptor localization","scopus_import":"1","abstract":[{"lang":"eng","text":"Long-term potentiation (LTP) of excitatory synapses is a leading model to explain the concept of information storage in the brain. Multiple mechanisms contribute to LTP, but central amongst them is an increased sensitivity of the postsynaptic membrane to neurotransmitter release. This sensitivity is predominantly determined by the abundance and localization of AMPA-type glutamate receptors (AMPARs). A combination of AMPAR structural data, super-resolution imaging of excitatory synapses, and an abundance of electrophysiological studies are providing an ever-clearer picture of how AMPARs are recruited and organized at synaptic junctions. Here, we review the latest insights into this process, and discuss how both cytoplasmic and extracellular receptor elements cooperate to tune the AMPAR response at the hippocampal CA1 synapse."}],"volume":46,"doi":"10.1002/bies.202400006","year":"2024","acknowledgement":"The authors thank Alexander Scrutton and James M. Krieger for comments on the manuscript. The authors also acknowledge Shraddha Nayak for help with Figure 1B design. This work was supported by grants from the Medical Research Council (MC_U105174197), the BBSRC (BB/N002113/1), and the Wellcome Trust (223194/Z/21/Z) to IHG.","day":"01","OA_type":"hybrid","fulldoi":"https://doi.org/10.1002/bies.202400006","pmid":1,"publisher":"Wiley","external_id":{"pmid":["38693811"],"isi":["001214545700001"]},"publication":"BioEssays","month":"07","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","citation":{"ama":"Stockwell I, Watson J, Greger IH. Tuning synaptic strength by regulation of AMPA glutamate receptor localization. <i>BioEssays</i>. 2024;46(7). doi:<a href=\"https://doi.org/10.1002/bies.202400006\">10.1002/bies.202400006</a>","apa":"Stockwell, I., Watson, J., &#38; Greger, I. H. (2024). Tuning synaptic strength by regulation of AMPA glutamate receptor localization. <i>BioEssays</i>. Wiley. <a href=\"https://doi.org/10.1002/bies.202400006\">https://doi.org/10.1002/bies.202400006</a>","ieee":"I. Stockwell, J. Watson, and I. H. Greger, “Tuning synaptic strength by regulation of AMPA glutamate receptor localization,” <i>BioEssays</i>, vol. 46, no. 7. Wiley, 2024.","chicago":"Stockwell, Imogen, Jake Watson, and Ingo H. Greger. “Tuning Synaptic Strength by Regulation of AMPA Glutamate Receptor Localization.” <i>BioEssays</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/bies.202400006\">https://doi.org/10.1002/bies.202400006</a>.","mla":"Stockwell, Imogen, et al. “Tuning Synaptic Strength by Regulation of AMPA Glutamate Receptor Localization.” <i>BioEssays</i>, vol. 46, no. 7, 2400006, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/bies.202400006\">10.1002/bies.202400006</a>.","ista":"Stockwell I, Watson J, Greger IH. 2024. Tuning synaptic strength by regulation of AMPA glutamate receptor localization. BioEssays. 46(7), 2400006.","short":"I. Stockwell, J. Watson, I.H. Greger, BioEssays 46 (2024)."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","file_date_updated":"2025-01-09T09:31:05Z","type":"journal_article","author":[{"full_name":"Stockwell, Imogen","first_name":"Imogen","last_name":"Stockwell"},{"full_name":"Watson, Jake","first_name":"Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Ingo H.","full_name":"Greger, Ingo H.","last_name":"Greger"}],"publication_status":"published","isi":1,"issue":"7","language":[{"iso":"eng"}],"ddc":["570"],"OA_place":"publisher","status":"public","has_accepted_license":"1","date_created":"2024-05-12T22:01:02Z","date_updated":"2025-09-08T07:25:02Z","file":[{"date_created":"2025-01-09T09:31:05Z","relation":"main_file","date_updated":"2025-01-09T09:31:05Z","file_name":"2024_BioEssays_Stockwell.pdf","creator":"dernst","success":1,"checksum":"dc8be74156657e8aab12a9d613233ee3","content_type":"application/pdf","file_id":"18801","file_size":775825,"access_level":"open_access"}]},{"day":"22","keyword":["nuclear magnetic resonance","NMR","cellwall","structural biology","spectroscopy"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:17042","status":"public","has_accepted_license":"1","year":"2024","doi":"10.15479/AT:ISTA:17042","related_material":{"record":[{"id":"17291","relation":"used_in_publication","status":"public"}]},"ddc":["570"],"abstract":[{"lang":"eng","text":"Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13C-13C and heteronuclear H-N, H-C and