[{"_id":"11373","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaLo"}],"ec_funded":1,"tmp":{"short":"CC BY (4.0)","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"},"has_accepted_license":"1","day":"12","publication":"Nature Communications","corr_author":"1","year":"2022","article_type":"original","date_created":"2022-05-13T09:06:28Z","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","first_name":"Natalia S.","last_name":"Baranova"},{"full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","first_name":"Paulo R","last_name":"Dos Santos Caldas"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Pelegrin, Maria D"},{"id":"B9577E20-AA38-11E9-AC9A-0930E6697425","full_name":"Michalik, David","last_name":"Michalik","first_name":"David"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724"}],"file_date_updated":"2022-05-13T09:10:51Z","intvolume":"        13","oa":1,"publication_status":"published","doi":"10.1038/s41467-022-30301-y","project":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division"}],"file":[{"creator":"dernst","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","file_name":"2022_NatureCommunications_Radler.pdf","access_level":"open_access","date_created":"2022-05-13T09:10:51Z","success":1,"file_id":"11374","file_size":6945191,"date_updated":"2022-05-13T09:10:51Z","content_type":"application/pdf","relation":"main_file"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"article_number":"2635","scopus_import":"1","abstract":[{"text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.","lang":"eng"}],"citation":{"apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>"},"oa_version":"Published Version","publisher":"Springer Nature","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-34485-1"}],"record":[{"relation":"research_data","id":"10934","status":"public"},{"id":"14280","relation":"dissertation_contains","status":"public"}]},"status":"public","type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"volume":13,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_published":"2022-05-12T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","title":"In vitro reconstitution of Escherichia coli divisome activation","date_updated":"2026-08-06T22:30:10Z","quality_controlled":"1","external_id":{"isi":["000795171100037"]},"month":"05"},{"date_published":"2022-08-05T00:00:00Z","article_processing_charge":"No","date_created":"2022-07-26T11:01:47Z","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","year":"2022","doi":"10.15479/AT:ISTA:11653","file":[{"description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","relation":"main_file","date_updated":"2022-08-08T22:30:04Z","content_type":"application/x-zip-compressed","embargo":"2022-08-07","file_size":2209382998,"file_id":"11655","title":"Supplementary Datasets","date_created":"2022-07-26T12:37:52Z","access_level":"open_access","file_name":"Data.zip","creator":"melkrewi","checksum":"5f1d7c6d7ab5375ed2564521432bed0c"}],"month":"08","oa":1,"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"}],"date_updated":"2025-04-15T08:34:17Z","ddc":["570"],"file_date_updated":"2022-08-08T22:30:04Z","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","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"},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","citation":{"ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","short":"M.N. Elkrewi, (2022).","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022."},"abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11653","status":"public","corr_author":"1","type":"research_data","day":"05","contributor":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","last_name":"Mrnjavac"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sax","first_name":"Luca"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K"},{"last_name":"Hontoria ","first_name":"Francisco"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"related_material":{"record":[{"status":"public","id":"12248","relation":"used_in_publication"}]}},{"year":"2022","date_created":"2023-01-12T12:04:33Z","article_type":"original","file_date_updated":"2023-05-30T17:07:05Z","author":[{"orcid":"0000-0001-9523-9089","first_name":"Vladyslav","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Petrova, Olga","id":"5D8C9660-5D49-11EA-8188-567B3DDC885E","first_name":"Olga","last_name":"Petrova"},{"last_name":"Kampjut","first_name":"Domen","orcid":"0000-0002-6018-3422","id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen"},{"full_name":"Wojciechowska-Bason, Anna","first_name":"Anna","last_name":"Wojciechowska-Bason"},{"full_name":"Breese, Zara","first_name":"Zara","last_name":"Breese"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"ddc":["572"],"doi":"10.1038/s41586-022-05199-7","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697"}],"file":[{"file_id":"13104","success":1,"date_created":"2023-05-30T17:05:31Z","access_level":"open_access","file_name":"EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf","creator":"lsazanov","checksum":"d42a93e24f59e883ef0b5429832391d0","content_type":"application/pdf","relation":"main_file","date_updated":"2023-05-30T17:05:31Z","file_size":1425655},{"success":1,"file_id":"13105","date_created":"2023-05-30T17:07:05Z","file_name":"EcCxI_manuscript_rev3_SI_All_opt_upd.pdf","access_level":"open_access","creator":"lsazanov","checksum":"5422bc0a73b3daadafa262c7ea6deae3","date_updated":"2023-05-30T17:07:05Z","relation":"main_file","content_type":"application/pdf","file_size":9842513}],"oa":1,"publication_status":"published","intvolume":"       