[{"OA_type":"free access","abstract":[{"text":"Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n","lang":"eng"}],"oa":1,"_id":"18648","OA_place":"repository","day":"10","language":[{"iso":"eng"}],"oa_version":"Preprint","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.12.06.570392"}],"doi":"10.1101/2023.12.06.570392","article_processing_charge":"No","corr_author":"1","title":"Causal inference for multiple risk factors and diseases from genomics data","department":[{"_id":"MaRo"}],"date_created":"2024-12-11T10:42:59Z","status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"apa":"Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., &#38; Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.12.06.570392\">https://doi.org/10.1101/2023.12.06.570392</a>","short":"N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024).","mla":"Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” <i>BioRxiv</i>, 2024, doi:<a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>.","ama":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. <i>bioRxiv</i>. 2024. doi:<a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>","chicago":"Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” <i>BioRxiv</i>, 2024. <a href=\"https://doi.org/10.1101/2023.12.06.570392\">https://doi.org/10.1101/2023.12.06.570392</a>.","ieee":"N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” <i>bioRxiv</i>. 2024.","ista":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, <a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>."},"date_updated":"2026-07-16T22:30:22Z","type":"preprint","year":"2024","acknowledgement":"We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). ","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"08","date_published":"2024-08-10T00:00:00Z","author":[{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","first_name":"Nick N","orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N","last_name":"Machnik"},{"full_name":"Mahmoudi, Seyed Mahdi","last_name":"Mahmoudi","id":"b9f6d5ef-7774-11eb-a47f-df2c75c02ee7","first_name":"Seyed Mahdi"},{"first_name":"Malgorzata","last_name":"Borczyk","full_name":"Borczyk, Malgorzata"},{"full_name":"Krätschmer, Ilse","last_name":"Krätschmer","orcid":"0000-0002-5636-9259","id":"30d4014e-7753-11eb-b44b-db6d61112e73","first_name":"Ilse"},{"first_name":"Markus J.","last_name":"Bauer","full_name":"Bauer, Markus J."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813"}],"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181"},{"_id":"bd936e6f-d553-11ed-ba76-a82299f63e8c","grant_number":"590359","name":"Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation"}],"publication":"bioRxiv","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18642"}]}},{"supervisor":[{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"doi":"10.15479/at:ista:18661","publication_status":"published","oa_version":"Published Version","OA_place":"publisher","day":"17","language":[{"iso":"eng"}],"ddc":["572","530"],"_id":"18661","oa":1,"abstract":[{"text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n","lang":"eng"}],"title":"Archaeal membranes : In silico modelling and design","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"date_created":"2024-12-16T10:53:39Z","status":"public","corr_author":"1","article_processing_charge":"No","page":"57","month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"year":"2024","type":"dissertation","citation":{"apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes : In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>","short":"M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes : In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>.","ama":"Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria."},"date_updated":"2026-04-07T13:22:29Z","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-046-6"]},"has_accepted_license":"1","related_material":{"record":[{"id":"18670","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","file_date_updated":"2025-06-18T22:30:03Z","author":[{"first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel"}],"file":[{"embargo_to":"open_access","content_type":"application/zip","creator":"mamaral","date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:27:01Z","file_id":"18671","access_level":"closed","file_name":"2024_msfa_thesis.zip","file_size":19161387,"checksum":"eca06497a29078558395455c890a32d9","relation":"source_file"},{"date_created":"2024-12-18T12:26:30Z","file_id":"18672","access_level":"open_access","file_name":"2024_msfa_thesis.pdf","file_size":16530084,"checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","relation":"main_file","content_type":"application/pdf","creator":"mamaral","embargo":"2025-06-18","date_updated":"2025-06-18T22:30:03Z"}],"date_published":"2024-12-17T00:00:00Z"},{"corr_author":"1","status":"public","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"department":[{"_id":"AnSa"}],"date_created":"2024-12-18T10:07:45Z","title":"Stability vs flexibility: Reshaping archaeal membranes in silico","publication":"bioRxiv","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"18661","status":"public"}]},"date_published":"2024-11-27T00:00:00Z","author":[{"last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"},{"full_name":"Frey, Felix F","last_name":"Frey","orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F"},{"first_name":"Xiuyun","full_name":"Jiang, Xiuyun","last_name":"Jiang"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.10.18.619072"}],"publication_status":"draft","acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","doi":"10.1101/2024.10.18.619072","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","oa":1,"abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties."}],"date_updated":"2026-07-16T22:30:24Z","citation":{"ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” <i>bioRxiv</i>. .","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>.","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.)."