N-C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples. "}],"file":[{"date_created":"2024-05-22T12:05:13Z","date_updated":"2024-05-22T12:05:13Z","relation":"main_file","creator":"pschanda","file_name":"Read_me.txt","success":1,"checksum":"eb55f0988342d927702353b75e07edfa","content_type":"text/plain","file_id":"17043","file_size":2132,"access_level":"open_access"},{"file_size":755704888,"access_level":"open_access","file_id":"17044","content_type":"application/zip","checksum":"3393592acaf5ee1e032052c236780914","creator":"pschanda","file_name":"raw_data_CryoMAS_cyronebacteria.zip","success":1,"relation":"main_file","date_created":"2024-05-22T12:17:10Z","date_updated":"2024-05-22T12:17:10Z"}],"publisher":"Institute of Science and Technology Austria","date_created":"2024-05-22T12:04:54Z","date_updated":"2025-09-09T12:01:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","corr_author":"1","oa":1,"department":[{"_id":"PaSc"}],"oa_version":"Published Version","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"citation":{"mla":"Schanda, Paul. <i>Raw Data to “MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17042\">10.15479/AT:ISTA:17042</a>.","short":"P. Schanda, (2024).","ista":"Schanda P. 2024. Raw data to ‘MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17042\">10.15479/AT:ISTA:17042</a>.","ama":"Schanda P. Raw data to “MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17042\">10.15479/AT:ISTA:17042</a>","apa":"Schanda, P. (2024). Raw data to “MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17042\">https://doi.org/10.15479/AT:ISTA:17042</a>","ieee":"P. Schanda, “Raw data to ‘MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.’” Institute of Science and Technology Austria, 2024.","chicago":"Schanda, Paul. “Raw Data to ‘MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17042\">https://doi.org/10.15479/AT:ISTA:17042</a>."},"month":"05","_id":"17042","type":"research_data","author":[{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul"}],"title":"Raw data to \"MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments\"","file_date_updated":"2024-05-22T12:17:10Z","date_published":"2024-05-22T00:00:00Z","contributor":[{"contributor_type":"data_collector","first_name":"Alicia","last_name":"Vallet"},{"first_name":"Isabel ","contributor_type":"data_collector","last_name":"Ayala"},{"last_name":"Perrone","contributor_type":"data_collector","first_name":"Barbara"},{"last_name":"Hassan","first_name":"Alia","contributor_type":"data_collector"},{"last_name":"Bougault","contributor_type":"data_collector","first_name":"Catherine"}]},{"article_type":"original","date_published":"2024-05-29T00:00:00Z","article_number":"401","intvolume":"        24","scopus_import":"1","title":"The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study","_id":"17122","publication_identifier":{"eissn":["1471-244X"]},"department":[{"_id":"PeJo"}],"oa":1,"publisher":"Springer Nature","external_id":{"pmid":["38811916"]},"publication":"BMC Psychiatry","pmid":1,"volume":24,"abstract":[{"text":"Background: Motor alterations and lowered physical activity are common in affective disorders. Previous research has indicated a link between depressive symptoms and declining muscle strength primarily focusing on the elderly but not younger individuals. Thus, we aimed to evaluate the relationship between mood and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy. The study was carried out as a prospective observational study at a German psychiatric university hospital between September 2021 and March 2022.\r\nMethods: Employing a standardized strength circuit consisting of computerized strength training devices, we measured the maximal muscle strength (Fmax) using three repetitions maximum across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3) over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood lipid profiling in a clinical setting. For analysis of psychopharmacotherapy, medication was split into activating (AM) and inhibiting (IM) medication and dosages were normalized by the respective WHO defined daily dose.\r\nResults: While we observed a significant decrease of the MADRS score and increase of the relative total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001), we did not reveal a significant bivariate correlation between disease severity (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with longer disease history displayed reduced rTFmax (p = .048). IM was significantly associated with decreased rTFmax (p = .032). Regression models provide a more substantial effect of gender, age, and IM on muscle strength than the depressive episode itself (p < .001).