609","department":[{"_id":"LeSa"}],"issue":"7928","ec_funded":1,"_id":"12138","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"page":"808-814","has_accepted_license":"1","day":"22","corr_author":"1","publication":"Nature","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"volume":609,"title":"A universal coupling mechanism of respiratory complex I","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance with collecting cryo-EM data and A. Charnagalov for the assistance with protein purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also supported by the Medical Research Council (UK).","isi":1,"article_processing_charge":"No","date_published":"2022-09-22T00:00:00Z","external_id":{"pmid":["36104567"],"isi":["000854788200001"]},"quality_controlled":"1","date_updated":"2026-08-06T22:30:11Z","month":"09","oa_version":"Submitted Version","citation":{"apa":"Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z., &#38; Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex I. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>","chicago":"Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason, Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>.","mla":"Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14, doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>.","short":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A. Sazanov, Nature 609 (2022) 808–814.","ista":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928), 808–814.","ieee":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” <i>Nature</i>, vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.","ama":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. A universal coupling mechanism of respiratory complex I. <i>Nature</i>. 2022;609(7928):808-814. doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>"},"scopus_import":"1","keyword":["Multidisciplinary"],"abstract":[{"lang":"eng","text":"Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes."}],"publisher":"Springer Nature","related_material":{"record":[{"id":"12781","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-022-05457-8"},{"relation":"press_release","url":"https://ista.ac.at/en/news/proton-dominos-kick-off-life/","description":"News on ISTA website"}]},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"type":"journal_article","status":"public"},{"month":"07","external_id":{"pmid":["35856919"],"isi":["000874717200001"]},"date_updated":"2026-08-06T22:30:13Z","quality_controlled":"1","title":"Plan your trip before you leave: The neutrophils’ search-and-run journey","isi":1,"date_published":"2022-07-20T00:00:00Z","article_processing_charge":"No","volume":221,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"type":"journal_article","status":"public","related_material":{"record":[{"status":"public","id":"14697","relation":"dissertation_contains"}]},"publisher":"Rockefeller University Press","oa_version":"Published Version","keyword":["Cell Biology"],"citation":{"ieee":"J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” <i>Journal of Cell Biology</i>, vol. 221, no. 8. Rockefeller University Press, 2022.","ama":"Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. 2022;221(8). doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>","chicago":"Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>.","apa":"Stopp, J. A., &#38; Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>","short":"J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).","ista":"Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127.","mla":"Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>."},"abstract":[{"text":"Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant.","lang":"eng"}],"scopus_import":"1","article_number":"e202206127","file":[{"date_created":"2023-01-30T10:39:34Z","file_id":"12451","success":1,"creator":"dernst","checksum":"6b1620743669679b48b9389bb40f5a11","access_level":"open_access","file_name":"2022_JourCellBiology_Stopp.pdf","file_size":969969,"content_type":"application/pdf","date_updated":"2023-01-30T10:39:34Z","relation":"main_file"}],"doi":"10.1083/jcb.202206127","publication_status":"published","oa":1,"intvolume":"       221","file_date_updated":"2023-01-30T10:39:34Z","author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"}],"ddc":["570"],"language":[{"iso":"eng"}],"date_created":"2023-01-16T10:01:08Z","article_type":"original","year":"2022","corr_author":"1","publication":"Journal of Cell Biology","day":"20","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"department":[{"_id":"MiSi"}],"issue":"8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12272","pmid":1},{"_id":"11420","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"130","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"tmp":{"short":"CC BY (4.0)","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"},"has_accepted_license":"1","page":"1-55","day":"01","publication":"Journal of Machine Learning Research","corr_author":"1","year":"2022","article_type":"original","date_created":"2022-05-29T22:01:54Z","language":[{"iso":"eng"}],"ddc":["000"],"author":[{"last_name":"Shevchenko","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"full_name":"Kungurtsev, Vyacheslav","first_name":"Vyacheslav","last_name":"Kungurtsev"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"file_date_updated":"2022-05-30T08:22:55Z","intvolume":"        23","publication_status":"published","oa":1,"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2022-05-30T08:22:55Z","file_size":1521701,"file_name":"21-1365.pdf","access_level":"open_access","creator":"cchlebak","checksum":"d4ff5d1affb34848b5c5e4002483fc62","success":1,"file_id":"11422","date_created":"2022-05-30T08:22:55Z"}],"citation":{"ama":"Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. 2022;23(130):1-55.","ieee":"A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.","mla":"Shevchenko, Alexander, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.","ista":"Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55.","apa":"Shevchenko, A., Kungurtsev, V., &#38; Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","chicago":"Shevchenko, Alexander, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2022."},"abstract":[{"lang":"eng","text":"Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory."}],"scopus_import":"1","oa_version":"Published Version","publisher":"Journal of Machine Learning Research","related_material":{"record":[{"status":"public","id":"17465","relation":"dissertation_contains"}],"link":[{"relation":"other","url":"https://www.jmlr.org/papers/v23/21-1365.html"}]},"status":"public","type":"journal_article","publication_identifier":{"eissn":["1533-7928"],"issn":["1532-4435"]},"volume":23,"article_processing_charge":"No","arxiv":1,"date_published":"2022-04-01T00:00:00Z","acknowledgement":"We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n","title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","quality_controlled":"1","date_updated":"2026-08-06T22:30:15Z","external_id":{"arxiv":["2111.02278"]},"month":"04"},{"author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570"}],"language":[{"iso":"eng"}],"ddc":["573"],"degree_awarded":"PhD","file_date_updated":"2023-06-20T22:30:04Z","file":[{"creator":"mnardin","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","embargo_to":"open_access","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","access_level":"closed","date_created":"2022-08-19T16:31:34Z","file_id":"11935","file_size":13515457,"content_type":"application/zip","date_updated":"2023-06-20T22:30:04Z","relation":"source_file"},{"date_updated":"2023-06-20T22:30:04Z","relation":"main_file","content_type":"application/pdf","embargo":"2023-06-19","file_size":9906458,"access_level":"open_access","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","checksum":"0ec94035ea35a47a9f589ed168e60b48","creator":"mnardin","file_id":"11941","date_created":"2022-08-22T09:43:50Z"}],"doi":"10.15479/at:ista:11932","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"publication_status":"published","oa":1,"year":"2022","alternative_title":["ISTA Thesis"],"date_created":"2022-08-19T08:52:30Z","day":"19","corr_author":"1","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"ec_funded":1,"_id":"11932","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"has_accepted_license":"1","page":"136","date_updated":"2026-07-06T12:47:25Z","month":"08","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","article_processing_charge":"No","date_published":"2022-08-19T00:00:00Z","title":"On the encoding, transfer, and consolidation of spatial memories","related_material":{"record":[{"status":"public","id":"6194","relation":"part_of_dissertation"},{"status":"public","id":"10077","relation":"part_of_dissertation"}]},"status":"public","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"citation":{"short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>.","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>.","apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022."},"publisher":"Institute of Science and Technology Austria"},{"publisher":"Oxford University Press","keyword":["Genetics"],"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"citation":{"ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>"},"article_number":"iyac123","scopus_import":"1","oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"issn":["1943-2631"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"11653"},{"status":"public","relation":"dissertation_contains","id":"19386"}]},"article_processing_charge":"No","date_published":"2022-10-01T00:00:00Z","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","isi":1,"title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","volume":222,"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"10","date_updated":"2026-08-06T22:30:26Z","quality_controlled":"1","external_id":{"pmid":["35977389"],"isi":["000850270300001"]},"tmp":{"short":"CC BY (4.0)","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"},"has_accepted_license":"1","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12248","issue":"2","ec_funded":1,"department":[{"_id":"BeVi"}],"publication":"Genetics","corr_author":"1","day":"01","article_type":"original","date_created":"2023-01-16T09:56:10Z","year":"2022","intvolume":"       222","oa":1,"publication_status":"published","doi":"10.1093/genetics/iyac123","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2023-01-30T08:59:58Z","file_size":1347136,"success":1,"file_id":"12440","date_created":"2023-01-30T08:59:58Z","file_name":"2022_Genetics_Elkrewi.pdf","access_level":"open_access","creator":"dernst","checksum":"f79ff5383e882ea3f95f3da47a78029d"}],"language":[{"iso":"eng"}],"ddc":["570"],"author":[{"last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"},{"first_name":"Uladzislava","last_name":"Khauratovich","id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","full_name":"Khauratovich, Uladzislava"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups"},{"first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Mrnjavac","first_name":"Andrea","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"Luca","last_name":"Sax","full_name":"Sax, Luca","id":"701c5602-97d8-11ed-96b5-b52773c70189"},{"orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hontoria, Francisco","last_name":"Hontoria","first_name":"Francisco"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"file_date_updated":"2023-01-30T08:59:58Z"},{"day":"09","corr_author":"1","publication":"Proceedings of the Royal Society B: Biological Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10767","ec_funded":1,"department":[{"_id":"BeVi"}],"issue":"1968","pmid":1,"page":"20211985","tmp":{"short":"CC BY (4.0)","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"},"has_accepted_license":"1","file_date_updated":"2022-02-21T08:17:38Z","ddc":["570"],"language":[{"iso":"eng"}],"author":[{"full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","last_name":"Kelemen","first_name":"Réka K"},{"last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"},{"first_name":"Anna K.","last_name":"Lindholm","full_name":"Lindholm, Anna K."},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa":1,"doi":"10.1098/rspb.2021.1985","file":[{"file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","access_level":"open_access","creator":"dernst","checksum":"27042a3706ae52a919fed1ac114bf7bb","success":1,"file_id":"10779","date_created":"2022-02-21T08:17:38Z","relation":"main_file","date_updated":"2022-02-21T08:17:38Z","content_type":"application/pdf","file_size":2366976}],"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"intvolume":"       289","year":"2022","date_created":"2022-02-20T23:01:31Z","article_type":"original","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19386"},{"status":"public","id":"17119","relation":"dissertation_contains"}]},"type":"journal_article","publication_identifier":{"eissn":["1471-2954"]},"status":"public","abstract":[{"lang":"eng","text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination."}],"scopus_import":"1","citation":{"ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>."},"oa_version":"Published Version","publisher":"The Royal Society","external_id":{"pmid":["35135349"],"isi":["000752812800012"]},"quality_controlled":"1","date_updated":"2026-08-06T22:30:27Z","month":"02","volume":289,"title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","date_published":"2022-02-09T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. "},{"publisher":"Springer Nature","abstract":[{"text":"Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only 0.16+0.02−0.01 microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with 0.41+0.02−0.02), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago.","lang":"eng"}],"citation":{"short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, Nature Communications 13 (2022).","ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 13, 1276.","mla":"Sahu, Rishabh, et al. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>, vol. 13, 1276, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>.","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>.","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., &#38; Fink, J. M. (2022). Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>","ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Quantum-enabled operation of a microwave-optical interface,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"scopus_import":"1","article_number":"1276","oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13175"},{"id":"12900","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18871"}]},"date_published":"2022-03-11T00:00:00Z","arxiv":1,"article_processing_charge":"No","acknowledgement":"The authors thank S. Wald and F. Diorico for their help with optical filtering, O. Hosten\r\nand M. Aspelmeyer for equipment, H.G.L. Schwefel for materials and discussions, L.\r\nDrmic and P. Zielinski for software support, and the MIBA workshop at IST Austria for\r\nmachining the microwave cavity. This work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG QUNNECT) and the European\r\nUnion’s Horizon 2020 research and innovation program under grant agreement no.