},"_id":"18670","OA_place":"repository","type":"preprint","language":[{"iso":"eng"}],"day":"27","year":"2024","oa_version":"Preprint"},{"article_type":"original","article_number":"e2301449121","article_processing_charge":"Yes (in subscription journal)","corr_author":"1","date_created":"2024-03-05T09:23:55Z","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","department":[{"_id":"RySh"},{"_id":"PeJo"}],"status":"public","issue":"8","ec_funded":1,"OA_type":"hybrid","oa":1,"abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n            <jats:sup>2+</jats:sup>\r\n            -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"_id":"15084","ddc":["570"],"oa_version":"Published Version","OA_place":"publisher","day":"20","language":[{"iso":"eng"}],"publication_status":"published","doi":"10.1073/pnas.2301449121","isi":1,"pmid":1,"date_published":"2024-02-20T00:00:00Z","file":[{"date_updated":"2024-03-12T13:42:42Z","success":1,"content_type":"application/pdf","creator":"dernst","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","relation":"main_file","file_size":13648221,"file_name":"2024_PNAS_Koppensteiner.pdf","file_id":"15110","date_created":"2024-03-12T13:42:42Z","access_level":"open_access"}],"author":[{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","last_name":"Bhandari"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","full_name":"Önal, Hüseyin C","last_name":"Önal","orcid":"0000-0002-2771-2011"},{"last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Le Monnier","full_name":"Le Monnier, Elodie","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2","first_name":"Utsa","full_name":"Roy, Utsa","last_name":"Roy"},{"last_name":"Nakamura","full_name":"Nakamura, Yukihiro","first_name":"Yukihiro"},{"last_name":"Sadakata","full_name":"Sadakata, Tetsushi","first_name":"Tetsushi"},{"last_name":"Sanbo","full_name":"Sanbo, Makoto","first_name":"Makoto"},{"first_name":"Masumi","last_name":"Hirabayashi","full_name":"Hirabayashi, Masumi"},{"last_name":"Rhee","full_name":"Rhee, JeongSeop","first_name":"JeongSeop"},{"first_name":"Nils","last_name":"Brose","full_name":"Brose, Nils"},{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       121","file_date_updated":"2024-03-12T13:42:42Z","volume":121,"project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"APC_amount":"5887,8 EUR","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","description":"News on ISTA Website"}],"record":[{"status":"public","id":"13173","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"19271"}]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"publisher":"National Academy of Sciences","external_id":{"isi":["001208567300006"],"pmid":["38346189"]},"date_updated":"2026-07-16T22:30:25Z","citation":{"apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(8). doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>.","ieee":"P. Koppensteiner <i>et al.</i>, “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8. National Academy of Sciences, 2024.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>."},"year":"2024","type":"journal_article","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"},"scopus_import":"1","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","month":"02","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"article_type":"original","article_processing_charge":"Yes","article_number":"010327","corr_author":"1","issue":"1","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"title":"Emergent macroscopic bistability induced by a single superconducting qubit","date_created":"2024-06-27T10:58:06Z","status":"public","ec_funded":1,"OA_type":"gold","oa":1,"abstract":[{"lang":"eng","text":"The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength 𝑔 to a superconducting cavity that is in situ bandwidth 𝜅 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of 𝑔/𝜅. For the highest realized 𝑔/𝜅 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology."}],"ddc":["530"],"_id":"17183","language":[{"iso":"eng"}],"OA_place":"publisher","day":"16","oa_version":"Published Version","publication_status":"published","doi":"10.1103/prxquantum.5.010327","isi":1,"date_published":"2024-02-16T00:00:00Z","file":[{"file_size":1443351,"checksum":"0833880d47f74ad1deda93a1d8ffa5a7","relation":"main_file","date_created":"2024-06-28T12:04:43Z","file_id":"17185","access_level":"open_access","file_name":"2024_PRXQuantum_Sett.pdf","content_type":"application/pdf","success":1,"creator":"cchlebak","date_updated":"2024-06-28T12:04:43Z"}],"author":[{"id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya","full_name":"Sett, Riya","last_name":"Sett","orcid":"0000-0001-7641-8348"},{"last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan","full_name":"Phan, Duc T"},{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"last_name":"Vukics","full_name":"Vukics, Andras","first_name":"Andras"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"file_date_updated":"2024-06-28T12:04:43Z","volume":5,"intvolume":"         5","APC_amount":"3782,54","project":[{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"publication":"PRX Quantum","related_material":{"record":[{"id":"18978","relation":"research_data","status":"public"},{"id":"19533","relation":"dissertation_contains","status":"public"}]},"has_accepted_license":"1","publication_identifier":{"eissn":["2691-3399"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"publisher":"American Physical Society","arxiv":1,"citation":{"short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024).","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” <i>PRX Quantum</i>, vol. 5, no. 1. American Physical Society, 2024.","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327.","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>","mla":"Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>."},"external_id":{"isi":["001171652500001"],"arxiv":["2210.14182"]},"date_updated":"2026-07-16T22:30:27Z","type":"journal_article","year":"2024","acknowledgement":"This work has received funding from the Austrian Science Fund (FWF) through BeyondC (F7105) and the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 862644 (FETopen QUARTET). A.V. acknowledges support from the National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary. The authors thank the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility for technical support. We are grateful to HUN-REN Cloud for providing us with suitable computational infrastructure for the simulations.","scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02"},{"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.10518320","open_access":"1"}],"doi":"10.5281/ZENODO.10518320","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","OA_type":"gold","publisher":"Zenodo","oa":1,"abstract":[{"text":"Data analysis files for the manuscript \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\".\r\n\r\nThis contains the raw data and the data analysis files for generating the figures in the manuscript.\r\n\r\n Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.