\r\nConclusions: The results of the study indicate that disease severity and muscle strength are not associated in young to middle-aged inpatients with affective disorders using a strength circuit as observational measurement. Future research will be needed to differentiate the effect of medication, gender, and age on muscle strength and to develop interventions for prevention of muscle weakness, especially in younger patients with chronic affective illnesses.","lang":"eng"}],"acknowledgement":"This work was supported by the project ‘Fellows Ride’ of the Thomas Lurz und Dieter Schneider Stiftung and by the ‘Würzburger Bündnis gegen Depression’ (to S.K.-S).\r\nOpen Access funding enabled and organized by Projekt DEAL.","day":"29","fulldoi":"https://doi.org/10.1186/s12888-024-05849-2","year":"2024","doi":"10.1186/s12888-024-05849-2","file_date_updated":"2024-06-10T10:44:26Z","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"last_name":"Ramming","full_name":"Ramming, Hannah","first_name":"Hannah"},{"last_name":"Theuerkauf","first_name":"Linda","full_name":"Theuerkauf, Linda"},{"first_name":"Olaf","full_name":"Hoos, Olaf","last_name":"Hoos"},{"id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","last_name":"Lichter","orcid":"0000-0002-1485-0351","first_name":"Katharina","full_name":"Lichter, Katharina"},{"last_name":"Kittel-Schneider","first_name":"Sarah","full_name":"Kittel-Schneider, Sarah"}],"citation":{"ista":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. 2024. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. BMC Psychiatry. 24, 401.","short":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, S. Kittel-Schneider, BMC Psychiatry 24 (2024).","mla":"Ramming, Hannah, et al. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>, vol. 24, 401, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>.","chicago":"Ramming, Hannah, Linda Theuerkauf, Olaf Hoos, Katharina Lichter, and Sarah Kittel-Schneider. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>.","ama":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. 2024;24. doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>","apa":"Ramming, H., Theuerkauf, L., Hoos, O., Lichter, K., &#38; Kittel-Schneider, S. (2024). The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>","ieee":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, and S. Kittel-Schneider, “The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study,” <i>BMC Psychiatry</i>, vol. 24. Springer Nature, 2024."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","date_updated":"2025-04-23T07:51:51Z","date_created":"2024-06-09T22:01:01Z","file":[{"file_size":2320147,"access_level":"open_access","file_id":"17131","checksum":"5df60d3c9388955c5b682ea34748d59d","content_type":"application/pdf","date_updated":"2024-06-10T10:44:26Z","date_created":"2024-06-10T10:44:26Z","relation":"main_file","file_name":"2024_BMCPsychiatry_Ramming.pdf","creator":"dernst","success":1}],"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1"},{"citation":{"ieee":"A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per CPU core is requested?,” in <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, Grundlsee, Austria, 2024, p. 46.","apa":"Schlögl, A., Khalid, W., Elefante, S., &#38; Stadlbauer, S. (2024). How much memory per CPU core is requested? In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i> (p. 46). Grundlsee, Austria: EuroCC Austria. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>","ama":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core is requested? In: <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>. EuroCC Austria; 2024:46. doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>","chicago":"Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer. “How Much Memory per CPU Core Is Requested?” In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, 46. EuroCC Austria, 2024. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>.","mla":"Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, EuroCC Austria, 2024, p. 46, doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>.","short":"A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46.","ista":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian HPC Meeting, 46."