\r\n899354 (FETopen SuperQuLAN). W.H. is the recipient of an ISTplus postdoctoral fellowship\r\nwith funding from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the\r\nrecipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F.\r\nacknowledges support from the Austrian Science Fund (FWF) through BeyondC (F7105)\r\nand the European Union’s Horizon 2020 research and innovation programs under grant\r\nagreement no. 862644 (FETopen QUARTET).","isi":1,"title":"Quantum-enabled operation of a microwave-optical interface","volume":13,"acknowledged_ssus":[{"_id":"M-Shop"}],"month":"03","date_updated":"2026-08-06T22:30:31Z","quality_controlled":"1","external_id":{"pmid":["35277488"],"isi":["000767892300013"],"arxiv":["2107.08303"]},"tmp":{"short":"CC BY (4.0)","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"},"has_accepted_license":"1","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10924","department":[{"_id":"JoFi"}],"ec_funded":1,"publication":"Nature Communications","corr_author":"1","day":"11","article_type":"original","date_created":"2022-03-27T22:01:45Z","year":"2022","intvolume":"        13","publication_status":"published","oa":1,"file":[{"file_size":1167492,"date_updated":"2022-03-28T08:02:12Z","content_type":"application/pdf","relation":"main_file","date_created":"2022-03-28T08:02:12Z","success":1,"file_id":"10929","creator":"dernst","checksum":"7c5176db7b8e2ed18a4e0c5aca70a72c","file_name":"2022_NatureCommunications_Sahu.pdf","access_level":"open_access"}],"project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"doi":"10.1038/s41467-022-28924-2","language":[{"iso":"eng"}],"ddc":["530"],"author":[{"first_name":"Rishabh","last_name":"Sahu","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh"},{"orcid":"0000-0001-9868-2166","last_name":"Hease","first_name":"William J","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","first_name":"Alfredo R","orcid":"0000-0001-6249-5860"},{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","last_name":"Arnold","first_name":"Georg M"},{"first_name":"Liu","last_name":"Qiu","orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"file_date_updated":"2022-03-28T08:02:12Z"},{"date_updated":"2026-04-07T14:30:18Z","month":"02","acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2022-02-07T00:00:00Z","article_processing_charge":"No","title":"Pathogen-mediated sexual selection and immunization in ant colonies","status":"public","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history."}],"citation":{"short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","mla":"Metzler, Sina. <i>Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>.","apa":"Metzler, S. (2022). <i>Pathogen-mediated sexual selection and immunization in ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022."},"publisher":"Institute of Science and Technology Austria","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","full_name":"Metzler, Sina","last_name":"Metzler","first_name":"Sina","orcid":"0000-0002-9547-2494"}],"language":[{"iso":"eng"}],"ddc":["570"],"degree_awarded":"PhD","file_date_updated":"2023-02-04T23:30:03Z","project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"file":[{"file_size":6757886,"date_updated":"2023-02-03T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"smetzler","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Sina_Metzler.docx","date_created":"2022-02-04T15:36:12Z","file_id":"10728"},{"file_name":"Thesis_Sina_Metzler_A2.pdf","access_level":"open_access","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","creator":"smetzler","file_id":"10730","date_created":"2022-02-04T15:36:43Z","relation":"main_file","content_type":"application/pdf","date_updated":"2023-02-03T23:30:03Z","embargo":"2023-02-02","file_size":6314921},{"date_created":"2022-02-07T10:35:02Z","file_id":"10742","checksum":"dedd14b7be7a75d63018dbfc68dd8113","creator":"smetzler","access_level":"open_access","file_name":"Thesis_Sina_Metzler_print.pdf","embargo":"2023-02-02","file_size":6882557,"relation":"main_file","content_type":"application/pdf","date_updated":"2023-02-04T23:30:03Z"}],"doi":"10.15479/AT:ISTA:10727","publication_status":"published","oa":1,"year":"2022","alternative_title":["ISTA Thesis"],"date_created":"2022-02-04T15:45:12Z","day":"07","OA_place":"publisher","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"ec_funded":1,"_id":"10727","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}]},{"year":"2022","article_type":"original","date_created":"2021-11-02T09:28:55Z","language":[{"iso":"eng"}],"ddc":["000"],"author":[{"first_name":"Samira","last_name":"Goudarzi","full_name":"Goudarzi, Samira"},{"first_name":"Mohammad","last_name":"Sharif","full_name":"Sharif, Mohammad"},{"last_name":"Karimipour","first_name":"Farid","orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","full_name":"Karimipour, Farid"}],"file_date_updated":"2022-12-20T23:30:08Z","intvolume":"        13","oa":1,"publication_status":"published","file":[{"file_id":"10279","date_created":"2021-11-12T19:38:05Z","access_level":"open_access","file_name":"A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf","creator":"fkarimip","checksum":"0a8961416a9bb2be5a1cebda65468bcf","relation":"main_file","date_updated":"2022-12-20T23:30:08Z","content_type":"application/pdf","file_size":1634958,"embargo":"2022-11-12"}],"doi":"10.1007/s12652-021-03569-z","project":[{"call_identifier":"FWF","name":"Mathematics, Computer