[{"publication":"Geo-Spatial Information Science","year":"2024","volume":27,"researchdata_availability":"no","ddc":["550"],"quality_controlled":"1","status":"public","scopus_import":"1","intvolume":"        27","author":[{"full_name":"Buri, Pascal","first_name":"Pascal","last_name":"Buri"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone","last_name":"Fatichi"},{"last_name":"Shaw","full_name":"Shaw, Thomas","orcid":"0000-0001-7640-6152","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas"},{"last_name":"Fyffe","id":"001b0422-8d15-11ed-bc51-cab6c037a228","first_name":"Catriona Louise","full_name":"Fyffe, Catriona Louise"},{"last_name":"Miles","full_name":"Miles, Evan S.","first_name":"Evan S."},{"last_name":"Mccarthy","full_name":"Mccarthy, Michael","first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f"},{"first_name":"Marin","full_name":"Kneib, Marin","last_name":"Kneib"},{"first_name":"Shaoting","full_name":"Ren, Shaoting","last_name":"Ren"},{"first_name":"Achille","full_name":"Jouberton, Achille","last_name":"Jouberton"},{"last_name":"Fugger","full_name":"Fugger, Stefan","first_name":"Stefan"},{"last_name":"Jia","first_name":"Li","full_name":"Jia, Li"},{"last_name":"Zhang","first_name":"Jing","full_name":"Zhang, Jing"},{"last_name":"Shen","full_name":"Shen, Cong","first_name":"Cong"},{"first_name":"Chaolei","full_name":"Zheng, Chaolei","last_name":"Zheng"},{"last_name":"Menenti","first_name":"Massimo","full_name":"Menenti, Massimo"},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca"}],"oa":1,"file_date_updated":"2024-07-29T11:34:54Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Mountains are important suppliers of freshwater to downstream areas, affecting large populations in particular in High Mountain Asia (HMA). Yet, the propagation of water from HMA headwaters to downstream areas is not fully understood, as interactions in the mountain water cycle between the cryo-, hydro- and biosphere remain elusive. We review the definition of blue and green water fluxes as liquid water that contributes to runoff at the outlet of the selected domain (blue) and water lost to the atmosphere through vapor fluxes, that is evaporation from water, ground, and interception plus transpiration (green) and propose to add the term white water to account for the (often neglected) evaporation and sublimation from snow and ice. We provide an assessment of models that can simulate the cryo-hydro-biosphere continuum and the interactions between spheres in high mountain catchments, going beyond disciplinary separations. Land surface models are uniquely able to account for such complexity, since they solve the coupled fluxes of water, energy, and carbon between the land surface and atmosphere. Due to the mechanistic nature of such models, specific variables can be compared systematically to independent remote sensing observations – providing vital insights into model accuracy and enabling the understanding of the complex watersheds of HMA. We discuss recent developments in spaceborne earth observation products that have the potential to support catchment modeling in high mountain regions. We then present a pilot study application of the mechanistic land surface model Tethys & Chloris to a glacierized watershed in the Nepalese Himalayas and discuss the use of high-resolution earth observation data to constrain the meteorological forcing uncertainty and validate model results. We use these insights to highlight the remaining challenges and future opportunities that remote sensing data presents for land surface modeling in HMA."}],"publisher":"Taylor & Francis","month":"03","license":"https://creativecommons.org/licenses/by/4.0/","supplementarymaterial":"yes","date_published":"2024-03-22T00:00:00Z","department":[{"_id":"FrPe"}],"date_created":"2024-04-07T22:00:56Z","acknowledgement":"This work was supported by the ESA and NRSCC Dragon 5 cooperation project “Cryosphere-hydrosphere interactions of the Asian water towers: using remote sensing to drive hyper-resolution ecohydrological modelling” [Grant no. 59199]. PB and FP acknowledge funding from the SNSF (High-elevation precipitation in High Mountain Asia, HOPE)) [Grant no. 183633]. ESM, MK, SFu and FP acknowledge funding from the ERC under the European Union’s Horizon 2020 research and innovation program (Rapid mass losses of debris-covered glaciers in High Mountain Asia, RAVEN) [Grant no. 772751]. LJ, CZ and MMe acknowledge the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) [grant no. 2019QZKK010308, no. 2019QZKK0206], the National Natural Science Foundation of China projects (Grant no. 42171039, no. 91737205), the Chinese Academy of Sciences President’s International Fellowship Initiative [Grant no. 2020VTA0001], and the MOST High-Level Foreign Expert Program [Grant no. G2022055010L].","file":[{"file_id":"17342","file_size":15678450,"relation":"main_file","content_type":"application/pdf","file_name":"2024_GeoSpatialInfo_Buri.pdf","date_created":"2024-07-29T11:34:54Z","success":1,"checksum":"afbfc4e9f1bf2a00711efc30ad667c40","creator":"dernst","date_updated":"2024-07-29T11:34:54Z","access_level":"open_access"}],"date_updated":"2026-10-02T09:12:24Z","das_tickbox":"0","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1080/10095020.2024.2330546","oa_version":"Published Version","_id":"15298","day":"22","doi":"10.1080/10095020.2024.2330546","article_processing_charge":"Yes","has_accepted_license":"1","type":"journal_article","page":"703-727","article_type":"original","issue":"3","isi":1,"title":"Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia","publication_identifier":{"issn":["1009-5020"]},"publication_status":"published","external_id":{"isi":["001189470100001"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"chicago":"Buri, Pascal, Simone Fatichi, Thomas Shaw, Catriona Louise Fyffe, Evan S. Miles, Michael McCarthy, Marin Kneib, et al. “Land Surface Modeling Informed by Earth Observation Data: Toward Understanding Blue–Green–White Water Fluxes in High Mountain Asia.” <i>Geo-Spatial Information Science</i>. Taylor &#38; Francis, 2024. <a href=\"https://doi.org/10.1080/10095020.2024.2330546\">https://doi.org/10.1080/10095020.2024.2330546</a>.","ista":"Buri P, Fatichi S, Shaw T, Fyffe CL, Miles ES, McCarthy M, Kneib M, Ren S, Jouberton A, Fugger S, Jia L, Zhang J, Shen C, Zheng C, Menenti M, Pellicciotti F. 2024. Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia. Geo-Spatial Information Science. 27(3), 703–727.","ama":"Buri P, Fatichi S, Shaw T, et al. Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia. <i>Geo-Spatial Information Science</i>. 2024;27(3):703-727. doi:<a href=\"https://doi.org/10.1080/10095020.2024.2330546\">10.1080/10095020.2024.2330546</a>","short":"P. Buri, S. Fatichi, T. Shaw, C.L. Fyffe, E.S. Miles, M. McCarthy, M. Kneib, S. Ren, A. Jouberton, S. Fugger, L. Jia, J. Zhang, C. Shen, C. Zheng, M. Menenti, F. Pellicciotti, Geo-Spatial Information Science 27 (2024) 703–727.","mla":"Buri, Pascal, et al. “Land Surface Modeling Informed by Earth Observation Data: Toward Understanding Blue–Green–White Water Fluxes in High Mountain Asia.” <i>Geo-Spatial Information Science</i>, vol. 27, no. 3, Taylor &#38; Francis, 2024, pp. 703–27, doi:<a href=\"https://doi.org/10.1080/10095020.2024.2330546\">10.1080/10095020.2024.2330546</a>.","ieee":"P. Buri <i>et al.</i>, “Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia,” <i>Geo-Spatial Information Science</i>, vol. 27, no. 3. Taylor &#38; Francis, pp. 703–727, 2024.","apa":"Buri, P., Fatichi, S., Shaw, T., Fyffe, C. L., Miles, E. S., McCarthy, M., … Pellicciotti, F. (2024). Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia. <i>Geo-Spatial Information Science</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10095020.2024.2330546\">https://doi.org/10.1080/10095020.2024.2330546</a>"}},{"article_type":"original","isi":1,"issue":"2","related_material":{"record":[{"status":"public","id":"14919","relation":"research_data"},{"relation":"research_data","id":"23030","status":"public"}]},"type":"journal_article","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","_id":"14885","day":"28","fulldoi":"https://doi.org/10.1029/2023JD040214","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1029/2023JD040214","citation":{"chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca Pellicciotti. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” <i>Journal of Geophysical Research: Atmospheres</i>. Wiley, 2024. <a href=\"https://doi.org/10.1029/2023JD040214\">https://doi.org/10.1029/2023JD040214</a>.","ista":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. 2024. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 129(2), e2023JD040214.","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E. S., &#38; Pellicciotti, F. (2024). Local controls on near-surface glacier cooling under warm atmospheric conditions. <i>Journal of Geophysical Research: Atmospheres</i>. Wiley. <a href=\"https://doi.org/10.1029/2023JD040214\">https://doi.org/10.1029/2023JD040214</a>","short":"T. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 129 (2024).","ama":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. Local controls on near-surface glacier cooling under warm atmospheric conditions. <i>Journal of Geophysical Research: Atmospheres</i>. 2024;129(2). doi:<a href=\"https://doi.org/10.1029/2023JD040214\">10.1029/2023JD040214</a>","ieee":"T. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pellicciotti, “Local controls on near-surface glacier cooling under warm atmospheric conditions,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 2. Wiley, 2024.","mla":"Shaw, Thomas, et al. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 2, e2023JD040214, Wiley, 2024, doi:<a href=\"https://doi.org/10.1029/2023JD040214\">10.1029/2023JD040214</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"e2023JD040214","title":"Local controls on near-surface glacier cooling under warm atmospheric conditions","external_id":{"isi":["001146838000001"]},"publication_status":"published","publication_identifier":{"issn":["2169-897X"],"eissn":["2169-8996"]},"publisher":"Wiley","file_date_updated":"2024-02-06T08:38:27Z","oa":1,"author":[{"last_name":"Shaw","full_name":"Shaw, Thomas","orcid":"0000-0001-7640-6152","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e"},{"first_name":"Pascal","id":"317987aa-9421-11ee-ac5a-b941b041abba","full_name":"Buri, Pascal","last_name":"Buri"},{"last_name":"Mccarthy","first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","full_name":"Mccarthy, Michael"},{"first_name":"Evan S.","full_name":"Miles, Evan S.","last_name":"Miles"},{"last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"The near-surface boundary layer can mediate the response of mountain glaciers to external climate, cooling the overlying air and promoting a density-driven glacier wind. The fundamental processes are conceptually well understood, though the magnitudes of cooling and presence of glacier winds are poorly quantified in space and time, increasing the forcing uncertainty for melt models. We utilize a new data set of on-glacier meteorological measurements on three neighboring glaciers in the Swiss Alps to explore their distinct response to regional climate under the extreme 2022 summer. We find that synoptic wind origins and local terrain modifications, not only glacier size, play an important role in the ability of a glacier to cool the near-surface air. Warm air intrusions from valley or synoptically-driven winds onto the glacier can occur between ∼19% and 64% of the time and contribute between 3% and 81% of the total sensible heat flux to the surface during warm afternoon hours, depending on the fetch of the glacier flowline and its susceptibility to boundary layer erosion. In the context of extreme summer warmth, indicative of future conditions, the boundary layer cooling (up to 6.5°C cooler than its surroundings) and resultant katabatic wind flow are highly heterogeneous between the study glaciers, highlighting the complex and likely non-linear response of glaciers to an uncertain future."