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"06","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"Grundlsee, Austria","name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2024-06-10","end_date":"2024-06-13"},"file_date_updated":"2024-06-17T09:36:51Z","quality_controlled":"1","publication_status":"published","author":[{"first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"first_name":"Waleed","full_name":"Khalid, Waleed","id":"097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1","last_name":"Khalid"},{"full_name":"Elefante, Stefano","first_name":"Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan","first_name":"Stephan"}],"type":"conference_abstract","language":[{"iso":"eng"}],"ddc":["000"],"has_accepted_license":"1","status":"public","date_updated":"2024-06-17T09:40:37Z","date_created":"2024-06-14T09:06:36Z","file":[{"access_level":"open_access","file_size":206746,"file_id":"17153","checksum":"f7d3dded6df2dcdb4818904cf2e1c183","content_type":"application/pdf","date_created":"2024-06-17T09:36:51Z","relation":"main_file","date_updated":"2024-06-17T09:36:51Z","success":1,"creator":"dernst","file_name":"2024_ASHPC_Schloegl.pdf"}],"_id":"17139","publication_identifier":{"isbn":["9783200096455"]},"department":[{"_id":"ScienComp"}],"oa":1,"date_published":"2024-06-13T00:00:00Z","title":"How much memory per CPU core is requested?","fulldoi":"https://doi.org/10.25365/phaidra.463","day":"13","doi":"10.25365/phaidra.463","year":"2024","publication":"ASHPC24 - Austrian-Slovenian HPC Meeting 2024","page":"46","publisher":"EuroCC Austria"},{"month":"12","citation":{"ama":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. Protein cage directed assembly of binary nanoparticle superlattices. <i>Advanced Science</i>. 2024;11(45). doi:<a href=\"https://doi.org/10.1002/advs.202408416\">10.1002/advs.202408416</a>","ieee":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J. V. I. Timonen, and M. A. Kostiainen, “Protein cage directed assembly of binary nanoparticle superlattices,” <i>Advanced Science</i>, vol. 11, no. 45. Wiley, 2024.","apa":"Zhou, Y., Shaukat, A., Seitsonen, J., Rigoni, C., Timonen, J. V. I., &#38; Kostiainen, M. A. (2024). Protein cage directed assembly of binary nanoparticle superlattices. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.202408416\">https://doi.org/10.1002/advs.202408416</a>","chicago":"Zhou, Yu, Ahmed Shaukat, Jani Seitsonen, Carlo Rigoni, Jaakko V.I. Timonen, and Mauri A. Kostiainen. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” <i>Advanced Science</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/advs.202408416\">https://doi.org/10.1002/advs.202408416</a>.","mla":"Zhou, Yu, et al. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” <i>Advanced Science</i>, vol. 11, no. 45, 2408416, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/advs.202408416\">10.1002/advs.202408416</a>.","short":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen, Advanced Science 11 (2024).","ista":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. 2024. Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. 11(45), 2408416."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","DOAJ_listed":"1","article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","file_date_updated":"2025-01-13T09:16:25Z","author":[{"last_name":"Zhou","first_name":"Yu","full_name":"Zhou, Yu"},{"full_name":"Shaukat, Ahmed","first_name":"Ahmed","last_name":"Shaukat"},{"first_name":"Jani","full_name":"Seitsonen, Jani","last_name":"Seitsonen"},{"id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0","last_name":"Rigoni","first_name":"Carlo","full_name":"Rigoni, Carlo"},{"last_name":"Timonen","full_name":"Timonen, Jaakko V.I.","first_name":"Jaakko V.I."},{"first_name":"Mauri A.","full_name":"Kostiainen, Mauri A.","last_name":"Kostiainen"}],"type":"journal_article","publication_status":"published","isi":1,"issue":"45","OA_place":"publisher","ddc":["540"],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","date_updated":"2025-09-08T14:20:31Z","date_created":"2024-10-20T22:02:07Z","file":[{"checksum":"00451eeb2c9eecf1ff41ad243c793a51","content_type":"application/pdf","date_created":"2025-01-13T09:16:25Z","date_updated":"2025-01-13T09:16:25Z","relation":"main_file","success":1,"file_name":"2024_AdvancedScience_Zhou.pdf","creator":"dernst","access_level":"open_access","file_size":7040083,"file_id":"18834"}],"_id":"18451","oa":1,"department":[{"_id":"RaKl"}],"publication_identifier":{"eissn":["2198-3844"]},"date_published":"2024-12-04T00:00:00Z","article_type":"original","title":"Protein cage directed assembly of binary nanoparticle superlattices","scopus_import":"1","intvolume":"        11","article_number":"2408416","abstract":[{"lang":"eng","text":"Inorganic nanoparticles