\r\n Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file\r\n Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.\r\nFigure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included.  ","lang":"eng"}],"date_updated":"2026-07-16T22:30:27Z","citation":{"apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024).","mla":"Sett, Riya, et al. <i>Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Data Analysis Files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>.","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024.","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>."},"ddc":["530"],"_id":"18978","day":"16","OA_place":"repository","type":"research_data_reference","oa_version":"Published Version","year":"2024","corr_author":"1","date_created":"2025-01-30T08:30:03Z","status":"public","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"title":"Data Analysis files for \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\"","related_material":{"record":[{"id":"17183","relation":"used_in_publication","status":"public"},{"status":"public","relation":"used_in_publication","id":"19533"}]},"has_accepted_license":"1","date_published":"2024-01-16T00:00:00Z","author":[{"full_name":"Sett, Riya","last_name":"Sett","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya"},{"orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Phan, Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"first_name":"Andras","full_name":"Vukics, Andras","last_name":"Vukics"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"article_processing_charge":"No"},{"publication_status":"published","doi":"10.1016/j.devcel.2024.04.021","isi":1,"pmid":1,"OA_type":"hybrid","oa":1,"abstract":[{"lang":"eng","text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering."}],"ddc":["570"],"_id":"17148","oa_version":"Published Version","OA_place":"publisher","language":[{"iso":"eng"}],"day":"01","title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","department":[{"_id":"AnKi"}],"status":"public","date_created":"2024-06-16T22:01:07Z","issue":"15","page":"1940-1953.e10","article_type":"original","article_processing_charge":"Yes (in subscription journal)","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"},"acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","scopus_import":"1","month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publisher":"Elsevier","citation":{"short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10.","apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>.","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","ieee":"T. Krammer <i>et al.</i>, “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” <i>Developmental Cell</i>, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>.","ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. 2024;59(15):1940-1953.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>"},"date_updated":"2026-07-16T22:30:29Z","external_id":{"isi":["001289684800001"],"pmid":["38776925"]},"year":"2024","type":"journal_article","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"publication":"Developmental Cell","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"has_accepted_license":"1","date_published":"2024-08-01T00:00:00Z","file":[{"file_name":"2024_DevelopmentalCell_Krammer.pdf","access_level":"open_access","file_id":"18841","date_created":"2025-01-13T10:59:12Z","relation":"main_file","checksum":"fefdea9c02862b4bb74de49b65ce638a","file_size":6249076,"date_updated":"2025-01-13T10:59:12Z","creator":"dernst","content_type":"application/pdf","success":1}],"author":[{"first_name":"Teresa","full_name":"Krammer, Teresa","last_name":"Krammer"},{"first_name":"Hannah T.","full_name":"Stuart, Hannah T.","last_name":"Stuart"},{"full_name":"Gromberg, Elena","last_name":"Gromberg","first_name":"Elena"},{"first_name":"Keisuke","full_name":"Ishihara, Keisuke","last_name":"Ishihara"},{"last_name":"Cislo","full_name":"Cislo, Dillon","first_name":"Dillon"},{"first_name":"Manuela","full_name":"Melchionda, Manuela","last_name":"Melchionda"},{"first_name":"Fernando","full_name":"Becerril Perez, Fernando","last_name":"Becerril Perez"},{"last_name":"Wang","full_name":"Wang, Jingkui","first_name":"Jingkui"},{"last_name":"Costantini","full_name":"Costantini, Elena","first_name":"Elena"},{"orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie"},{"first_name":"Laura","last_name":"Arbanas","full_name":"Arbanas, Laura"},{"full_name":"Hörmann, Alexandra","last_name":"Hörmann","first_name":"Alexandra"},{"last_name":"Neumüller","full_name":"Neumüller, Ralph A.","first_name":"Ralph A."},{"full_name":"Elvassore, Nicola","last_name":"Elvassore","first_name":"Nicola"},{"first_name":"Eric","full_name":"Siggia, Eric","last_name":"Siggia"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"first_name":"Elly M.","full_name":"Tanaka, Elly M.","last_name":"Tanaka"}],"intvolume":"        59","file_date_updated":"2025-01-13T10:59:12Z","volume":59},{"date_published":"2024-12-20T00:00:00Z","file":[{"date_updated":"2024-12-03T10:53:23Z","creator":"dernst","success":1,"content_type":"application/pdf","relation":"main_file","checksum":"0c61a6f9978608a103865905e06f4581","file_size":4989169,"file_name":"2024_STARProtoc_Lehr.pdf","access_level":"open_access","date_created":"2024-12-03T10:53:23Z","file_id":"18610"}],"author":[{"last_name":"Rus","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093","first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"full_name":"Kulig, Monika Aleksandra","last_name":"Kulig","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","first_name":"Monika Aleksandra"},{"last_name":"Minchington","full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"         5","file_date_updated":"2024-12-03T10:53:23Z","volume":5,"project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"APC_amount":"804 EUR","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"publication":"STAR Protocols","publication_identifier":{"eissn":["2666-1667"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"NanoFab"}],"publisher":"Elsevier","external_id":{"pmid":["39602310"]},"date_updated":"2026-07-16T22:30:29Z","citation":{"short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., &#38; Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>","ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” <i>STAR Protocols</i>, vol. 5, no. 4. Elsevier, 2024.","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>.","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>, vol. 5, no. 4, 103187, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>."