}],"corr_author":"1","scopus_import":"1","quality_controlled":"1","status":"public","ddc":["550"],"intvolume":"       129","year":"2024","volume":129,"publication":"Journal of Geophysical Research: Atmospheres","researchdata_availability":"yes","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2024-02-06T08:38:27Z","checksum":"cad5b93caadb40c14e5faedc34f7bba7","success":1,"date_created":"2024-02-06T08:38:27Z","file_name":"2024_JGRAtmospheres_Shaw.pdf","relation":"main_file","content_type":"application/pdf","file_size":7481087,"file_id":"14943"}],"das_tickbox":"1","date_updated":"2026-10-02T08:59:02Z","department":[{"_id":"FrPe"}],"acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101026058. The authors acknowledge the invaluable field assistance of Marta Corrà, Achille Jouberton, Marin Kneib, Stefan Fugger, Celine Ducret and Alexander Groos. The authors would also like to thank Luca Carturan for advice regarding AWS setup and maintenance and Simone Fatichi for provision and support in the use of the Tethys-Chloris model. Open access funding provided by ETH-Bereich Forschungsanstalten.","date_created":"2024-01-28T23:01:42Z","dataavailabilitystatement":"The meteorological data used in this analysis (Shaw, Buri, McCarthy, Miles, & Pelliciotti, 2023) are made publicly available at the following repository: https://zenodo.org/record/8277285. The source code of the T&C model is available at https://doi.org/10.24433/CO.0905087.v2. Reanalysis data are openly available from the ECMWF (https://cds.climate.copernicus.eu/). MeteoSwiss data can be acquired through direct request to the company.","date_published":"2024-01-28T00:00:00Z","month":"01","supplementarymaterial":"yes"},{"publisher":"MDPI","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Arctic tidewater glaciers are retreating, serving as key indicators of global warming. This study aims to assess how subglacial hydrology affects glacier front retreat by comparing two glacier–fjord models of the Hansbreen glacier: one incorporating a detailed subglacial hydrology model and another simplifying the subglacial discharge to a single channel centered in the flow line. We first validate the subglacial hydrology model by comparing its discharge channels with observations of plume activity. Simulations conducted from April to December 2010 revealed that the glacier front position aligns more closely with the observations in the coupled model than in the simplified version. Furthermore, the mass loss due to calving and submarine melting is greater in the coupled model, with the calving mass loss reaching 6 Mt by the end of the simulation compared to 4 Mt in the simplified model. These findings highlight the critical role of subglacial hydrology in predicting glacier dynamics and emphasize the importance of detailed modeling in understanding the responses of Arctic tidewater glaciers to climate change."}],"author":[{"last_name":"De Andrés","first_name":"Eva","full_name":"De Andrés, Eva"},{"last_name":"Muñoz Hermosilla","full_name":"Muñoz Hermosilla, José M","first_name":"José M","id":"e1037a6d-646e-11ef-b402-e0ed9ab0901e","orcid":"0000-0002-1990-8508"},{"first_name":"Kaian","full_name":"Shahateet, Kaian","last_name":"Shahateet"},{"full_name":"Otero, Jaime","first_name":"Jaime","last_name":"Otero"}],"oa":1,"file_date_updated":"2024-12-09T09:43:33Z","intvolume":"        11","status":"public","OA_type":"gold","ddc":["550"],"quality_controlled":"1","DOAJ_listed":"1","scopus_import":"1","researchdata_availability":"yes","publication":"Hydrology","volume":11,"year":"2024","date_updated":"2026-10-02T09:16:55Z","das_tickbox":"1","file":[{"relation":"main_file","content_type":"application/pdf","file_size":5709093,"file_id":"18635","access_level":"open_access","date_updated":"2024-12-09T09:43:33Z","creator":"dernst","checksum":"0665c5bfca97782bf0b041f23dd7e8d7","success":1,"date_created":"2024-12-09T09:43:33Z","file_name":"2024_Hydrology_deAndres.pdf"}],"date_created":"2024-12-08T23:01:55Z","acknowledgement":"E. De Andrés is supported by Margarita-Salas Grant No. UP2021-035 under the Next Generation-EU program. This research was also funded by grant PID2020-113051RB-C31 from MCIN/AEI/10.13039/501100011033/FEDER, UE.\r\nWe gratefully acknowledge Michal Cieply and Dariusz Ignatiuk from the Faculty of Natural Sciences, University of Silesia in Katowice, Poland, for their essential contributions to the Hansbreen data collection. We also extend our sincere thanks to Waldemar Walczowski from the Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland, for providing Hansbuka data. Additionally, we would like to thank two anonymous reviewers for their constructive feedback, which helped to enhance the quality and clarity of this work.","department":[{"_id":"FrPe"}],"date_published":"2024-11-12T00:00:00Z","dataavailabilitystatement":"The data that support the results of this study and form the basis for all the figures presented in this paper are openly available from Zenodo at https://doi.org/10.5281/zenodo.8005258 (accessed on 6 November 2024).","OA_place":"publisher","supplementarymaterial":"no","month":"11","related_material":{"record":[{"id":"18634","status":"public","relation":"used_in_publication"},{"relation":"research_data","id":"23031","status":"public"}]},"issue":"11","article_type":"original","has_accepted_license":"1","type":"journal_article","article_processing_charge":"Yes","doi":"10.3390/hydrology11110193","fulldoi":"https://doi.org/10.3390/hydrology11110193","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"12","_id":"18628","citation":{"chicago":"De Andrés, Eva, José M Muñoz Hermosilla, Kaian Shahateet, and Jaime Otero. “The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” <i>Hydrology</i>. MDPI, 2024. <a href=\"https://doi.org/10.3390/hydrology11110193\">https://doi.org/10.3390/hydrology11110193</a>.","ista":"De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. 2024. The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. Hydrology. 11(11), 193.","apa":"De Andrés, E., Muñoz Hermosilla, J. M., Shahateet, K., &#38; Otero, J. (2024). The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. <i>Hydrology</i>. MDPI. <a href=\"https://doi.org/10.3390/hydrology11110193\">https://doi.org/10.3390/hydrology11110193</a>","ama":"De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. <i>Hydrology</i>. 2024;11(11). doi:<a href=\"https://doi.org/10.3390/hydrology11110193\">10.3390/hydrology11110193</a>","short":"E. De Andrés, J.M. Muñoz Hermosilla, K. Shahateet, J. Otero, Hydrology 11 (2024).","mla":"De Andrés, Eva, et al. “The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” <i>Hydrology</i>, vol. 11, no. 11, 193, MDPI, 2024, doi:<a href=\"https://doi.org/10.3390/hydrology11110193\">10.3390/hydrology11110193</a>.","ieee":"E. De Andrés, J. M. Muñoz Hermosilla, K. Shahateet, and J. Otero, “The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard,” <i>Hydrology</i>, vol. 11, no. 11. MDPI, 2024."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"193","publication_status":"published","publication_identifier":{"eissn":["2306-5338"]},"title":"The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard"},{"month":"07","supplementarymaterial":"yes","OA_place":"publisher","dataavailabilitystatement":"DNA sequencing data are deposited in the European Genome-Phenome Archive (EGA) with accession code EGAS00001006434. Called de novo and somatic mutations are available online (https://figshare.com/account/home#/projects/156404).","date_published":"2024-07-01T00:00:00Z","department":[{"_id":"FyKo"}],"acknowledgement":"This study was funded by the Spanish Ministry of Science and Innovation (Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe [PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234 (LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR 2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL (FK)].","date_created":"2024-05-05T22:01:04Z","ec_funded":1,"file":[{"file_size":3060724,"file_id":"18799","relation":"main_file","content_type":"application/pdf","checksum":"e45fc987f4e9ebafdd0ec4f0e9027de4","date_created":"2025-01-09T09:21:25Z","file_name":"2024_EJHG_Andrianova.pdf","success":1,"creator":"dernst","access_level":"open_access","date_updated":"2025-01-09T09:21:25Z"}],"date_updated":"2026-10-02T09:48:07Z","das_tickbox":"1","publication":"European Journal of Human Genetics","volume":32,"year":"2024","researchdata_availability":"yes","quality_controlled":"1","status":"public","ddc":["570"],"OA_type":"hybrid","pmid":1,"scopus_import":"1","intvolume":"        32","author":[{"last_name":"Andrianova","first_name":"Maria A.","full_name":"Andrianova, Maria A."},{"full_name":"Seplyarskiy, Vladimir B.","first_name":"Vladimir B.","last_name":"Seplyarskiy"},{"last_name":"Terradas","first_name":"Mariona","full_name":"Terradas, Mariona"},{"full_name":"Sánchez-Heras, Ana Beatriz","first_name":"Ana Beatriz","last_name":"Sánchez-Heras"},{"last_name":"Mur","full_name":"Mur, Pilar","first_name":"Pilar"},{"last_name":"Soto","full_name":"Soto, José Luis","first_name":"José Luis"},{"first_name":"Gemma","full_name":"Aiza, Gemma","last_name":"Aiza"},{"first_name":"Emma","full_name":"Borràs, Emma","last_name":"Borràs"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"last_name":"Kondrashov","first_name":"Alexey S.","full_name":"Kondrashov, Alexey S."},{"first_name":"Georgii A.","full_name":"Bazykin, Georgii A.","last_name":"Bazykin"},{"last_name":"Valle","first_name":"Laura","full_name":"Valle, Laura"}],"oa":1,"file_date_updated":"2025-01-09T09:21:25Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.","lang":"eng"}],"publisher":"Springer Nature","title":"Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells","publication_identifier":{"eissn":["1476-5438"],"issn":["1018-4813"]},"publication_status":"published","external_id":{"isi":["001207703200001"],"pmid":["38658779"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"chicago":"Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>.","ista":"Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. 32, 837–845.","apa":"Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B., Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>","short":"M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur, J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L. Valle, European Journal of Human Genetics 32 (2024) 837–845.","ama":"Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. 2024;32:837-845. doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>","mla":"Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>, vol. 32, Springer Nature, 2024, pp. 837–45, doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>.","ieee":"M. A. Andrianova <i>et al.</i>, “Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells,” <i>European Journal of Human Genetics</i>, vol. 32. Springer Nature, pp. 837–845, 2024."