can be assembled into superlattices with unique optical and magnetic properties arising from collective behavior. Protein cages can be utilized to guide this assembly by encapsulating nanoparticles and promoting their assembly into ordered structures. However, creating ordered multi-component structures with different protein cage types and sizes remains a challenge. Here, the co-crystallization of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized by opposing surface charges and unequal diameter is shown. Precise tuning of the electrostatic attraction between the cages enabled the preparation of binary crystals with dimensions up to several tens of micrometers. Additionally, binary metal nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles inside the cavities of the protein cages. The resulting structure adopts an AB2FCC configuration that also impacts the dipolar coupling between the particles and hence the optical properties of the crystals, providing key insight for the future preparation of plasmonic and magnetic nanoparticle metamaterials."}],"volume":11,"year":"2024","doi":"10.1002/advs.202408416","fulldoi":"https://doi.org/10.1002/advs.202408416","OA_type":"gold","day":"04","acknowledgement":"This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 101002258). The authors acknowledge the provision of facilities and technical support by Aalto University Bioeconomy Facilities and OtaNanoNanomicroscopy Center (Aalto-NMC). This work was carried out under the Academy of Finland's Centers of Excellence Programme, Life Inspired Hybrid Materials (LIBER) Center of Excellence (2022–2029), project number 346110 and 346112.","pmid":1,"publication":"Advanced Science","external_id":{"pmid":["39401426"],"isi":["001330745600001"]},"publisher":"Wiley"},{"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","has_accepted_license":"1","ddc":["570"],"OA_place":"publisher","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"19076"}]},"file":[{"file_id":"18625","file_size":800647957,"access_level":"open_access","creator":"symonova","file_name":"electro_physiology_data.zip","date_created":"2024-12-06T13:28:18Z","date_updated":"2024-12-09T10:24:25Z","relation":"main_file","content_type":"application/x-zip-compressed","checksum":"8b13990ca1a458ae3f3ae54c2e888564"},{"file_id":"18636","access_level":"open_access","file_size":828410832,"success":1,"file_name":"NN_vLGN_Ca_data.zip","creator":"symonova","date_updated":"2024-12-09T10:21:10Z","relation":"main_file","date_created":"2024-12-09T10:21:10Z","content_type":"application/x-zip-compressed","checksum":"c5a4d71c5f29c009c3d96a3244532afa"},{"file_id":"18637","file_size":505,"access_level":"open_access","relation":"main_file","date_created":"2024-12-09T12:54:55Z","date_updated":"2024-12-09T12:54:55Z","file_name":"readme.txt","creator":"symonova","success":1,"checksum":"63651df0186196969553dc48b467f6ab","content_type":"text/plain"}],"date_created":"2024-11-22T13:48:12Z","date_updated":"2026-06-18T18:12:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","citation":{"mla":"Vega Zuniga, Tomas A., et al. <i>A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","short":"T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024).","ista":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","ieee":"T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024.","apa":"Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., &#38; Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>","ama":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>","chicago":"Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"12","type":"research_data","author":[{"first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga"},{"last_name":"Sumser","id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","first_name":"Anton L"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","orcid":"0000-0003-2012-9947","first_name":"Olga","full_name":"Symonova, Olga"},{"orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"first_name":"Florian","full_name":"Schmidt, Florian","id":"A2EF226A-AF19-11E9-924C-0525E6697425","last_name":"Schmidt"},{"first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch"}],"file_date_updated":"2024-12-09T12:54:55Z","day":"09","acknowledgement":"Freyja Lange, Michael Schunn, and Todor Asenov","fulldoi":"https://doi.org/10.15479/AT:ISTA:18579","year":"2024","doi":"10.15479/AT:ISTA:18579","project":[{"grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425"},{"_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256"},{"name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"756502"},{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580"}],"abstract":[{"text":"Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al.  