},"year":"2024","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","scopus_import":"1","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","DOAJ_listed":"1","article_type":"original","article_processing_charge":"Yes","article_number":"103187","corr_author":"1","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","date_created":"2024-12-01T23:01:53Z","status":"public","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"issue":"4","OA_type":"gold","abstract":[{"text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1","lang":"eng"}],"oa":1,"ddc":["570"],"_id":"18601","oa_version":"Published Version","OA_place":"publisher","day":"20","language":[{"iso":"eng"}],"publication_status":"published","doi":"10.1016/j.xpro.2024.103187","pmid":1},{"corr_author":"1","issue":"6678","status":"public","date_created":"2024-01-14T23:00:56Z","title":"The genetic basis of a recent transition to live-bearing in marine snails","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"page":"114-119","article_type":"original","article_processing_charge":"No","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241"}],"doi":"10.1126/science.adi2982","pmid":1,"isi":1,"OA_type":"green","abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"oa":1,"_id":"14796","language":[{"iso":"eng"}],"day":"05","OA_place":"repository","oa_version":"Submitted Version","publication":"Science","related_material":{"record":[{"status":"public","relation":"research_data","id":"14812"},{"status":"public","relation":"dissertation_contains","id":"20694"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/"}]},"publication_identifier":{"eissn":["1095-9203"]},"date_published":"2024-01-05T00:00:00Z","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"first_name":"Martin D.","last_name":"Garlovsky","full_name":"Garlovsky, Martin D."},{"orcid":"0000-0002-4530-8469","last_name":"Pal","full_name":"Pal, Arka","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226"},{"first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando"},{"first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz","full_name":"Lifchitz, Hila"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"last_name":"Leder","full_name":"Leder, Erica","first_name":"Erica"},{"last_name":"Reeve","full_name":"Reeve, James","first_name":"James"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"volume":383,"intvolume":"       383","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","month":"01","publisher":"American Association for the Advancement of Science","date_updated":"2026-07-16T22:30:38Z","citation":{"apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. 2024;383(6678):114-119. doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>.","ieee":"S. Stankowski <i>et al.</i>, “The genetic basis of a recent transition to live-bearing in marine snails,” <i>Science</i>, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>."},"external_id":{"pmid":["38175895"],"isi":["001138156400003"]},"type":"journal_article","year":"2024"},{"date_created":"2024-12-23T11:03:59Z","title":"Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"status":"public","page":"1-29","article_type":"original","article_processing_charge":"Yes","publication_status":"epub_ahead","main_file_link":[{"url":"https://doi.org/10.1017/S0956792524000810","open_access":"1"}],"doi":"10.1017/s0956792524000810","isi":1,"OA_type":"gold","abstract":[{"lang":"eng","text":"We prove discrete-to-continuum convergence for dynamical optimal transport on  Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of  1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations."}],"oa":1,"ddc":["500"],"_id":"18706","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"20","OA_place":"publisher","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"related_material":{"record":[{"status":"public","id":"20563","relation":"dissertation_contains"}]},"publication":"European Journal of Applied Mathematics","publication_identifier":{"eissn":["1469-4425"],"issn":["0956-7925"]},"date_published":"2024-12-20T00:00:00Z","author":[{"last_name":"Portinale","full_name":"Portinale, Lorenzo","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","orcid":"0009-0000-9773-1931","last_name":"Quattrocchi","full_name":"Quattrocchi, Filippo"}],"scopus_import":"1","acknowledgement":"L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","month":"12","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","DOAJ_listed":"1","publisher":"Cambridge University Press","external_id":{"isi":["001381435800001"]},"date_updated":"2026-07-16T22:30:39Z","citation":{"ista":"Portinale L, Quattrocchi F. 2024. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics., 1–29.","ieee":"L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” <i>European Journal of Applied Mathematics</i>. Cambridge University Press, pp. 1–29, 2024.","chicago":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>. Cambridge University Press, 2024. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>.","ama":"Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. 2024:1-29. doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>","mla":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>, Cambridge University Press, 2024, pp. 1–29, doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>.","short":"L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics (2024) 1–29.","apa":"Portinale, L., &#38; Quattrocchi, F. (2024). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>"},"year":"2024","type":"journal_article"},{"date_updated":"2026-07-16T22:30:39Z","citation":{"ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>","mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, 2403.07803, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>.","ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” <i>arXiv</i>. .","ista":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv, 2403.07803.","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>.","apa":"Quattrocchi, F. (n.d.). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>","short":"F. Quattrocchi, ArXiv (n.d.)."},"external_id":{"arxiv":["2403.07803"]},"year":"2024","type":"preprint","arxiv":1,"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["gradient flows","Jordan–Kinderlehrer–Otto scheme","curves of maximal slope","optimal transport","Dirichlet boundary conditions","Fokker–Planck equation"],"acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful\r\ncomments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, and Oliver Tse for pointing out the reference [15]. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.\r\n","author":[{"orcid":"0009-0000-9773-1931","last_name":"Quattrocchi","full_name":"Quattrocchi, Filippo","first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308"}],"date_published":"2024-04-09T00:00:00Z","related_material":{"record":[{"id":"20865","relation":"later_version","status":"public"},{"id":"20563","relation":"dissertation_contains","status":"public"}]},"publication":"arXiv","project":[{"grant_number":"F06504","name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"20571","oa_version":"Preprint","OA_place":"repository","day":"09","language":[{"iso":"eng"}],"OA_type":"green","oa":1,"abstract":[{"lang":"eng","text":"We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\\Omega \\Subset \\mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum.   In the special case where $\\Omega$ is an interval in $\\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.\r\nOur discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\\partial \\Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\\overline \\Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\\Omega$ is an interval in $\\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. "}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2403.07803","open_access":"1"}],"publication_status":"draft","doi":"10.48550/arXiv.2403.07803","article_processing_charge":"No","article_number":"2403.07803","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","date_created":"2025-10-28T13:12:56Z","status":"public"},{"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"title":"Asymptotics for optimal empirical quantization of measures","date_created":"2025-10-28T13:12:22Z","status":"public","article_number":"2408.12924","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.12924"}],"publication_status":"draft","doi":"10.48550/arXiv.2408.12924","_id":"20570","OA_place":"repository","day":"23","language":[{"iso":"eng"}],"oa_version":"Preprint","OA_type":"green","oa":1,"abstract":[{"text":"We investigate the minimal error in approximating a general probability\r\nmeasure $\\mu$ on $\\mathbb{R}^d$ by the uniform measure on a finite set with\r\nprescribed cardinality $n$. The error is measured in the $p$-Wasserstein\r\ndistance. In particular, when $1\\le p<d$, we establish asymptotic upper and\r\nlower bounds as $n \\to \\infty$ on the rescaled minimal error that have the\r\nsame, explicit dependency on $\\mu$.\r\n  In some instances, we prove that the rescaled minimal error has a limit.\r\nThese include general measures in dimension $d = 2$ with $1 \\le p < 2$, and\r\nuniform measures in arbitrary dimension with $1 \\le p < d$. For some uniform\r\nmeasures, we prove the limit existence for $p \\ge d$ as well.\r\n  For a class of compactly supported measures with H\\\"older densities, we\r\ndetermine the convergence speed of the minimal error for every $p \\ge 1$.\r\n  Furthermore, we establish a new Pierce-type (i.e., nonasymptotic) upper\r\nestimate of the minimal error when $1 \\le p < d$.\r\n  In the initial sections, we survey the state of the art and draw connections\r\nwith similar problems, such as classical and random quantization.","lang":"eng"}],"publication":"arXiv","related_material":{"record":[{"relation":"dissertation_contains","id":"20563","status":"public"}]},"project":[{"call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Differential Systems","grant_number":"F06504"}],"author":[{"full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi","orcid":"0009-0000-9773-1931","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","first_name":"Filippo"}],"date_published":"2024-08-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","keyword":["optimal empirical quantization","vector quantization","Wasserstein distance","semidiscrete optimal transport","Zador’s Theorem","Pierce’s Lemma"],"acknowledgement":"The author is thankful to Nicolas Clozeau, Lorenzo Dello Schiavo, Jan Maas, Dejan Slepčev,\r\nand Dario Trevisan for many fruitful discussions and comments. The author gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","external_id":{"arxiv":["2408.12924"]},"citation":{"short":"F. Quattrocchi, ArXiv (n.d.).","apa":"Quattrocchi, F. (n.d.). Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>","chicago":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>.","ieee":"F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” <i>arXiv</i>. .","ista":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924.","mla":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, 2408.12924, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>.","ama":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>"},"date_updated":"2026-07-16T22:30:39Z","type":"preprint","year":"2024","arxiv":1},{"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2024","type":"dissertation","date_updated":"2026-04-07T13:03:22Z","citation":{"chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","ieee":"J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.","ista":"Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>.","ama":"Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>","short":"J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024.","apa":"Raices, J. (2024). <i>Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>"},"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"ThesisRaices2024_postDefense.docx","file_id":"17223","date_created":"2024-07-11T07:18:01Z","access_level":"closed","checksum":"d5e9234bde8667b005a8cfe18bb467d3","relation":"source_file","file_size":13788479,"embargo_to":"open_access","date_updated":"2025-01-11T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak"},{"relation":"main_file","checksum":"f5ed0139aa3e11ce58369f0915647c5c","file_size":5580296,"file_name":"ThesisRaices2024_nosignature.pdf","access_level":"open_access","file_id":"17224","date_created":"2024-07-11T07:22:32Z","date_updated":"2025-01-11T23:30:04Z","embargo":"2025-01-11","creator":"cchlebak","content_type":"application/pdf"}],"date_published":"2024-07-05T00:00:00Z","file_date_updated":"2025-01-11T23:30:04Z","author":[{"id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Raices, Julia","last_name":"Raices"}],"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","abstract":[{"text":"Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. ","lang":"eng"}],"oa":1,"oa_version":"Published Version","day":"05","language":[{"iso":"eng"}],"OA_place":"publisher","_id":"17206","ddc":["570"],"doi":"10.15479/at:ista:17206","publication_status":"published","supervisor":[{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"page":"82","article_processing_charge":"No","date_created":"2024-07-05T14:15:29Z","status":"public","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"corr_author":"1","ec_funded":1},{"citation":{"apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>","mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>."