},"fulldoi":"https://doi.org/10.1038/s41431-024-01598-8","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"01","_id":"15362","doi":"10.1038/s41431-024-01598-8","article_processing_charge":"No","has_accepted_license":"1","project":[{"_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716","name":"Evolution of Sensorimotor Transformation Across Diptera"},{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation","grant_number":"I05127"}],"type":"journal_article","page":"837-845","article_type":"original","isi":1},{"researchdata_availability":"yes (supplementary data)","volume":10,"year":"2024","publication":"Science Advances","intvolume":"        10","pmid":1,"scopus_import":"1","DOAJ_listed":"1","status":"public","quality_controlled":"1","ddc":["580"],"OA_type":"gold","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.","lang":"eng"}],"oa":1,"file_date_updated":"2024-03-25T09:42:10Z","author":[{"full_name":"Palkina, Kseniia A.","first_name":"Kseniia A.","last_name":"Palkina"},{"first_name":"Tatiana A.","full_name":"Karataeva, Tatiana A.","last_name":"Karataeva"},{"full_name":"Perfilov, Maxim M.","first_name":"Maxim M.","last_name":"Perfilov"},{"first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova"},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383"},{"last_name":"Garcia-Perez","first_name":"Elena","full_name":"Garcia-Perez, Elena"},{"last_name":"Vazquez-Vilar","full_name":"Vazquez-Vilar, Marta","first_name":"Marta"},{"last_name":"Rodriguez-Rodriguez","full_name":"Rodriguez-Rodriguez, Marta","first_name":"Marta"},{"full_name":"Vazquez-Vilriales, Victor","first_name":"Victor","last_name":"Vazquez-Vilriales"},{"first_name":"Ekaterina S.","full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova"},{"last_name":"Mitiouchkina","first_name":"Tatiana","full_name":"Mitiouchkina, Tatiana"},{"last_name":"Belozerova","first_name":"Olga A.","full_name":"Belozerova, Olga A."},{"full_name":"Kovalchuk, Sergey I.","first_name":"Sergey I.","last_name":"Kovalchuk"},{"first_name":"Anna","full_name":"Alekberova, Anna","last_name":"Alekberova"},{"first_name":"Alena K.","full_name":"Malyshevskaia, Alena K.","last_name":"Malyshevskaia"},{"full_name":"Bugaeva, Evgenia N.","first_name":"Evgenia N.","last_name":"Bugaeva"},{"first_name":"Elena B.","full_name":"Guglya, Elena B.","last_name":"Guglya"},{"first_name":"Anastasia","full_name":"Balakireva, Anastasia","last_name":"Balakireva"},{"full_name":"Sytov, Nikita","first_name":"Nikita","last_name":"Sytov"},{"last_name":"Bezlikhotnova","full_name":"Bezlikhotnova, Anastasia","first_name":"Anastasia"},{"first_name":"Daria I.","full_name":"Boldyreva, Daria I.","last_name":"Boldyreva"},{"first_name":"Vladislav V.","full_name":"Babenko, Vladislav V.","last_name":"Babenko"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"last_name":"Choob","full_name":"Choob, Vladimir V.","first_name":"Vladimir V."},{"last_name":"Orzaez","full_name":"Orzaez, Diego","first_name":"Diego"},{"first_name":"Ilia V.","full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"first_name":"Karen S.","full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan"}],"publisher":"American Association for the Advancement of Science","supplementarymaterial":"yes","OA_place":"publisher","month":"03","date_published":"2024-03-01T00:00:00Z","dataavailabilitystatement":"All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The plasmids used in this study will be made available for noncommercial use through Addgene under the terms of UBMTA (www.addgene.org/agreement/1). The data are available at https://doi.org/10.6084/m9.figshare.24772872.","date_created":"2024-03-25T08:54:33Z","acknowledgement":"We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund).","department":[{"_id":"FyKo"}],"das_tickbox":"1","date_updated":"2026-10-02T09:22:29Z","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2024-03-25T09:42:10Z","checksum":"a19c43b260ea0bbaf895a29712e3153c","success":1,"file_name":"2024_ScienceAdv_Palkina.pdf","date_created":"2024-03-25T09:42:10Z","content_type":"application/pdf","relation":"main_file","file_size":1499302,"file_id":"15185"}],"doi":"10.1126/sciadv.adk1992","_id":"15179","day":"01","fulldoi":"https://doi.org/10.1126/sciadv.adk1992","language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"Yes","type":"journal_article","has_accepted_license":"1","isi":1,"issue":"10","related_material":{"record":[{"status":"public","id":"23032","relation":"research_data"}]},"article_type":"original","external_id":{"pmid":["38457503"],"isi":["001187580500013"]},"publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","title":"A hybrid pathway for self-sustained luminescence","article_number":"adk1992","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” <i>Science Advances</i>, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk1992\">10.1126/sciadv.adk1992</a>.","ieee":"K. A. Palkina <i>et al.</i>, “A hybrid pathway for self-sustained luminescence,” <i>Science Advances</i>, vol. 10, no. 10. American Association for the Advancement of Science, 2024.","short":"K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. <i>Science Advances</i>. 2024;10(10). doi:<a href=\"https://doi.org/10.1126/sciadv.adk1992\">10.1126/sciadv.adk1992</a>","apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk1992\">https://doi.org/10.1126/sciadv.adk1992</a>","ista":"Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992.","chicago":"Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk1992\">https://doi.org/10.1126/sciadv.adk1992</a>."}},{"date_updated":"2026-10-02T09:53:20Z","das_tickbox":"1","file":[{"checksum":"1d64265f62a3bf14550b4f5c684f1782","file_name":"2024_eLife_David.pdf","success":1,"date_created":"2025-01-08T13:33:05Z","access_level":"open_access","date_updated":"2025-01-08T13:33:05Z","creator":"dernst","file_size":9992462,"file_id":"18780","content_type":"application/pdf","relation":"main_file"}],"acknowledgement":"This research was supported by the Wellcome Trust (ZN, LA). In addition, LA was supported by an ERC Advanced Grant (FRONTHAL, 742595) and the European Union project RRF-2.3.1-\r\n21-2022-00004 within the framework of the Artificial Intelligence National Laboratory and Lendület_2023_90. ZN is the recipient of a Hungarian Academy of Sciences Momentum Grant (Lendület, LP2012-29) and an ERC Advanced Grant (293681). We thank the Light Microscopy Center at Institute of Experimental Medicine for kindly providing microscopy support. Authors would like to express their deepest gratitude to Prof Luc Anselin (Center for Spatial Data Science, University of Chicago) and Dr Szabolcs Káli (Instiute of Experimental Medicine, Budapest) for the valuable discussion about analysis of spatial association, and to Krisztina Faddi for the excellent technical assistance. ","date_created":"2025-01-08T13:25:45Z","department":[{"_id":"GaNo"}],"date_published":"2024-12-10T00:00:00Z","dataavailabilitystatement":"The code for the analysis is available online as a user-friendly MATLAB script at: https://github.com/dcsabaCD225/Moran_Matlab/blob/main/moran_local.m (copy archived at Csaba, 2024). All source data relevant to figures and charts are included in source data files.","OA_place":"publisher","supplementarymaterial":"yes","month":"12","publisher":"eLife Sciences Publications","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Unsupervised segmentation in biological and non-biological images is only partially resolved. Segmentation either requires arbitrary thresholds or large teaching datasets. Here, we propose a spatial autocorrelation method based on Local Moran’s <jats:italic>I</jats:italic> coefficient to differentiate signal, background, and noise in any type of image. The method, originally described for geoinformatics, does not require a predefined intensity threshold or teaching algorithm for image segmentation and allows quantitative comparison of samples obtained in different conditions. It utilizes relative intensity as well as spatial information of neighboring elements to select spatially contiguous groups of pixels. We demonstrate that Moran’s method outperforms threshold-based method in both artificially generated as well as in natural images especially when background noise is substantial. This superior performance can be attributed to the exclusion of false positive pixels resulting from isolated, high intensity pixels in high noise conditions. To test the method’s power in real situation, we used high power confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3 (A-type) voltage-gated potassium channels in mice. Moran’s method identified high-intensity Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution of these clusters displayed strong correlation with large sensory axon terminals of subcortical origin. The unique association of the special presynaptic terminals and a postsynaptic voltage-gated ion channel cluster was confirmed with electron microscopy. These data demonstrate that Moran’s method is a rapid, simple image segmentation method optimal for variable and high noise conditions.","lang":"eng"}],"author":[{"last_name":"Dávid","full_name":"Dávid, Csaba","first_name":"Csaba"},{"full_name":"Giber, Kristóf","first_name":"Kristóf","last_name":"Giber"},{"first_name":"Margit Katalin","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9500-8758","full_name":"Szigeti, Margit Katalin","last_name":"Szigeti"},{"first_name":"Mihály","full_name":"Köllő, Mihály","last_name":"Köllő"},{"last_name":"Nusser","first_name":"Zoltan","full_name":"Nusser, Zoltan"},{"last_name":"Acsady","first_name":"Laszlo","full_name":"Acsady, Laszlo"}],"oa":1,"file_date_updated":"2025-01-08T13:33:05Z","intvolume":"        12","OA_type":"gold","quality_controlled":"1","status":"public","ddc":["570"],"scopus_import":"1","DOAJ_listed":"1","researchdata_availability":"yes","publication":"eLife","volume":12,"year":"2024","citation":{"ista":"Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. 2024. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. eLife. 12, 89361.","chicago":"Dávid, Csaba, Kristóf Giber, Margit Katalin Szigeti, Mihály Köllő, Zoltan Nusser, and Laszlo Acsady. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.89361\">https://doi.org/10.7554/elife.89361</a>.","ieee":"C. Dávid, K. Giber, M. K. Szigeti, M. Köllő, Z. Nusser, and L. Acsady, “A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024.","mla":"Dávid, Csaba, et al. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” <i>ELife</i>, vol. 12, 89361, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.89361\">10.7554/elife.89361</a>.","ama":"Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.89361\">10.7554/elife.89361</a>","short":"C. Dávid, K. Giber, M.K. Szigeti, M. Köllő, Z. Nusser, L. Acsady, ELife 12 (2024).","apa":"Dávid, C., Giber, K., Szigeti, M. K., Köllő, M., Nusser, Z., &#38; Acsady, L. (2024). A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.89361\">https://doi.org/10.7554/elife.89361</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"89361","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"title":"A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus","article_type":"original","has_accepted_license":"1","type":"journal_article","article_processing_charge":"Yes","doi":"10.7554/elife.89361","fulldoi":"https://doi.org/10.7554/elife.89361","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"18779","day":"10"},{"title":"Hereditary amyloidosis: Insights into a fibrinogen A variant protein","external_id":{"isi":["001272128100001"],"pmid":["39031927"]},"publication_identifier":{"eissn":["1097-0134"],"issn":["0887-3585"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://doi.org/10.22541/au.171804763.37967262/v1","open_access":"1"}],"citation":{"chicago":"Cattaneo, Elizabeth R, Romina A Gisonno, Martín C Abba, Marianela Santana, Silvana A Rosú, Elsa Nucifora, María A Aguirre, María C Giordani, M. Alejandra Tricerri, and Nahuel A Ramella. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/prot.26732\">https://doi.org/10.1002/prot.26732</a>.","ista":"Cattaneo ER, Gisonno RA, Abba MC, Santana M, Rosú SA, Nucifora E, Aguirre MA, Giordani MC, Tricerri MA, Ramella NA. 2024. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. 92(12), 1366–1374.","apa":"Cattaneo, E. R., Gisonno, R. A., Abba, M. C., Santana, M., Rosú, S. A., Nucifora, E., … Ramella, N. A. (2024). Hereditary amyloidosis: Insights into a fibrinogen A variant protein. <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley. <a href=\"https://doi.org/10.1002/prot.26732\">https://doi.org/10.1002/prot.26732</a>","short":"E.R. Cattaneo, R.A. Gisonno, M.C. Abba, M. Santana, S.A. Rosú, E. Nucifora, M.A. Aguirre, M.C. Giordani, M.A. Tricerri, N.A. Ramella, Proteins: Structure, Function and Bioinformatics 92 (2024) 1366–1374.","ama":"Cattaneo ER, Gisonno RA, Abba MC, et al. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. <i>Proteins: Structure, Function and Bioinformatics</i>. 2024;92(12):1366-1374. doi:<a href=\"https://doi.org/10.1002/prot.26732\">10.1002/prot.26732</a>","mla":"Cattaneo, Elizabeth R., et al. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 92, no. 12, Wiley, 2024, pp. 1366–74, doi:<a href=\"https://doi.org/10.1002/prot.26732\">10.1002/prot.26732</a>.","ieee":"E. R. Cattaneo <i>et al.</i>, “Hereditary amyloidosis: Insights into a fibrinogen A variant protein,” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 92, no. 12. Wiley, pp. 1366–1374, 2024."},"day":"01","_id":"17331","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1002/prot.26732","oa_version":"Preprint","doi":"10.1002/prot.26732","article_processing_charge":"No","type":"journal_article","article_type":"original","page":"1366-1374","isi":1,"issue":"12","month":"12","OA_place":"repository","supplementarymaterial":"yes","dataavailabilitystatement":"The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.","date_published":"2024-12-01T00:00:00Z","department":[{"_id":"GaNo"}],"acknowledgement":"The authors acknowledge Rosana del Cid for her help with English corrections, Mario Ramos for the figure editions, and Gabriela Finarelli for technical assistance. S.A. Rosú, N.A. Ramella, and M.A. Tricerri acknowledge support from Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Grant PIP 11220200102381), Agencia Nacional de Promoción Científica y Tecnológica (PICT 2019-03592), Universidad Nacional de La Plata (UNLP) (Grants M234 and PPID M014), and Fundación Florencio Fiorini. The authors warmly thank M.P. for her willingness to conduct these studies.","date_created":"2024-07-28T22:01:10Z","das_tickbox":"1","date_updated":"2026-10-02T09:56:43Z","year":"2024","volume":92,"publication":"Proteins: Structure, Function and Bioinformatics","researchdata_availability":"upon request","scopus_import":"1","pmid":1,"status":"public","quality_controlled":"1","OA_type":"green","intvolume":"        92","oa":1,"author":[{"last_name":"Cattaneo","first_name":"Elizabeth R","full_name":"Cattaneo, Elizabeth R"},{"first_name":"Romina A","id":"a9e08d76-6a98-11ec-8f7b-c777fe5ca519","full_name":"Gisonno, Romina A","last_name":"Gisonno"},{"full_name":"Abba, Martín C","first_name":"Martín C","last_name":"Abba"},{"first_name":"Marianela","full_name":"Santana, Marianela","last_name":"Santana"},{"full_name":"Rosú, Silvana A","first_name":"Silvana A","last_name":"Rosú"},{"full_name":"Nucifora, Elsa","first_name":"Elsa","last_name":"Nucifora"},{"last_name":"Aguirre","first_name":"María A","full_name":"Aguirre, María A"},{"full_name":"Giordani, María C","first_name":"María C","last_name":"Giordani"},{"first_name":"M. Alejandra","full_name":"Tricerri, M. Alejandra","last_name":"Tricerri"},{"first_name":"Nahuel A","full_name":"Ramella, Nahuel A","last_name":"Ramella"}],"abstract":[{"text":"Amyloidosis are a group of diseases in which soluble proteins aggregate and deposit in fibrillar conformation extracellularly in tissues. The effectiveness of therapeutic strategies depends on the specific protein involved, being crucial to accurately determine its nature. Moreover, following the diagnosis, the search for the mutation within relatives allows the clinical advice. Here we report the precise diagnosis and explored the possible reasons of the structural pathogenicity for a renal amyloidosis related to a fibrinogen Aα-chain variant. Whole-exome sequencing and GATK calling pipeline were leveraged to characterize the protein variant present in a patient with kidney failure. Bioinformatics strategies were applied to suggest potential explanations of the variants aggregation. Our pipeline allowed the identification of a single-point variant of fibrinogen Aα-chain, which opened the possibility of curative transplantation. In silico structural analysis suggested that the pathogenicity of the variant may be attributed to a heightened susceptibility to yield a peptide prone to deposit as an oligomer with a β-sheet structure. Exploiting the comprehensive coverage of whole-genome sequencing, we managed to fill a vacant stage in the diagnosis of hereditary amyloidosis and to stimulate the advancement in biomedicine.","lang":"eng"}],"publisher":"Wiley"},{"citation":{"apa":"Novarino, G., &#38; Bock, C. (2024). Mapping the brain’s gene-regulatory maze. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adp4663\">https://doi.org/10.1126/science.adp4663</a>","ieee":"G. Novarino and C. Bock, “Mapping the brain’s gene-regulatory maze,” <i>Science</i>, vol. 384, no. 6698. AAAS, pp. 860–861, 2024.","mla":"Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” <i>Science</i>, vol. 384, no. 6698, AAAS, 2024, pp. 860–61, doi:<a href=\"https://doi.org/10.1126/science.adp4663\">10.1126/science.adp4663</a>.","short":"G. Novarino, C. Bock, Science 384 (2024) 860–861.","ama":"Novarino G, Bock C. Mapping the brain’s gene-regulatory maze. <i>Science</i>. 2024;384(6698):860-861. doi:<a href=\"https://doi.org/10.1126/science.adp4663\">10.1126/science.adp4663</a>","ista":"Novarino G, Bock C. 2024. Mapping the brain’s gene-regulatory maze. Science. 384(6698), 860–861.","chicago":"Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adp4663\">https://doi.org/10.1126/science.adp4663</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Mapping the brain’s gene-regulatory maze","publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"external_id":{"isi":["001230076500007"],"pmid":["38781359"]},"page":"860-861","article_type":"letter_note","issue":"6698","isi":1,"type":"journal_article","article_processing_charge":"No","fulldoi":"https://doi.org/10.1126/science.adp4663","oa_version":"None","language":[{"iso":"eng"}],"_id":"17091","day":"24","doi":"10.1126/science.adp4663","date_updated":"2026-10-02T09:50:30Z","das_tickbox":"0","department":[{"_id":"GaNo"}],"date_created":"2024-06-02T22:00:57Z","date_published":"2024-05-24T00:00:00Z","month":"05","supplementarymaterial":"no","publisher":"AAAS","author":[{"full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"first_name":"Christoph","full_name":"Bock, Christoph","last_name":"Bock"}],"corr_author":"1","abstract":[{"lang":"eng","text":"DNA sequences are connected to genes and functions in the developing and adult brain"}],"quality_controlled":"1","status":"public","scopus_import":"1","pmid":1,"intvolume":"       384","publication":"Science","volume":384,"year":"2024","researchdata_availability":"no"},{"_id":"18307","day":"01","fulldoi":"https://doi.org/10.1093/evolut/qpae106","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1093/evolut/qpae106","article_processing_charge":"Yes (via OA deal)","type":"journal_article","has_accepted_license":"1","article_type":"original","page":"1722-1738","isi":1,"issue":"10","related_material":{"link":[{"relation":"software","url":"https://github.com/Simon-Re/complex-vaccination"}],"record":[{"relation":"research_data","status":"public","id":"14862"},{"relation":"dissertation_contains","id":"20811","status":"public"}]},"title":"Complex vaccination strategies prevent the emergence of vaccine resistance","external_id":{"isi":["001286581900001"],"pmid":["38990788"]},"publication_status":"published","publication_identifier":{"eissn":["1558-5646"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. 2024. Complex vaccination strategies prevent the emergence of vaccine resistance. Evolution: International journal of organic evolution. 78(10), 1722–1738.","chicago":"Rella, Simon, Yuliya A. Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/evolut/qpae106\">https://doi.org/10.1093/evolut/qpae106</a>.","apa":"Rella, S., Kulikova, Y. A., Minnegalieva, A., &#38; Kondrashov, F. (2024). Complex vaccination strategies prevent the emergence of vaccine resistance. <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpae106\">https://doi.org/10.1093/evolut/qpae106</a>","ieee":"S. Rella, Y. A. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” <i>Evolution: International journal of organic evolution</i>, vol. 78, no. 10. Oxford University Press, pp. 1722–1738, 2024.","mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” <i>Evolution: International Journal of Organic Evolution</i>, vol. 78, no. 10, Oxford University Press, 2024, pp. 1722–38, doi:<a href=\"https://doi.org/10.1093/evolut/qpae106\">10.1093/evolut/qpae106</a>.","short":"S. Rella, Y.A. Kulikova, A. Minnegalieva, F. Kondrashov, Evolution: International Journal of Organic Evolution 78 (2024) 1722–1738.","ama":"Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. <i>Evolution: International journal of organic evolution</i>. 2024;78(10):1722-1738. doi:<a href=\"https://doi.org/10.1093/evolut/qpae106\">10.1093/evolut/qpae106</a>"},"volume":78,"year":"2024","publication":"Evolution: International journal of organic evolution","researchdata_availability":"yes","scopus_import":"1","pmid":1,"quality_controlled":"1","ddc":["570"],"status":"public","OA_type":"hybrid","intvolume":"        78","file_date_updated":"2024-10-21T09:34:50Z","oa":1,"author":[{"last_name":"Rella","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","first_name":"Simon","full_name":"Rella, Simon"},{"full_name":"Kulikova, Yuliya A.","first_name":"Yuliya A.","last_name":"Kulikova"},{"last_name":"Minnegalieva","first_name":"Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","full_name":"Minnegalieva, Aygul"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"corr_author":"1","abstract":[{"lang":"eng","text":"Vaccination is the most effective tool to control infectious diseases. However, the evolution of vaccine resistance, exemplified by vaccine resistance in SARS-CoV-2, remains a concern. Here, we model complex vaccination strategies against a pathogen with multiple epitopes—molecules targeted by the vaccine. We found that a vaccine targeting one epitope was ineffective in preventing vaccine escape. Vaccine resistance in highly infectious pathogens was prevented by the full-epitope vaccine, that is, one targeting all available epitopes, but only when the rate of pathogen evolution was low. Strikingly, a bet-hedging strategy of random administration of vaccines targeting different epitopes was the most effective in preventing vaccine resistance in pathogens with the low rate of infection and high rate of evolution. Thus, complex vaccination strategies, when biologically feasible, may be preferable to the currently used single-vaccine approaches for long-term control of disease outbreaks, especially when applied to livestock with near 100% vaccination rates."