Relevant information can be found in the 'README.txt' files. ","lang":"eng"}],"ec_funded":1,"publisher":"Institute of Science and Technology Austria","corr_author":"1","department":[{"_id":"MaJö"}],"oa":1,"_id":"18579","title":"A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics","date_published":"2024-12-09T00:00:00Z"},{"status":"public","isi":1,"OA_place":"repository","language":[{"iso":"eng"}],"date_updated":"2025-09-09T12:00:51Z","date_created":"2025-01-05T23:01:56Z","conference":{"location":"Kolkata, India","end_date":"2024-12-13","name":"ASIACRYPT: Conference on the Theory and Application of Cryptology and Information Security","start_date":"2024-12-09"},"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"12","citation":{"mla":"Brzuska, Chris, et al. “Evasive LWE Assumptions: Definitions, Classes, and Counterexamples.” <i>30th International Conference on the Theory and Application of Cryptology and Information Security</i>, vol. 15487, Springer Nature, 2024, pp. 418–49, doi:<a href=\"https://doi.org/10.1007/978-981-96-0894-2_14\">10.1007/978-981-96-0894-2_14</a>.","ista":"Brzuska C, Ünal A, Woo IKY. 2024. Evasive LWE assumptions: Definitions, classes, and counterexamples. 30th International Conference on the Theory and Application of Cryptology and Information Security. ASIACRYPT: Conference on the Theory and Application of Cryptology and Information Security, LNCS, vol. 15487, 418–449.","short":"C. Brzuska, A. Ünal, I.K.Y. Woo, in:, 30th International Conference on the Theory and Application of Cryptology and Information Security, Springer Nature, 2024, pp. 418–449.","ama":"Brzuska C, Ünal A, Woo IKY. Evasive LWE assumptions: Definitions, classes, and counterexamples. In: <i>30th International Conference on the Theory and Application of Cryptology and Information Security</i>. Vol 15487. Springer Nature; 2024:418-449. doi:<a href=\"https://doi.org/10.1007/978-981-96-0894-2_14\">10.1007/978-981-96-0894-2_14</a>","apa":"Brzuska, C., Ünal, A., &#38; Woo, I. K. Y. (2024). Evasive LWE assumptions: Definitions, classes, and counterexamples. In <i>30th International Conference on the Theory and Application of Cryptology and Information Security</i> (Vol. 15487, pp. 418–449). Kolkata, India: Springer Nature. <a href=\"https://doi.org/10.1007/978-981-96-0894-2_14\">https://doi.org/10.1007/978-981-96-0894-2_14</a>","ieee":"C. Brzuska, A. Ünal, and I. K. Y. Woo, “Evasive LWE assumptions: Definitions, classes, and counterexamples,” in <i>30th International Conference on the Theory and Application of Cryptology and Information Security</i>, Kolkata, India, 2024, vol. 15487, pp. 418–449.","chicago":"Brzuska, Chris, Akin Ünal, and Ivy K.Y. Woo. “Evasive LWE Assumptions: Definitions, Classes, and Counterexamples.” In <i>30th International Conference on the Theory and Application of Cryptology and Information Security</i>, 15487:418–49. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-981-96-0894-2_14\">https://doi.org/10.1007/978-981-96-0894-2_14</a>."},"oa_version":"Preprint","author":[{"last_name":"Brzuska","first_name":"Chris","full_name":"Brzuska, Chris"},{"first_name":"Akin","full_name":"Ünal, Akin","orcid":"0000-0002-8929-0221","id":"f6b56fb6-dc63-11ee-9dbf-f6780863a85a","last_name":"Ünal"},{"last_name":"Woo","full_name":"Woo, Ivy K.Y.","first_name":"Ivy K.Y."}],"type":"conference","alternative_title":["LNCS"],"publication_status":"published","quality_controlled":"1","year":"2024","doi":"10.1007/978-981-96-0894-2_14","fulldoi":"https://doi.org/10.1007/978-981-96-0894-2_14","OA_type":"green","day":"13","acknowledgement":"The authors thank the anonymous reviewers for insightful comments which very much improved this work, in particular, sharing with us the counterexamples against a prior version of Hiding Evasive LWE, and against public-coin Evasive LWE when the sampler inputs B. Chris Brzuska and Ivy K. Y. Woo are supported by Research Council of Finland grant 358950. We thank Russell W. F. Lai and Hoeteck Wee for helpful discussions.","abstract":[{"text":"The evasive LWE assumption, proposed by Wee [Eurocrypt’22 Wee] for constructing a lattice-based optimal broadcast encryption, has shown to be a powerful assumption, adopted by subsequent works to construct advanced primitives ranging from ABE variants to obfuscation for null circuits. However, a closer look reveals significant differences among the precise assumption statements involved in different works, leading to the fundamental question of how these assumptions compare to each other. In this work, we initiate a more systematic study on evasive LWE assumptions:\r\n(i) Based on the standard LWE assumption, we construct simple counterexamples against three private-coin evasive LWE variants, used in [Crypto’22 Tsabary, Asiacrypt’22 VWW, Crypto’23 ARYY] respectively, showing that these assumptions are unlikely to hold.