},"date_updated":"2026-04-07T13:21:01Z","type":"dissertation","year":"2024","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","author":[{"id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","first_name":"Dario J","full_name":"Porley, Dario J","last_name":"Porley"}],"file_date_updated":"2025-03-25T23:30:03Z","date_published":"2024-09-26T00:00:00Z","file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dporley","date_updated":"2025-03-25T23:30:03Z","file_id":"18149","date_created":"2024-09-26T13:40:33Z","access_level":"closed","file_name":"PhD_thesis_DPorley_final_20240919.docx","file_size":14213128,"checksum":"3b8b0bacfe61112f3852744f3170e468","relation":"source_file"},{"checksum":"6c3a652a8eede874118e11d66a63652f","relation":"main_file","file_size":18583031,"file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","file_id":"18150","date_created":"2024-09-26T13:41:39Z","access_level":"open_access","embargo":"2025-03-25","date_updated":"2025-03-25T23:30:03Z","content_type":"application/pdf","creator":"dporley"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"degree_awarded":"PhD","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A"}],"_id":"18101","ddc":["570"],"day":"26","language":[{"iso":"eng"}],"OA_place":"publisher","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies."}],"oa":1,"supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur"}],"publication_status":"published","doi":"10.15479/at:ista:18101","article_processing_charge":"No","page":"131","ec_funded":1,"corr_author":"1","status":"public","date_created":"2024-09-20T10:21:03Z","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"title":"Structural characterization of spumavirus capsid assemblies"},{"supervisor":[{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","doi":"10.15479/at:ista:17319","ddc":["580"],"_id":"17319","OA_place":"publisher","day":"26","language":[{"iso":"eng"}],"oa_version":"Published Version","oa":1,"abstract":[{"text":"This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor.","lang":"eng"}],"corr_author":"1","title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","status":"public","date_created":"2024-07-26T09:05:55Z","department":[{"_id":"LeSa"},{"_id":"GradSch"}],"article_processing_charge":"No","page":"224","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"07","date_updated":"2026-04-07T13:20:44Z","citation":{"apa":"Lukic, K. (2024). <i>Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>","short":"K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.","mla":"Lukic, Kristina. <i>Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>.","ama":"Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>","chicago":"Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>.","ista":"Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.","ieee":"K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024."},"type":"dissertation","year":"2024","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","author":[{"id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","first_name":"Kristina","orcid":"0000-0003-1581-881X","full_name":"Lukic, Kristina","last_name":"Lukic"}],"file_date_updated":"2025-01-26T23:30:04Z","date_published":"2024-07-26T00:00:00Z","file":[{"file_size":24639084,"relation":"main_file","checksum":"95517e697ea6a87e267e649cad560989","access_level":"open_access","date_created":"2024-07-26T13:14:24Z","file_id":"17320","file_name":"Thesis_Kristina_Lukic.pdf","creator":"cchlebak","content_type":"application/pdf","date_updated":"2025-01-26T23:30:04Z","embargo":"2025-01-26"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","date_updated":"2025-01-26T23:30:04Z","file_id":"17321","date_created":"2024-07-26T13:14:50Z","access_level":"closed","file_name":"Thesis_Kristina_Lukic.docx","file_size":96334272,"checksum":"74325746a9a05078fb9935dbf2aef752","relation":"source_file"}]},{"keyword":["Memory","Hippocampus","Consolidation"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"07","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T13:21:20Z","citation":{"apa":"Bollmann, L. (2024). <i>Stability and change in the memory system during rest</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>","short":"L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024.","ama":"Bollmann L. Stability and change in the memory system during rest. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>","mla":"Bollmann, Lars. <i>Stability and Change in the Memory System during Rest</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>.","ista":"Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria.","ieee":"L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024.","chicago":"Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>."},"type":"dissertation","year":"2024","degree_awarded":"PhD","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"date_published":"2024-07-31T00:00:00Z","file":[{"embargo":"2025-01-31","date_updated":"2025-01-31T23:30:03Z","content_type":"application/pdf","creator":"lbollman","checksum":"12c76297cc27449da80c60d79127770d","relation":"main_file","file_size":12920169,"file_name":"PhD_Thesis_Lars_Bollmann.pdf","date_created":"2024-07-31T18:37:19Z","file_id":"17359","access_level":"open_access"},{"file_name":"Latex_source.zip","access_level":"closed","date_created":"2024-07-31T18:38:39Z","file_id":"17360","relation":"source_file","checksum":"19a0265079dec8038830ad6e35c5106e","file_size":27568807,"embargo_to":"open_access","date_updated":"2025-01-31T23:30:03Z","creator":"lbollman","content_type":"application/zip"}],"author":[{"last_name":"Bollmann","full_name":"Bollmann, Lars","first_name":"Lars","id":"47AD3038-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2025-01-31T23:30:03Z","publication_status":"published","doi":"10.15479/at:ista:17346","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"oa":1,"abstract":[{"text":"Acquiring, retaining, and retrieving information over a wide range of timescales are crucial\r\nfunctions of the brain. The successful processing of memories affects many aspects of our\r\nlives and enables us and many other organisms to operate in a complex environment and\r\nto interact with it. In this context, the hippocampus and functionally connected brain\r\nareas, such as the prefrontal cortex, are central and have been subject to intensive research\r\nin the past decades. Storage of memories is believed to rely on distributed neural activity\r\nwithin these neural circuits. Additionally, neural memory traces of recent experience are\r\nreinstated during periods of rest or sleep. These reactivations are thought to play an\r\noutstanding role in the consolidation of memories and potentially facilitate the transfer of\r\ninformation from the hippocampus to cortical areas for long-term storage and integration\r\ninto existing knowledge.