}],"publisher":"Oxford University Press","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"10","OA_place":"publisher","supplementarymaterial":"yes","dataavailabilitystatement":"Results and figures derive from the model, described in detail in the main text. The code is available at github.com/Simon-Re/complex-vaccination.","date_published":"2024-10-01T00:00:00Z","department":[{"_id":"GaTk"}],"date_created":"2024-10-13T22:01:50Z","acknowledgement":"We thank Raimundo Julian Saona Urmeneta, Maike Morrison, Sergey Kryazhimskiy, Hiroki Ishikawa, Simone Pigolotti, and Shingo Miyauchi for fruitful discussions. We also thank the participants of the FRISBI seminar at ISTA for useful comments.","file":[{"file_size":29360811,"file_id":"18453","content_type":"application/pdf","relation":"main_file","checksum":"5c6e8475bb88b07d424a5130d5e91e74","file_name":"2024_Evolution_Rella.pdf","date_created":"2024-10-21T09:34:50Z","success":1,"creator":"dernst","access_level":"open_access","date_updated":"2024-10-21T09:34:50Z"}],"das_tickbox":"1","date_updated":"2026-10-02T10:12:20Z"},{"date_published":"2024-01-02T00:00:00Z","dataavailabilitystatement":"All experimental data included in this work are available at https://zenodo.org/records/10119346.","supplementarymaterial":"yes","OA_place":"publisher","month":"01","date_updated":"2026-10-02T10:23:53Z","das_tickbox":"1","file":[{"file_id":"14825","file_size":2336595,"content_type":"application/pdf","relation":"main_file","date_created":"2024-01-17T11:03:00Z","file_name":"2024_NatureComm_Valentini.pdf","success":1,"checksum":"ef79173b45eeaf984ffa61ef2f8a52ab","date_updated":"2024-01-17T11:03:00Z","access_level":"open_access","creator":"dernst"}],"acknowledgement":"We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290.","date_created":"2024-01-14T23:00:56Z","ec_funded":1,"department":[{"_id":"GeKa"}],"intvolume":"        15","status":"public","quality_controlled":"1","OA_type":"gold","ddc":["530"],"scopus_import":"1","DOAJ_listed":"1","pmid":1,"researchdata_availability":"yes","APC_amount":"6468 EUR","publication":"Nature Communications","year":"2024","volume":15,"publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on  the same silicon technology compatible platform.","lang":"eng"}],"corr_author":"1","author":[{"full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini"},{"full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi"},{"id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","first_name":"Levon","full_name":"Baghumyan, Levon","last_name":"Baghumyan"},{"last_name":"de Gijsel","full_name":"de Gijsel, Thijs","first_name":"Thijs","id":"a0ece13c-b527-11ee-929d-bad130106eee"},{"last_name":"Jung","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","first_name":"Jason","full_name":"Jung, Jason"},{"first_name":"Stefano","full_name":"Calcaterra, Stefano","last_name":"Calcaterra"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"full_name":"Aguilera Servin, Juan L","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin"},{"full_name":"Aggarwal, Kushagra","first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293","last_name":"Aggarwal"},{"full_name":"Janik, Marian","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","last_name":"Janik"},{"id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Adletzberger, Thomas","last_name":"Adletzberger"},{"full_name":"Seoane Souto, Rubén","first_name":"Rubén","last_name":"Seoane Souto"},{"first_name":"Martin","full_name":"Leijnse, Martin","last_name":"Leijnse"},{"full_name":"Danon, Jeroen","first_name":"Jeroen","last_name":"Danon"},{"last_name":"Schrade","first_name":"Constantin","full_name":"Schrade, Constantin"},{"first_name":"Erik","full_name":"Bakkers, Erik","last_name":"Bakkers"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","first_name":"Giovanni","last_name":"Isella"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"file_date_updated":"2024-01-17T11:03:00Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"169","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","external_id":{"isi":["001142794000839"],"pmid":["38167818"]},"title":"Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium","citation":{"apa":"Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>","mla":"Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>, vol. 15, 169, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>.","ieee":"M. Valentini <i>et al.</i>, “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","ista":"Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169.","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>."},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_processing_charge":"Yes","doi":"10.1038/s41467-023-44114-0","fulldoi":"https://doi.org/10.1038/s41467-023-44114-0","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"14793","day":"02","related_material":{"record":[{"status":"public","id":"13312","relation":"earlier_version"},{"relation":"research_data","id":"23036","status":"public"}]},"isi":1,"article_type":"original","project":[{"call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046"},{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515","name":"Integrated Germanium Quantum Technology"},{"_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811","name":"Quantum bits with Kitaev Transmons","grant_number":"101115315"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"has_accepted_license":"1","type":"journal_article"},{"citation":{"ama":"Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>","short":"M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024).","ieee":"M. Zagorski <i>et al.</i>, “Assessing the precision of morphogen gradients in neural tube development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","mla":"Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>, vol. 15, 929, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>.","apa":"Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe, J., &#38; Kicheva, A. (2024). Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>","chicago":"Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>.","ista":"Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva A. 2024. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 15, 929."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"929","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","external_id":{"isi":["001156218500022"],"pmid":["38302459"]},"title":"Assessing the precision of morphogen gradients in neural tube development","isi":1,"article_type":"letter_note","project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"}],"has_accepted_license":"1","type":"journal_article","article_processing_charge":"Yes","doi":"10.1038/s41467-024-45148-8","fulldoi":"https://doi.org/10.1038/s41467-024-45148-8","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"18902","day":"01","date_updated":"2026-10-02T10:12:59Z","das_tickbox":"1","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"18903","file_size":4723831,"date_updated":"2025-01-27T13:04:03Z","access_level":"open_access","creator":"dernst","success":1,"date_created":"2025-01-27T13:04:03Z","file_name":"2024_NatureComm_Zagorski.pdf","checksum":"acf75f2b6fa84a64d1f590dd4a53cbf7"}],"acknowledgement":"MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188, the Polish National Agency for Academic Exchange, and by a grant from the Priority Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian University. Work in JB’s lab is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Neural Stem Cell Modulation).","date_created":"2025-01-27T13:01:01Z","department":[{"_id":"GaTk"},{"_id":"AnKi"}],"date_published":"2024-02-01T00:00:00Z","dataavailabilitystatement":"Source data for Figs. 1, 2 is provided in the Source data file. All published data is available from us to interested researchers. Source data are provided with this paper.","OA_place":"publisher","supplementarymaterial":"yes","month":"02","publisher":"Springer Nature","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"author":[{"first_name":"Marcin","full_name":"Zagorski, Marcin","last_name":"Zagorski"},{"last_name":"Brandenberg","first_name":"Nathalie","full_name":"Brandenberg, Nathalie"},{"last_name":"Lutolf","first_name":"Matthias","full_name":"Lutolf, Matthias"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva"}],"oa":1,"file_date_updated":"2025-01-27T13:04:03Z","intvolume":"        15","ddc":["570"],"status":"public","OA_type":"gold","quality_controlled":"1","pmid":1,"scopus_import":"1","DOAJ_listed":"1","researchdata_availability":"yes","publication":"Nature Communications","volume":15,"year":"2024"},{"citation":{"mla":"Seoane Souto, Rubén, et al. “Tuning the Josephson Diode Response with an Ac Current.” <i>Physical Review Research</i>, vol. 6, no. 2, L022002, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">10.1103/PhysRevResearch.6.L022002</a>.","ieee":"R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, and J. Danon, “Tuning the Josephson diode response with an ac current,” <i>Physical Review Research</i>, vol. 6, no. 2. American Physical Society, 2024.","short":"R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, J. Danon, Physical Review Research 6 (2024).","ama":"Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. Tuning the Josephson diode response with an ac current. <i>Physical Review Research</i>. 2024;6(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">10.1103/PhysRevResearch.6.L022002</a>","apa":"Seoane Souto, R., Leijnse, M., Schrade, C., Valentini, M., Katsaros, G., &#38; Danon, J. (2024). Tuning the Josephson diode response with an ac current. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">https://doi.org/10.1103/PhysRevResearch.6.L022002</a>","ista":"Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. 2024. Tuning the Josephson diode response with an ac current. Physical Review Research. 6(2), L022002.","chicago":"Seoane Souto, Rubén, Martin Leijnse, Constantin Schrade, Marco Valentini, Georgios Katsaros, and Jeroen Danon. “Tuning the Josephson Diode Response with an Ac Current.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">https://doi.org/10.1103/PhysRevResearch.6.L022002</a>."},"publication_identifier":{"eissn":["2643-1564"]},"publication_status":"published","title":"Tuning the Josephson diode response with an ac current","article_number":"L022002","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","has_accepted_license":"1","issue":"2","article_type":"letter_note","doi":"10.1103/PhysRevResearch.6.L022002","day":"01","_id":"15320","fulldoi":"https://doi.org/10.1103/PhysRevResearch.6.L022002","language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"Yes","date_created":"2024-04-14T22:01:02Z","acknowledgement":"We acknowledge support from research grants Spanish CM Talento Program (Project No. 2022-T1/IND-24070), Spanish Ministry of Science, innovation, and Universities through Grant No. PID2022-140552NA-I00, Swedish Research Council under Grant Agreement No. 2020-03412, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 856526, Nanolund, FWF Project with [82],\r\nand Microsoft Corporation. ","department":[{"_id":"GeKa"}],"das_tickbox":"0","date_updated":"2026-10-02T10:26:37Z","file":[{"checksum":"7b9cb3b17d89f392bd582e30d7a72a29","file_name":"2024_PhysReviewResearch_Souto.pdf","date_created":"2024-04-17T07:14:53Z","success":1,"creator":"dernst","access_level":"open_access","date_updated":"2024-04-17T07:14:53Z","file_size":1073544,"file_id":"15327","content_type":"application/pdf","relation":"main_file"}],"supplementarymaterial":"yes","month":"04","date_published":"2024-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"Josephson diodes are superconducting elements that show an asymmetry in the critical current depending on the direction of the current. Here, we theoretically explore how an alternating current bias can tune the response of such a diode. We show that for slow driving there is always a regime where the system can only carry zero-voltage dc current in one direction, thus effectively behaving as an ideal Josephson diode. Under fast driving, the diode efficiency is also tunable, although the ideal regime cannot be reached in this case. We also investigate the residual dissipation due to the time-dependent current bias and show that it remains small. All our conclusions are solely based on the critical current asymmetry of the junction, and are thus compatible with any Josephson diode."