\r\n\r\n(ii) Based on existing evasive LWE variants and our counterexamples, we propose and define three classes of plausible evasive LWE assumptions, suitably capturing all existing variants for which we are not aware of non-obfuscation-based counterexamples.\r\n\r\n(iii) We show that under our assumption formulations, the security proofs of [Asiacrypt’22 VWW] and [Crypto’23 ARYY] can be recovered, and we reason why the security proof of [Crypto’22 Tsabary] is also plausibly repairable using an appropriate evasive LWE assumption.","lang":"eng"}],"volume":15487,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2024/2000"}],"external_id":{"isi":["001443890800014"]},"publication":"30th International Conference on the Theory and Application of Cryptology and Information Security","page":"418-449","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"oa":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9789819608935"]},"_id":"18756","scopus_import":"1","title":"Evasive LWE assumptions: Definitions, classes, and counterexamples","intvolume":"     15487","date_published":"2024-12-13T00:00:00Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ista":"Draganov O, Skiena S. 2024. The shape of word embeddings: Quantifying non-isometry with topological data analysis. Findings of the Association for Computational Linguistics: EMNLP 2024. EMNLP: Conference on Empirical Methods in Natural Language Processing, 12080–12099.","short":"O. Draganov, S. Skiena, in:, Findings of the Association for Computational Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp. 12080–12099.","mla":"Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” <i>Findings of the Association for Computational Linguistics: EMNLP 2024</i>, Association for Computational Linguistics, 2024, pp. 12080–99, doi:<a href=\"https://doi.org/10.18653/v1/2024.findings-emnlp.705\">10.18653/v1/2024.findings-emnlp.705</a>.","chicago":"Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” In <i>Findings of the Association for Computational Linguistics: EMNLP 2024</i>, 12080–99. Association for Computational Linguistics, 2024. <a href=\"https://doi.org/10.18653/v1/2024.findings-emnlp.705\">https://doi.org/10.18653/v1/2024.findings-emnlp.705</a>.","ama":"Draganov O, Skiena S. The shape of word embeddings: Quantifying non-isometry with topological data analysis. In: <i>Findings of the Association for Computational Linguistics: EMNLP 2024</i>. Association for Computational Linguistics; 2024:12080-12099. doi:<a href=\"https://doi.org/10.18653/v1/2024.findings-emnlp.705\">10.18653/v1/2024.findings-emnlp.705</a>","ieee":"O. Draganov and S. Skiena, “The shape of word embeddings: Quantifying non-isometry with topological data analysis,” in <i>Findings of the Association for Computational Linguistics: EMNLP 2024</i>, Miami, FL, United States, 2024, pp. 12080–12099.","apa":"Draganov, O., &#38; Skiena, S. (2024). The shape of word embeddings: Quantifying non-isometry with topological data analysis. In <i>Findings of the Association for Computational Linguistics: EMNLP 2024</i> (pp. 12080–12099). Miami, FL, United States: Association for Computational Linguistics. <a href=\"https://doi.org/10.18653/v1/2024.findings-emnlp.705\">https://doi.org/10.18653/v1/2024.findings-emnlp.705</a>"},"oa_version":"Published Version","month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","conference":{"location":"Miami, FL, United States","end_date":"2024-11-16","start_date":"2024-11-12","name":"EMNLP: Conference on Empirical Methods in Natural Language