\r\nHowever, there is growing evidence that memory-related neural representations in the\r\nhippocampus are not as stable as initially thought and that they change even in the\r\nabsence of learning. It has been suggested that these changes reflect the accumulation of\r\nexperience, but the influence of interspersed consolidation periods has not been considered.\r\nPrevious studies have analyzed consolidation periods by detecting activity that strongly\r\nresembled neural activity during the acquisition of memory. Besides being often limited\r\nto only non-rapid eye movement (NREM) sleep, the used approaches were not capable of\r\ntracking changes in neural representations over extended temporal periods. More fluid\r\nrepresentations do not only challenge our understanding of how information is stored, but\r\nthey also affect the transfer of information between brain areas during the consolidation\r\nprocess.\r\nFor this thesis, I investigated the evolution of memory-related activity during sleep\r\nperiods expected to be involved in consolidation in the hippocampus and between the\r\nhippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus\r\ngradually transformed during prolonged periods of sleep and inactivity. In the beginning,\r\nneural activity strongly resembled acquisition activity, whereas, with the progression of\r\ntime, it became more similar to the subsequent recall activity. NREM periods drove\r\nthis process, while rapid-eye movement (REM) periods showed a resetting effect. This\r\nreactivation drift was due to firing rate changes of a subset of cells and mirrored the\r\nrepresentational changes from the acquisition to the recall. A stable subset of cells\r\nwithstood the drift and maintained their activity. Therefore, my results indicate that\r\nmemory-related representations undergo spontaneous modifications during consolidation\r\nperiods and that these changes are predictive of representational drift.\r\nFurthermore, I found that the amount of change in the neural activity during subsequent\r\nsleep periods was biased by prior behavioral performance. Observed changes in the\r\nhippocampus and the prefrontal cortex were synchronized and increased after poor\r\nperformance, highlighting a potential role in the exchange of information. Low-variance\r\nvii\r\nperiods with distinct, more stable activity from a subset of cells significantly contributed\r\nto the heightened synchrony between both areas. Hence, interleaved phases of more stable\r\nneural activity could facilitate the information transfer between brain areas.\r\nIn conclusion, my investigations underline the fluidity of memory-related representations\r\nand assign a prominent role to sleep reactivation periods in their evolution. In addition, I\r\nidentified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling\r\nand integrating findings from both spontaneous and behaviorally-related representational\r\nchanges in functionally related brain areas will help to broaden our understanding of how\r\nknowledge is stored, maintained, updated, and transferred between brain areas.","lang":"eng"}],"_id":"17346","ddc":["573"],"language":[{"iso":"eng"}],"day":"31","OA_place":"publisher","oa_version":"Published Version","corr_author":"1","status":"public","title":"Stability and change in the memory system during rest","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"date_created":"2024-07-29T15:08:42Z","page":"103","article_processing_charge":"No"},{"article_processing_charge":"No","page":"60","corr_author":"1","status":"public","date_created":"2024-08-02T10:52:40Z","title":"Bayesian linear regression for analyzing general omics data with time-to-event phenotypes","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"_id":"17368","ddc":["610"],"day":"13","language":[{"iso":"eng"}],"OA_place":"publisher","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n"}],"oa":1,"supervisor":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813"}],"publication_status":"published","doi":"10.15479/at:ista:17368","author":[{"full_name":"Villanueva Marijuan, Ariadna","last_name":"Villanueva Marijuan","id":"e0ae4864-133f-11ed-8f02-adaa8dd27540","first_name":"Ariadna"}],"file_date_updated":"2025-02-14T23:30:03Z","date_published":"2024-08-13T00:00:00Z","file":[{"date_updated":"2025-02-14T23:30:03Z","embargo":"2025-02-14","creator":"avillanu","content_type":"application/pdf","file_name":"Masters_thesis_AriadnaVillanueva.pdf","access_level":"open_access","file_id":"17433","date_created":"2024-08-14T11:51:24Z","relation":"main_file","checksum":"0c2daa174609f0c00919dccc5701d375","file_size":13052436},{"file_size":45642547,"relation":"source_file","checksum":"e9ed4465dfa539ac4c3a8d4d0b6271a1","access_level":"closed","date_created":"2024-08-14T11:51:57Z","file_id":"17434","file_name":"Masters thesis-AriadnaVillanueva.zip","creator":"avillanu","content_type":"application/zip","date_updated":"2025-02-14T23:30:03Z","embargo_to":"open_access"}],"has_accepted_license":"1","publication_identifier":{"issn":["2791-4585"]},"degree_awarded":"MS","citation":{"chicago":"Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>.","ista":"Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria.","ieee":"A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024.","mla":"Villanueva Marijuan, Ariadna. <i>Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>.","ama":"Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>","short":"A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024.","apa":"Villanueva Marijuan, A. (2024). <i>Bayesian linear regression for analyzing general omics data with time-to-event phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>"},"date_updated":"2026-04-07T13:03:41Z","type":"dissertation","year":"2024","alternative_title":["ISTA Master's Thesis"],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"08","keyword":["Epigenetics","Multi-omics","Bayesian regression"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"}},{"acknowledged_ssus":[{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","citation":{"apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>","mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>."