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa":1,"file_date_updated":"2024-04-17T07:14:53Z","author":[{"last_name":"Seoane Souto","full_name":"Seoane Souto, Rubén","first_name":"Rubén"},{"last_name":"Leijnse","full_name":"Leijnse, Martin","first_name":"Martin"},{"last_name":"Schrade","first_name":"Constantin","full_name":"Schrade, Constantin"},{"full_name":"Valentini, Marco","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"}],"publisher":"American Physical Society","researchdata_availability":"no","volume":6,"year":"2024","publication":"Physical Review Research","intvolume":"         6","scopus_import":"1","DOAJ_listed":"1","status":"public","ddc":["530"],"quality_controlled":"1"},{"file":[{"file_id":"17390","file_size":2255741,"relation":"main_file","content_type":"application/pdf","file_name":"2024_ScientificReports_Severin.pdf","date_created":"2024-08-05T08:52:14Z","success":1,"checksum":"0b34b89e5f4f3f7b32ffadf104394594","date_updated":"2024-08-05T08:52:14Z","access_level":"open_access","creator":"dernst"}],"das_tickbox":"1","date_updated":"2026-10-02T11:04:33Z","department":[{"_id":"GeKa"}],"date_created":"2024-08-05T08:50:51Z","acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant (EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the NCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units of IST Austria through resources provided by the nanofabrication facility, the FWF-I 05060 and the FWF-P 30207 project.","dataavailabilitystatement":"The data acquired by the algorithm during experiments is available from the corresponding author upon reasonable request.","date_published":"2024-07-27T00:00:00Z","month":"07","supplementarymaterial":"yes","publisher":"Springer Nature","oa":1,"file_date_updated":"2024-08-05T08:52:14Z","author":[{"first_name":"B.","full_name":"Severin, B.","last_name":"Severin"},{"last_name":"Lennon","first_name":"D. T.","full_name":"Lennon, D. T."},{"last_name":"Camenzind","first_name":"L. C.","full_name":"Camenzind, L. C."},{"first_name":"F.","full_name":"Vigneau, F.","last_name":"Vigneau"},{"full_name":"Fedele, F.","first_name":"F.","last_name":"Fedele"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec"},{"last_name":"Ballabio","first_name":"A.","full_name":"Ballabio, A."},{"first_name":"D.","full_name":"Chrastina, D.","last_name":"Chrastina"},{"first_name":"G.","full_name":"Isella, G.","last_name":"Isella"},{"first_name":"M.","full_name":"de Kruijf, M.","last_name":"de Kruijf"},{"full_name":"Carballido, M. J.","first_name":"M. J.","last_name":"Carballido"},{"last_name":"Svab","full_name":"Svab, S.","first_name":"S."},{"first_name":"A. V.","full_name":"Kuhlmann, A. V.","last_name":"Kuhlmann"},{"last_name":"Geyer","full_name":"Geyer, S.","first_name":"S."},{"full_name":"Froning, F. N. M.","first_name":"F. N. M.","last_name":"Froning"},{"last_name":"Moon","full_name":"Moon, H.","first_name":"H."},{"full_name":"Osborne, M. A.","first_name":"M. A.","last_name":"Osborne"},{"full_name":"Sejdinovic, D.","first_name":"D.","last_name":"Sejdinovic"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X"},{"full_name":"Zumbühl, D. M.","first_name":"D. M.","last_name":"Zumbühl"},{"last_name":"Briggs","full_name":"Briggs, G. A. D.","first_name":"G. A. D."},{"last_name":"Ares","full_name":"Ares, N.","first_name":"N."}],"abstract":[{"text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions and each device realisation requires a different tuning protocol. We demonstrate that it is possible to automate the tuning of a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate Ge/SiGe heterostructure double quantum dot device from scratch with the same algorithm. We achieve tuning times of 30, 10, and 92 min, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices, allowing for the characterization of the regions where double quantum dot regimes are found. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","pmid":1,"ddc":["530"],"status":"public","quality_controlled":"1","intvolume":"        14","year":"2024","volume":14,"publication":"Scientific Reports","researchdata_availability":"upon request","citation":{"ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, de Kruijf M, Carballido MJ, Svab S, Kuhlmann AV, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. 2024. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. Scientific Reports. 14, 17281.","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>Scientific Reports</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41598-024-67787-z\">https://doi.org/10.1038/s41598-024-67787-z</a>.","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (2024). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-024-67787-z\">https://doi.org/10.1038/s41598-024-67787-z</a>","ieee":"B. Severin <i>et al.</i>, “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” <i>Scientific Reports</i>, vol. 14. Springer Nature, 2024.","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>Scientific Reports</i>, vol. 14, 17281, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41598-024-67787-z\">10.1038/s41598-024-67787-z</a>.","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>Scientific Reports</i>. 2024;14. doi:<a href=\"https://doi.org/10.1038/s41598-024-67787-z\">10.1038/s41598-024-67787-z</a>","short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, Scientific Reports 14 (2024)."},"acknowledged_ssus":[{"_id":"NanoFab"}],"article_number":"17281","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","external_id":{"pmid":["39068242"],"arxiv":["2107.12975"],"isi":["001281273100062"]},"publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"article_type":"original","isi":1,"arxiv":1,"related_material":{"record":[{"relation":"earlier_version","id":"10066","status":"public"}]},"type":"journal_article","has_accepted_license":"1","project":[{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"article_processing_charge":"Yes","_id":"17389","day":"27","fulldoi":"https://doi.org/10.1038/s41598-024-67787-z","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1038/s41598-024-67787-z"},{"das_tickbox":"1","date_updated":"2026-10-02T11:02:23Z","file":[{"checksum":"ef9f99a84089c388904cc8aa8d89c55a","date_created":"2024-12-03T11:00:15Z","success":1,"file_name":"2024_NatureComm_dePalma.pdf","creator":"dernst","access_level":"open_access","date_updated":"2024-12-03T11:00:15Z","file_size":5288092,"file_id":"18611","content_type":"application/pdf","relation":"main_file"}],"acknowledgement":"The authors thank Simone Frasca, Vincent Jouanny, Guillaume Beaulieu, Camille Roy, Dominic Dahinden, Davide Lombardo, Daniel Chrastina, and Siddhart Gautam for contributing to some cleanroom fabrication steps, the measurement setup, device simulations, data analysis, and for the useful discussions. P.S. acknowledges support from the Swiss National Science Foundation (SNSF) through the grants Ref. No. 200021 200418 and Ref. No. 206021_205335, and from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 01042765 SEFRI MB22.00081. W.J. acknowledges support from the EPFL QSE Postdoctoral Fellowship Grant. S.B., D.L., and P.S. acknowledge support from the NCCR Spin Qubit in Silicon (NCCR-SPIN) Grant No. 51NF40-180604. M.J., G.K., G.I., and S.C. acknowledge support from the Horizon Europe Project IGNITE ID 101070193. G.K. acknowledges support from the FWF via the P32235 and I05060 projects.","date_created":"2024-12-01T23:01:53Z","department":[{"_id":"GeKa"}],"date_published":"2024-12-01T00:00:00Z","dataavailabilitystatement":"The datasets generated during the current study are available in Zenodo with the identifier https://doi.org/10.5281/zenodo.13935167.","supplementarymaterial":"yes","OA_place":"publisher","month":"12","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Semiconductor quantum dots (QDs) in planar germanium (Ge) heterostructures have emerged as front-runners for future hole-based quantum processors. Here, we present strong coupling between a hole charge qubit, defined in a double quantum dot (DQD) in planar Ge, and microwave photons in a high-impedance (Zr = 1.3 kΩ) resonator based on an array of superconducting quantum interference devices (SQUIDs). Our investigation reveals vacuum-Rabi splittings with coupling strengths up to g0/2π = 260 MHz, and a cooperativity of C ~ 100, dependent on DQD tuning. Furthermore, utilizing the frequency tunability of our resonator, we explore the quenched energy splitting associated with strong Coulomb correlation effects in Ge QDs. The observed enhanced coherence of the strongly correlated excited state signals the presence of distinct symmetries within related spin functions, serving as a precursor to the strong coupling between photons and spin-charge hybrid qubits in planar Ge. This work paves the way towards coherent quantum connections between remote hole qubits in planar Ge, required to scale up hole-based quantum processors.","lang":"eng"}],"oa":1,"file_date_updated":"2024-12-03T11:00:15Z","author":[{"full_name":"De Palma, Franco","first_name":"Franco","last_name":"De Palma"},{"full_name":"Oppliger, Fabian","first_name":"Fabian","last_name":"Oppliger"},{"first_name":"Wonjin","full_name":"Jang, Wonjin","last_name":"Jang"},{"full_name":"Bosco, Stefano","first_name":"Stefano","last_name":"Bosco"},{"full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","orcid":"0009-0003-9037-8831","last_name":"Janik"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"last_name":"Loss","first_name":"Daniel","full_name":"Loss, Daniel"},{"full_name":"Scarlino, Pasquale","first_name":"Pasquale","last_name":"Scarlino"}],"intvolume":"        15","scopus_import":"1","DOAJ_listed":"1","pmid":1,"quality_controlled":"1","status":"public","ddc":["530"],"OA_type":"gold","researchdata_availability":"yes","volume":15,"year":"2024","publication":"Nature Communications","citation":{"chicago":"De Palma, Franco, Fabian Oppliger, Wonjin Jang, Stefano Bosco, Marian Janik, Stefano Calcaterra, Georgios Katsaros, Giovanni Isella, Daniel Loss, and Pasquale Scarlino. “Strong Hole-Photon Coupling in Planar Ge for Probing Charge Degree and Strongly Correlated States.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-54520-7\">https://doi.org/10.1038/s41467-024-54520-7</a>.","ista":"De Palma F, Oppliger F, Jang W, Bosco S, Janik M, Calcaterra S, Katsaros G, Isella G, Loss D, Scarlino P. 2024. Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states. Nature Communications. 15, 10177.","apa":"De Palma, F., Oppliger, F., Jang, W., Bosco, S., Janik, M., Calcaterra, S., … Scarlino, P. (2024). Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-54520-7\">https://doi.org/10.1038/s41467-024-54520-7</a>","short":"F. De Palma, F. Oppliger, W. Jang, S. Bosco, M. Janik, S. Calcaterra, G. Katsaros, G. Isella, D. Loss, P. Scarlino, Nature Communications 15 (2024).","ama":"De Palma F, Oppliger F, Jang W, et al. Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-54520-7\">10.1038/s41467-024-54520-7</a>","mla":"De Palma, Franco, et al. “Strong Hole-Photon Coupling in Planar Ge for Probing Charge Degree and Strongly Correlated States.” <i>Nature Communications</i>, vol. 15, 10177, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-54520-7\">10.1038/s41467-024-54520-7</a>.","ieee":"F. De Palma <i>et al.</i>, “Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024."},"article_number":"10177","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"pmid":["39580488"],"isi":["001362684200001"]},"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"title":"Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states","isi":1,"related_material":{"record":[{"status":"public","id":"23037","relation":"research_data"}]},"article_type":"original","type":"journal_article","has_accepted_license":"1","project":[{"_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","grant_number":"P32235"},{"name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"}],"article_processing_charge":"Yes","doi":"10.1038/s41467-024-54520-7","_id":"18602","day":"01","fulldoi":"https://doi.org/10.1038/s41467-024-54520-7","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"article_type":"original","issue":"6","isi":1,"has_accepted_license":"1","project":[{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515","name":"Integrated Germanium Quantum Technology"}],"type":"journal_article","article_processing_charge":"No","fulldoi":"https://doi.org/10.1103/PhysRevApplied.22.064026","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"18653","day":"01","doi":"10.1103/PhysRevApplied.22.064026","citation":{"apa":"Hickie, J., Van Straaten, B., Fedele, F., Jirovec, D., Ballabio, A., Chrastina, D., … Ares, N. (2024). Automated long-range compensation of an rf quantum dot sensor. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">https://doi.org/10.1103/PhysRevApplied.22.064026</a>","short":"J. Hickie, B. Van Straaten, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, G. Katsaros, N. Ares, Physical Review Applied 22 (2024).","ama":"Hickie J, Van Straaten B, Fedele F, et al. Automated long-range compensation of an rf quantum dot sensor. <i>Physical Review Applied</i>. 2024;22(6). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">10.1103/PhysRevApplied.22.064026</a>","ieee":"J. Hickie <i>et al.</i>, “Automated long-range compensation of an rf quantum dot sensor,” <i>Physical Review Applied</i>, vol. 22, no. 6. American Physical Society, 2024.","mla":"Hickie, Joseph, et al. “Automated Long-Range Compensation of an Rf Quantum Dot Sensor.” <i>Physical Review Applied</i>, vol. 22, no. 6, 064026, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">10.1103/PhysRevApplied.22.064026</a>.","chicago":"Hickie, Joseph, Barnaby Van Straaten, Federico Fedele, Daniel Jirovec, Andrea Ballabio, Daniel Chrastina, Giovanni Isella, Georgios Katsaros, and Natalia Ares. “Automated Long-Range Compensation of an Rf Quantum Dot Sensor.” <i>Physical Review Applied</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">https://doi.org/10.1103/PhysRevApplied.22.064026</a>.","ista":"Hickie J, Van Straaten B, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Katsaros G, Ares N. 2024. Automated long-range compensation of an rf quantum dot sensor. Physical Review Applied. 22(6), 064026."},"acknowledged_ssus":[{"_id":"NanoFab"}],"article_number":"064026","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Automated long-range compensation of an rf quantum dot sensor","publication_identifier":{"eissn":["2331-7019"]},"publication_status":"published","external_id":{"isi":["001379155900003"]},"publisher":"American Physical Society","author":[{"full_name":"Hickie, Joseph","first_name":"Joseph","last_name":"Hickie"},{"last_name":"Van Straaten","first_name":"Barnaby","full_name":"Van Straaten, Barnaby"},{"first_name":"Federico","full_name":"Fedele, Federico","last_name":"Fedele"},{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","first_name":"Giovanni","last_name":"Isella"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros"},{"full_name":"Ares, Natalia","first_name":"Natalia","last_name":"Ares"}],"oa":1,"file_date_updated":"2024-12-16T11:13:48Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Charge sensing is a sensitive technique for probing quantum devices, of particular importance for spin-qubit readout. To achieve good readout sensitivities, the proximity of the charge sensor to the device to be measured is a necessity. However, this proximity also means that the operation of the device affects, in turn, the sensor tuning and ultimately the readout sensitivity. We present an approach for compensating for this crosstalk effect allowing for the gate voltages of the measured device to be swept in a 1-V × 1-V window while maintaining a sensor configuration chosen by a Bayesian optimizer. Our algorithm will hopefully be a major contribution to the suite of fully automated solutions required for the operation of large quantum device architectures."}],"ddc":["530"],"OA_type":"hybrid","quality_controlled":"1","status":"public","scopus_import":"1","intvolume":"        22","publication":"Physical Review Applied","year":"2024","volume":22,"researchdata_availability":"no","file":[{"creator":"dernst","date_updated":"2024-12-16T11:13:48Z","access_level":"open_access","date_created":"2024-12-16T11:13:48Z","success":1,"file_name":"2024_PhysicalReviewApplied_Hickie.pdf","checksum":"bc29a40819abc4969867b6cd6563f7ad","relation":"main_file","content_type":"application/pdf","file_id":"18662","file_size":3560132}],"date_updated":"2026-10-02T11:04:04Z","das_tickbox":"0","department":[{"_id":"GeKa"}],"acknowledgement":"We thank Nicholas Sim for providing help with the experiment and Sebastian Orbell for helpful discussions. This work was supported by the Royal Society, the Engineering and Physical Sciences Research Council (EPSRC) National Quantum Technology Hub in Networked Quantum Information Technology (Grant No. EP/M013243/1), Quantum Technology Capital (Grant No. EP/N014995/1), the EPSRC Platform Grant (Grant No. EP/R029229/1), the European Research Council (Grant Agreement No. 948932), the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the nanofabrication facility and, the FWF-I 05060 and HORIZON-RIA 101069515 projects.","date_created":"2024-12-15T23:01:50Z","date_published":"2024-12-01T00:00:00Z","month":"12","supplementarymaterial":"yes","OA_place":"publisher"},{"contributor":[{"first_name":"Fabian","contributor_type":"project_member","last_name":"Oppliger"}],"_id":"23037","year":"2024","day":"15","oa_version":"None","fulldoi":"https://doi.org/10.5281/zenodo.13935166","doi":"10.5281/zenodo.13935166","status":"public","ddc":["530"],"OA_type":"green","article_processing_charge":"No","type":"research_data_reference","oa":1,"author":[{"first_name":"Franco","full_name":"De Palma, Franco","last_name":"De Palma"},{"first_name":"Fabian","full_name":"Oppliger, Fabian","last_name":"Oppliger"},{"first_name":"Wonjin","full_name":"Jang, Wonjin","last_name":"Jang"},{"full_name":"Bosco, Stefano","first_name":"Stefano","last_name":"Bosco"},{"first_name":"Marián","full_name":"Janík, Marián","last_name":"Janík"},{"first_name":"Stefano","full_name":"Calcaterra, Stefano","last_name":"Calcaterra"},{"first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros"},{"full_name":"Isella, Giovanni","first_name":"Giovanni","last_name":"Isella"},{"first_name":"Daniel","full_name":"Loss, Daniel","last_name":"Loss"},{"first_name":"Pasquale","full_name":"Scarlino, Pasquale","last_name":"Scarlino"}],"abstract":[{"lang":"eng","text":"The data for all figures in the main text can be found in csv files in ASCII format in the corresponing folders. For Figures 4-6, the panels are numbered from top to bottom."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"18602"}]},"publisher":"Zenodo","month":"10","title":"Online data of \"Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states\"","OA_place":"repository","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-15T00:00:00Z","department":[{"_id":"GeKa"}],"date_created":"2026-10-02T11:02:18Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.13935166"}],"citation":{"ista":"De Palma F, Oppliger F, Jang W, Bosco S, Janík M, Calcaterra S, Katsaros G, Isella G, Loss D, Scarlino P. 2024. Online data of ‘Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states’, Zenodo, <a href=\"https://doi.org/10.5281/zenodo.13935166\">10.5281/zenodo.13935166</a>.","chicago":"De Palma, Franco, Fabian Oppliger, Wonjin Jang, Stefano Bosco, Marián Janík, Stefano Calcaterra, Georgios Katsaros, Giovanni Isella, Daniel Loss, and Pasquale Scarlino. “Online Data of ‘Strong Hole-Photon Coupling in Planar Ge for Probing Charge Degree and Strongly Correlated States.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/zenodo.13935166\">https://doi.org/10.5281/zenodo.13935166</a>.","apa":"De Palma, F., Oppliger, F., Jang, W., Bosco, S., Janík, M., Calcaterra, S., … Scarlino, P. (2024). Online data of “Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states.” Zenodo. <a href=\"https://doi.org/10.5281/zenodo.13935166\">https://doi.org/10.5281/zenodo.13935166</a>","ieee":"F. De Palma <i>et al.</i>, “Online data of ‘Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states.’” Zenodo, 2024.","mla":"De Palma, Franco, et al. <i>Online Data of “Strong Hole-Photon Coupling in Planar Ge for Probing Charge Degree and Strongly Correlated States.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/zenodo.13935166\">10.5281/zenodo.13935166</a>.","ama":"De Palma F, Oppliger F, Jang W, et al. Online data of “Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states.” 2024. doi:<a href=\"https://doi.org/10.5281/zenodo.13935166\">10.5281/zenodo.13935166</a>","short":"F. De Palma, F. Oppliger, W. Jang, S. Bosco, M. Janík, S. Calcaterra, G. Katsaros, G. Isella, D. Loss, P. Scarlino, (2024)."},"date_updated":"2026-10-02T11:02:23Z"},{"has_accepted_license":"1","project":[{"grant_number":"101069515","name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"}],"type":"journal_article","article_type":"original","issue":"5","isi":1,"oa_version":"Published Version","fulldoi":"https://doi.org/10.1016/j.mssp.2024.108231","language":[{"iso":"eng"}],"keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"_id":"15018","day":"20","doi":"10.1016/j.mssp.2024.108231","article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>.","ieee":"Y. Shimura <i>et al.</i>, “Compressively strained epitaxial Ge layers for quantum computing applications,” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5. Elsevier, 2024.","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5, 108231, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>.","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. 