Processing"},"file_date_updated":"2025-02-10T08:20:34Z","quality_controlled":"1","publication_status":"published","type":"conference","author":[{"first_name":"Ondrej","full_name":"Draganov, Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov","orcid":"0000-0003-0464-3823"},{"full_name":"Skiena, Steven","first_name":"Steven","last_name":"Skiena"}],"OA_place":"publisher","language":[{"iso":"eng"}],"ddc":["500"],"status":"public","has_accepted_license":"1","date_updated":"2025-02-10T08:21:37Z","date_created":"2025-02-04T16:19:28Z","file":[{"file_name":"2024_EMNLP_Draganov.pdf","creator":"dernst","success":1,"date_created":"2025-02-10T08:20:34Z","date_updated":"2025-02-10T08:20:34Z","relation":"main_file","content_type":"application/pdf","checksum":"f4416a5962194f0181ab0dc7f9ef93c0","file_id":"19016","file_size":1312638,"access_level":"open_access"}],"_id":"18998","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"oa":1,"date_published":"2024-11-01T00:00:00Z","scopus_import":"1","title":"The shape of word embeddings: Quantifying non-isometry with topological data analysis","abstract":[{"text":"Word embeddings represent language vocabularies as clouds of d-dimensional points. We investigate how information is conveyed by the general shape of these clouds, instead of representing the semantic meaning of each token. Specifically, we use the notion of persistent homology from topological data analysis (TDA) to measure the distances between language pairs from the shape of their unlabeled embeddings. These distances quantify the degree of non-isometry of the embeddings. To distinguish whether these differences are random training errors or capture real information about the languages, we use the computed distance matrices to construct language phylogenetic trees over 81 Indo-European languages. Careful evaluation shows that our reconstructed trees exhibit strong and statistically-significant similarities to the reference.","lang":"eng"}],"day":"01","OA_type":"gold","fulldoi":"https://doi.org/10.18653/v1/2024.findings-emnlp.705","doi":"10.18653/v1/2024.findings-emnlp.705","year":"2024","arxiv":1,"publisher":"Association for Computational Linguistics","external_id":{"arxiv":["2404.00500"]},"publication":"Findings of the Association for Computational Linguistics: EMNLP 2024","page":"12080-12099"},{"author":[{"first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832"},{"first_name":"Ondrej","full_name":"Draganov, Ondrej","orcid":"0000-0003-0464-3823","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"first_name":"Morteza","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","last_name":"Saghafian"}],"type":"preprint","publication_status":"submitted","month":"06","citation":{"chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Topological Data Analysis.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2406.04102\">https://doi.org/10.48550/ARXIV.2406.04102</a>.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic topological data analysis. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2406.04102\">10.48550/ARXIV.2406.04102</a>","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Chromatic topological data analysis. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2406.04102\">https://doi.org/10.48550/ARXIV.2406.04102</a>","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic topological data analysis,” <i>arXiv</i>. .","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic topological data analysis. arXiv, 2406.04102.","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Topological Data Analysis.” <i>ArXiv</i>, 2406.04102, doi:<a href=\"https://doi.org/10.48550/ARXIV.2406.04102\">10.48550/ARXIV.2406.04102</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Preprint","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-02-10T08:14:27Z","date_created":"2025-02-04T16:21:21Z","language":[{"iso":"eng"}],"ddc":["510"],"OA_place":"repository","has_accepted_license":"1","status":"public","date_published":"2024-06-06T00:00:00Z","title":"Chromatic topological data analysis","article_number":"2406.04102","_id":"18999","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"oa":1,"corr_author":"1","publication":"arXiv","external_id":{"arxiv":["2406.04102"]},"arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.04102","open_access":"1"}],"abstract":[{"text":"Exploring the shape of point configurations has been a key driver in the evolution of TDA (short for topological data analysis) since its infancy. This survey illustrates the recent efforts to broaden these ideas to model spatial interactions among multiple configurations, each distinguished by a color. It describes advances in this area and prepares the ground for further exploration by mentioning unresolved questions and promising research avenues while focusing on the overlap with discrete geometry.","lang":"eng"}],"doi":"10.48550/ARXIV.2406.04102","year":"2024","fulldoi":"https://doi.org/10.48550/ARXIV.2406.04102","day":"06","OA_type":"green"}]