},"date_updated":"2026-06-18T17:55:53Z","type":"dissertation","year":"2024","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"08","date_published":"2024-08-29T00:00:00Z","file":[{"creator":"ashevche","content_type":"application/pdf","date_updated":"2024-10-05T22:30:05Z","embargo":"2024-10-04","file_size":4468610,"relation":"main_file","checksum":"da6dd3166078934577f6af93d27000e2","access_level":"open_access","date_created":"2024-09-02T09:23:32Z","file_id":"17482","file_name":"thesis_a2b.pdf"},{"access_level":"closed","date_created":"2024-09-02T09:23:46Z","file_id":"17483","file_name":"Thesis Alex - ISTA.zip","file_size":15930999,"relation":"source_file","checksum":"76a39ef252239560923cdda4ce0a31a4","embargo_to":"open_access","creator":"ashevche","content_type":"application/zip","date_updated":"2024-10-05T22:30:05Z"}],"author":[{"last_name":"Shevchenko","full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"}],"file_date_updated":"2024-10-05T22:30:05Z","degree_awarded":"PhD","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":"W1260-N35","name":"Vienna Graduate School on Computational Optimization"}],"related_material":{"record":[{"status":"public","id":"11420","relation":"part_of_dissertation"},{"id":"14459","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9198"},{"status":"public","id":"17469","relation":"part_of_dissertation"}]},"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"oa":1,"abstract":[{"text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n","lang":"eng"}],"_id":"17465","ddc":["519"],"language":[{"iso":"eng"}],"OA_place":"repository","day":"29","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:17465","supervisor":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"page":"232","article_processing_charge":"No","corr_author":"1","title":"High-dimensional limits in artificial neural networks","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"date_created":"2024-08-28T15:14:25Z","status":"public"},{"page":"82","article_processing_charge":"No","corr_author":"1","date_created":"2024-09-08T10:23:25Z","status":"public","title":"Thermal effects in one dimensional Josephson chains","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"oa":1,"_id":"17881","ddc":["539"],"language":[{"iso":"eng"}],"OA_place":"publisher","day":"10","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:17881","supervisor":[{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"}],"date_published":"2024-09-10T00:00:00Z","file":[{"access_level":"open_access","date_created":"2024-09-12T10:46:04Z","file_id":"18059","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","file_size":10297052,"relation":"main_file","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","creator":"smukhopa","content_type":"application/pdf","date_updated":"2025-03-13T23:30:04Z","embargo":"2025-03-13"},{"embargo_to":"open_access","content_type":"application/zip","creator":"smukhopa","date_updated":"2025-03-13T23:30:04Z","file_id":"18060","date_created":"2024-09-12T10:50:58Z","access_level":"closed","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","file_size":29178634,"checksum":"e352667482701dd18a9a0e7418aef465","relation":"source_file"}],"author":[{"orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","first_name":"Soham"}],"file_date_updated":"2025-03-13T23:30:04Z","degree_awarded":"PhD","project":[{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"14032","status":"public"},{"status":"public","id":"18057","relation":"part_of_dissertation"}]},"has_accepted_license":"1","publication_identifier":{"isbn":["978-3-99078-043-5"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","citation":{"mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024."},"date_updated":"2026-06-03T07:16:04Z","type":"dissertation","year":"2024","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09"},{"oa":1,"abstract":[{"lang":"eng","text":"Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST."}],"ddc":["000"],"_id":"17469","day":"01","language":[{"iso":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v235/kogler24a.html"}],"publication_status":"published","page":"24964-25015","article_processing_charge":"No","corr_author":"1","department":[{"_id":"DaAl"},{"_id":"MaMo"}],"conference":{"name":"ICML: International Conference on Machine Learning","location":"Vienna, Austria","start_date":"2024-07-21","end_date":"2024-07-27"},"title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth","status":"public","date_created":"2024-08-29T11:47:57Z","publisher":"ML Research Press","alternative_title":["PMLR"],"arxiv":1,"date_updated":"2026-07-16T22:30:49Z","external_id":{"arxiv":["2402.05013"]},"citation":{"apa":"Kögler, K., Shevchenko, A., Hassani, H., &#38; Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.","short":"K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015.","mla":"Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 24964–5015.","ama":"Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:24964-25015.","chicago":"Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:24964–15. ML Research Press, 2024.","ista":"Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.","ieee":"K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 24964–25015."},"type":"conference","year":"2024","acknowledgement":"Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","month":"07","date_published":"2024-07-01T00:00:00Z","author":[{"full_name":"Kögler, Kevin","last_name":"Kögler","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","first_name":"Kevin"},{"last_name":"Shevchenko","full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"last_name":"Hassani","full_name":"Hassani, Hamed","first_name":"Hamed"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"}],"volume":235,"intvolume":"       235","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"publication":"Proceedings of the 41st International Conference on Machine Learning","related_material":{"record":[{"relation":"dissertation_contains","id":"17465","status":"public"}]}}]