2024;174(5). doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>"},"title":"Compressively strained epitaxial Ge layers for quantum computing applications","publication_status":"published","publication_identifier":{"issn":["1369-8001"]},"external_id":{"isi":["001188520000001"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"108231","author":[{"full_name":"Shimura, Yosuke","first_name":"Yosuke","last_name":"Shimura"},{"first_name":"Clement","full_name":"Godfrin, Clement","last_name":"Godfrin"},{"last_name":"Hikavyy","first_name":"Andriy","full_name":"Hikavyy, Andriy"},{"last_name":"Li","full_name":"Li, Roy","first_name":"Roy"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin"},{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios"},{"first_name":"Paola","full_name":"Favia, Paola","last_name":"Favia"},{"last_name":"Han","first_name":"Han","full_name":"Han, Han"},{"full_name":"Wan, Danny","first_name":"Danny","last_name":"Wan"},{"last_name":"de Greve","first_name":"Kristiaan","full_name":"de Greve, Kristiaan"},{"last_name":"Loo","first_name":"Roger","full_name":"Loo, Roger"}],"oa":1,"file_date_updated":"2024-07-22T11:56:08Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"publisher":"Elsevier","publication":"Materials Science in Semiconductor Processing","volume":174,"year":"2024","researchdata_availability":"not applicable","ddc":["530"],"OA_type":"hybrid","quality_controlled":"1","status":"public","scopus_import":"1","intvolume":"       174","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","date_created":"2024-02-22T14:10:40Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"17312","file_size":4220165,"creator":"dernst","date_updated":"2024-07-22T11:56:08Z","access_level":"open_access","success":1,"file_name":"2024_MaterialsScience_Shimura.pdf","date_created":"2024-07-22T11:56:08Z","checksum":"62e8e9ae960387a3dca32ec7f5e413ab"}],"date_updated":"2026-10-02T11:06:21Z","das_tickbox":"1","month":"05","OA_place":"publisher","supplementarymaterial":"no","dataavailabilitystatement":"No data was used for the research described in the article.","date_published":"2024-05-20T00:00:00Z"},{"supplementarymaterial":"no","month":"06","date_published":"2024-06-11T00:00:00Z","date_created":"2024-06-12T07:01:52Z","acknowledgement":"I am grateful to Matthew Kwan for setting the problem, providing useful literature,\r\nfruitful discussions, text review, mentorship, general encouragement and support.","department":[{"_id":"GradSch"}],"das_tickbox":"0","date_updated":"2026-10-02T11:06:38Z","researchdata_availability":"yes","year":"2024","publication":"arXiv","status":"public","abstract":[{"text":"This paper focuses on Majority Dynamics in sparse graphs, in particular, as a\r\ntool to study internal cuts. It is known that, in Majority Dynamics on a finite\r\ngraph, each vertex eventually either comes to a fixed state, or oscillates with\r\nperiod two. The empirical evidence acquired by simulations suggests that for\r\nrandom odd-regular graphs, approximately half of the vertices end up\r\noscillating with high probability. We notice a local symmetry between\r\noscillating and non-oscillating vertices, that potentially can explain why the\r\nfraction of the oscillating vertices is concentrated around $\\frac{1}{2}$. In\r\nour simulations, we observe that the parts of random odd-regular graph under\r\nMajority Dynamics with high probability do not contain $\\lceil \\frac{d}{2}\r\n\\rceil$-cores at any timestep, and thus, one cannot use Majority Dynamics to\r\nprove that internal cuts exist in odd-regular graphs almost surely. However, we\r\nsuggest a modification of Majority Dynamics, that yields parts with desired\r\ncores with high probability.","lang":"eng"}],"oa":1,"author":[{"id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","first_name":"Pavel","full_name":"Arkhipov, Pavel","last_name":"Arkhipov"}],"external_id":{"arxiv":["2406.07026"]},"publication_status":"submitted","title":"Majority dynamics and internal partitions of random regular graphs: Experimental results","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"2406.07026","citation":{"chicago":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>.","ista":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. arXiv, 2406.07026.","apa":"Arkhipov, P. (n.d.). Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>","short":"P. Arkhipov, ArXiv (n.d.).","ama":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>","mla":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, 2406.07026, doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>.","ieee":"P. Arkhipov, “Majority dynamics and internal partitions of random regular graphs: Experimental results,” <i>arXiv</i>. ."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.07026","open_access":"1"}],"doi":"10.48550/arXiv.2406.07026","_id":"17136","day":"11","fulldoi":"https://doi.org/10.48550/arXiv.2406.07026","oa_version":"Preprint","language":[{"iso":"eng"}],"article_processing_charge":"No","type":"preprint","arxiv":1},{"department":[{"_id":"GradSch"}],"date_created":"2024-10-06T22:01:12Z","acknowledgement":"The computational results presented here were enabled via a generous share of CPU time, offered by the Vienna Scientific Cluster (VSC) under Project No. 71263. The authors thank Ms. Katrin Muck for her guidance related to the use of HPC. A.J.A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1.","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2024-10-07T11:25:00Z","checksum":"f3874e64ef94e94b2376f00a1fee24c3","date_created":"2024-10-07T11:25:00Z","success":1,"file_name":"2024_JourChemicalPhysics_Wassermair.pdf","content_type":"application/pdf","relation":"main_file","file_size":15009000,"file_id":"18185"}],"das_tickbox":"1","date_updated":"2026-10-02T11:10:03Z","month":"09","supplementarymaterial":"yes","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","date_published":"2024-09-28T00:00:00Z","oa":1,"file_date_updated":"2024-10-07T11:25:00Z","author":[{"full_name":"Wassermair, Michael","id":"23d132c4-4e98-11ef-b275-9e8d4cd8c917","first_name":"Michael","orcid":"0009-0003-6339-4051","last_name":"Wassermair"},{"last_name":"Kahl","full_name":"Kahl, Gerhard","first_name":"Gerhard"},{"full_name":"Roth, Roland","first_name":"Roland","last_name":"Roth"},{"last_name":"Archer","full_name":"Archer, Andrew J.","first_name":"Andrew J."}],"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"We investigate the phase ordering (pattern formation) of systems of two-dimensional core–shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases. In DFT, the hard core part of the potential is treated using either fundamental measure theory or a simple local density approximation, whereas the soft shoulder is treated using the random phase approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities and shortcomings. We find that having the liquid state static structure factor S(k) for wavenumber k is sufficient to identify the Fourier modes governing both the liquid and solid phases. This allows us to identify from easier-to-obtain liquid state data the wavenumbers relevant to the periodic phases and to predict roughly where in the phase diagram these patterned phases arise."}],"publisher":"AIP Publishing","volume":161,"year":"2024","publication":"The Journal of chemical physics","researchdata_availability":"upon request","pmid":1,"scopus_import":"1","ddc":["530"],"status":"public","quality_controlled":"1","intvolume":"       161","citation":{"short":"M. Wassermair, G. Kahl, R. Roth, A.J. Archer, The Journal of Chemical Physics 161 (2024).","ama":"Wassermair M, Kahl G, Roth R, Archer AJ. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. <i>The Journal of chemical physics</i>. 2024;161(12). doi:<a href=\"https://doi.org/10.1063/5.0226954\">10.1063/5.0226954</a>","ieee":"M. Wassermair, G. Kahl, R. Roth, and A. J. Archer, “Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system,” <i>The Journal of chemical physics</i>, vol. 161, no. 12. AIP Publishing, 2024.","mla":"Wassermair, Michael, et al. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” <i>The Journal of Chemical Physics</i>, vol. 161, no. 12, 124503, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0226954\">10.1063/5.0226954</a>.","apa":"Wassermair, M., Kahl, G., Roth, R., &#38; Archer, A. J. (2024). Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0226954\">https://doi.org/10.1063/5.0226954</a>","chicago":"Wassermair, Michael, Gerhard Kahl, Roland Roth, and Andrew J. Archer. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0226954\">https://doi.org/10.1063/5.0226954</a>.","ista":"Wassermair M, Kahl G, Roth R, Archer AJ. 2024. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of chemical physics. 161(12), 124503."},"title":"Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system","external_id":{"arxiv":["2409.06447"],"isi":["001325268300004"],"pmid":["39344889"]},"publication_identifier":{"eissn":["1089-7690"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"124503 ","type":"journal_article","has_accepted_license":"1","article_type":"original","isi":1,"arxiv":1,"issue":"12","_id":"18174","day":"28","fulldoi":"https://doi.org/10.1063/5.0226954","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1063/5.0226954","article_processing_charge":"Yes (in subscription journal)"},{"intvolume":"       495","scopus_import":"1","status":"public","ddc":["540"],"quality_controlled":"1","researchdata_availability":"upon request","volume":495,"year":"2024","publication":"International Journal of Mass Spectrometry","publisher":"Elsevier","abstract":[{"text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"file_date_updated":"2024-07-16T08:27:34Z","oa":1,"author":[{"full_name":"Kluibenschedl, Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","orcid":"0000-0003-4695-5526","last_name":"Kluibenschedl"},{"last_name":"Ploner","full_name":"Ploner, Anna","first_name":"Anna"},{"first_name":"Christina","full_name":"Meisenbichler, Christina","last_name":"Meisenbichler"},{"first_name":"Robert","full_name":"Konrat, Robert","last_name":"Konrat"},{"full_name":"Müller, Thomas","first_name":"Thomas","last_name":"Müller"}],"date_published":"2024-01-01T00:00:00Z","dataavailabilitystatement":"Data will be made available on request.","supplementarymaterial":"yes","month":"01","das_tickbox":"1","date_updated":"2026-10-02T11:07:09Z","file":[{"checksum":"6c5eb6dc07af70a59251d2c6fed38894","file_name":"2024_IJMS_Kluibenschedl.pdf","date_created":"2024-07-16T08:27:34Z","success":1,"creator":"dernst","access_level":"open_access","date_updated":"2024-07-16T08:27:34Z","file_size":3003139,"file_id":"17256","relation":"main_file","content_type":"application/pdf"}],"date_created":"2023-12-10T23:00:57Z","acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","department":[{"_id":"GradSch"}],"article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.ijms.2023.117168","day":"01","_id":"14653","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.ijms.2023.117168","oa_version":"Published Version","isi":1,"article_type":"original","type":"journal_article","has_accepted_license":"1","article_number":"117168","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001125054400001"]},"publication_status":"published","publication_identifier":{"issn":["1387-3806"]},"title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)","citation":{"ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2024. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>.","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., &#38; Müller, T. (2024). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>","mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>, vol. 495, 117168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>.","ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” <i>International Journal of Mass Spectrometry</i>, vol. 495. Elsevier, 2024.","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2024).","ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. 2024;495. doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>"}}]