Science","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"_id":"10208","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"}],"has_accepted_license":"1","page":"2621–2635","day":"01","publication":"Journal of Ambient Intelligence and Humanized Computing","volume":13,"date_published":"2022-05-01T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","title":"A context-aware dimension reduction framework for trajectory and health signal analyses","quality_controlled":"1","date_updated":"2025-04-15T07:16:55Z","external_id":{"isi":["000712198000001"]},"month":"05","citation":{"ista":"Goudarzi S, Sharif M, Karimipour F. 2022. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 13, 2621–2635.","short":"S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635.","mla":"Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>.","chicago":"Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>.","apa":"Goudarzi, S., Sharif, M., &#38; Karimipour, F. (2022). A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>","ama":"Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. 2022;13:2621–2635. doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>","ieee":"S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction framework for trajectory and health signal analyses,” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13. Springer Nature, pp. 2621–2635, 2022."},"abstract":[{"text":"It is practical to collect a huge amount of movement data and environmental context information along with the health signals of individuals because there is the emergence of new generations of positioning and tracking technologies and rapid advancements of health sensors. The study of the relations between these datasets and their sequence similarity analysis is of interest to many applications such as health monitoring and recommender systems. However, entering all movement parameters and health signals can lead to the complexity of the problem and an increase in its computational load. In this situation, dimension reduction techniques can be used to avoid consideration of simultaneous dependent parameters in the process of similarity measurement of the trajectories. The present study provides a framework, named CaDRAW, to use spatial–temporal data and movement parameters along with independent context information in the process of measuring the similarity of trajectories. In this regard, the omission of dependent movement characteristic signals is conducted by using an unsupervised feature selection dimension reduction technique. To evaluate the effectiveness of the proposed framework, it was applied to a real contextualized movement and related health signal datasets of individuals. The results indicated the capability of the proposed framework in measuring the similarity and in decreasing the characteristic signals in such a way that the similarity results -before and after reduction of dependent characteristic signals- have small differences. The mean differences between the obtained results before and after reducing the dimension were 0.029 and 0.023 for the round path, respectively.","lang":"eng"}],"scopus_import":"1","keyword":["general computer science"],"oa_version":"Submitted Version","publisher":"Springer Nature","status":"public","type":"journal_article","publication_identifier":{"eissn":["1868-5145"],"issn":["1868-5137"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7577","issue":"1","department":[{"_id":"VlKo"}],"ec_funded":1,"page":"192-216","has_accepted_license":"1","day":"01","corr_author":"1","publication":"Applicable Analysis","year":"2022","date_created":"2020-03-09T07:06:52Z","article_type":"original","file_date_updated":"2021-03-16T23:30:06Z","ddc":["510","515","518"],"language":[{"iso":"eng"}],"author":[{"full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","last_name":"Shehu","first_name":"Yekini"},{"first_name":"Olaniyi S.","last_name":"Iyiola","full_name":"Iyiola, Olaniyi S."}],"publication_status":"published","oa":1,"doi":"10.1080/00036811.2020.1736287","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2021-03-16T23:30:06Z","embargo":"2021-03-15","file_size":4282586,"access_level":"open_access","file_name":"2020_ApplicAnalysis_Shehu.pdf","creator":"dernst","checksum":"869efe8cb09505dfa6012f67d20db63d","file_id":"8648","date_created":"2020-10-12T10:42:54Z"}],"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"intvolume":"       101","citation":{"chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>.","apa":"Shehu, Y., &#38; Iyiola, O. S. (2022). Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>","ista":"Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 101(1), 192–216.","short":"Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>, vol. 101, no. 1, Taylor &#38; Francis, 2022, pp. 192–216, doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>.","ieee":"Y. Shehu and O. S. Iyiola, “Weak convergence for variational inequalities with inertial-type method,” <i>Applicable Analysis</i>, vol. 101, no. 1. Taylor &#38; Francis, pp. 192–216, 2022.","ama":"Shehu Y, Iyiola OS. Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. 2022;101(1):192-216. doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>"},"abstract":[{"lang":"eng","text":"Weak convergence of inertial iterative method for solving variational inequalities is the focus of this paper. The cost function is assumed to be non-Lipschitz and monotone. We propose a projection-type method with inertial terms and give weak convergence analysis under appropriate conditions. Some test results are performed and compared with relevant methods in the literature to show the efficiency and advantages given by our proposed methods."}],"scopus_import":"1","oa_version":"Submitted Version","publisher":"Taylor & Francis","type":"journal_article","publication_identifier":{"eissn":["1563-504X"],"issn":["0003-6811"]},"status":"public","volume":101,"title":"Weak convergence for variational inequalities with inertial-type method","arxiv":1,"date_published":"2022-01-01T00:00:00Z","article_processing_charge":"No","acknowledgement":"The project of the first author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","isi":1,"external_id":{"arxiv":["2101.08057"],"isi":["000518364100001"]},"date_updated":"2024-11-04T13:52:44Z","quality_controlled":"1","month":"01"},{"year":"2022","article_processing_charge":"No","date_published":"2022-05-09T00:00:00Z","date_created":"2022-08-23T11:07:59Z","title":"Saturated reconstruction of living brain tissue","author":[{"orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Miguel Villalba","first_name":"Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","full_name":"Miguel Villalba, Eder"},{"orcid":"0000-0003-3862-1235","last_name":"Michalska","first_name":"Julia M","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"last_name":"Lin","first_name":"Zudi","full_name":"Lin, Zudi"},{"orcid":"0000-0002-8698-3823","first_name":"Jake","last_name":"Watson","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Troidl, Jakob","first_name":"Jakob","last_name":"Troidl"},{"full_name":"Beyer, Johanna","first_name":"Johanna","last_name":"Beyer"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","first_name":"Wiebke","last_name":"Jahr","orcid":"0000-0003-0201-2315"},{"last_name":"Cenameri","first_name":"Alban","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"first_name":"Johannes","last_name":"Broichhagen","full_name":"Broichhagen, Johannes"},{"first_name":"Seth G. N.","last_name":"Grant","full_name":"Grant, Seth G. N."},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"},{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G"}],"date_updated":"2026-08-06T22:30:59Z","language":[{"iso":"eng"}],"doi":"10.1101/2022.03.16.484431","month":"05","publication_status":"draft","oa":1,"oa_version":"Preprint","citation":{"ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>","ieee":"P. Velicky <i>et al.</i>, “Saturated reconstruction of living brain tissue,” <i>bioRxiv</i>. .","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, BioRxiv (n.d.).","ista":"Velicky P, Miguel Villalba E, Michalska JM, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. Saturated reconstruction of living brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","mla":"Velicky, Philipp, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Donglai Wei, Zudi Lin, Jake Watson, Jakob Troidl, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Wei, D., Lin, Z., Watson, J., … Danzl, J. G. (n.d.). Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>"},"abstract":[{"lang":"eng","text":"Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full <jats:italic>in-silico</jats:italic> reconstruction<jats:sup>1–5</jats:sup>, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches<jats:sup>6–12</jats:sup> facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy<jats:sup>6,13</jats:sup> in extracellularly labelled tissue<jats:sup>14</jats:sup> for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue."}],"department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"}],"_id":"11943","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","das_tickbox":"1","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.16.484431","open_access":"1"}],"day":"09","related_material":{"record":[{"status":"public","relation":"later_version","id":"13267"},{"status":"public","relation":"dissertation_contains","id":"12470"}]},"status":"public","publication":"bioRxiv","corr_author":"1","OA_place":"repository","type":"preprint"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.08.17.504272"}],"das_tickbox":"1","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11950","oa_version":"Preprint","citation":{"ama":"Michalska JM, Lyudchik J, Velicky P, et al. Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>","ieee":"J. M. Michalska <i>et al.</i>, “Uncovering brain tissue architecture across scales with super-resolution light microscopy,” <i>bioRxiv</i>. .","mla":"Michalska, Julia M., et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Venturino A, Roessler K, Czech T, Siegert S, Novarino G, Jonas PM, Danzl JG. Uncovering brain tissue architecture across scales with super-resolution light microscopy. bioRxiv, <a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, A. Venturino, K. Roessler, T. Czech, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, BioRxiv (n.d.).","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (n.d.). Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>."},"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanoscopic synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS leverages fixation-compatible extracellular labeling and advanced optical readout, in particular stimulated-emission depletion and expansion microscopy, to comprehensively delineate cellular structures. It enables 3D-reconstructing single synapses and mapping synaptic connectivity by identification and tailored analysis of putative synaptic cleft regions. Applying CATS to the hippocampal mossy fiber circuitry, we demonstrate its power to reveal the system’s molecularly informed ultrastructure across spatial scales and assess local connectivity by reconstructing and quantifying the synaptic input and output structure of identified neurons.","lang":"eng"}],"corr_author":"1","type":"preprint","status":"public","publication":"bioRxiv","related_material":{"record":[{"id":"12470","relation":"dissertation_contains","status":"public"}]},"day":"18","date_created":"2022-08-24T08:24:52Z","title":"Uncovering brain tissue architecture across scales with super-resolution light microscopy","date_published":"2022-08-18T00:00:00Z","article_processing_charge":"No","year":"2022","month":"08","doi":"10.1101/2022.08.17.504272","oa":1,"publication_status":"draft","date_updated":"2026-08-06T22:30:59Z","author":[{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","last_name":"Michalska","first_name":"Julia M"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia"},{"orcid":"0000-0002-2340-7431","last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana","last_name":"Korinkova"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake"},{"first_name":"Alban","last_name":"Cenameri","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alessandro","last_name":"Venturino","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro"},{"full_name":"Roessler, Karl","first_name":"Karl","last_name":"Roessler"},{"full_name":"Czech, Thomas","first_name":"Thomas","last_name":"Czech"},{"first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}]},{"related_material":{"record":[{"relation":"dissertation_contains","id":"17208","status":"public"},{"id":"14622","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"issn":["2691-3399"]},"type":"journal_article","status":"public","oa_version":"Published Version","citation":{"ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>","ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>.","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.","short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., &#38; Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>."},"keyword":["General Medicine"],"scopus_import":"1","abstract":[{"lang":"eng","text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. "}],"article_number":"020365","publisher":"American Physical Society","external_id":{"arxiv":["2201.08194"],"isi":["000822564300001"]},"quality_controlled":"1","date_updated":"2026-08-06T22:31:04Z","month":"06","volume":3,"title":"Avoiding barren plateaus using classical shadows","isi":1,"acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","arxiv":1,"article_processing_charge":"No","date_published":"2022-06-29T00:00:00Z","day":"29","corr_author":"1","publication":"PRX Quantum","ec_funded":1,"issue":"2","department":[{"_id":"MaSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11471","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","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"},"file_date_updated":"2022-06-30T07:14:48Z","author":[{"first_name":"Stefan","last_name":"Sack","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan"},{"id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A","last_name":"Medina Ramos","first_name":"Raimel A","orcid":"0000-0002-5383-2869"},{"last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"last_name":"Kueng","first_name":"Richard","full_name":"Kueng, Richard"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym"}],"language":[{"iso":"eng"}],"ddc":["530"],"doi":"10.1103/prxquantum.3.020365","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"file":[{"date_created":"2022-06-30T07:14:48Z","success":1,"file_id":"11472","checksum":"a7706b28d24a0e32a55ea04b82a2df43","creator":"dernst","file_name":"2022_PRXQuantum_Sack.pdf","access_level":"open_access","file_size":4231591,"date_updated":"2022-06-30T07:14:48Z","content_type":"application/pdf","relation":"main_file"}],"oa":1,"publication_status":"published","intvolume":"         3","year":"2022","date_created":"2022-06-29T20:21:32Z","article_type":"original"},{"language":[{"iso":"eng"}],"ddc":["540"],"author":[{"full_name":"Fiedler, Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","last_name":"Fiedler","first_name":"Christine"},{"full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","orcid":"0000-0003-1537-7436","first_name":"Tobias","last_name":"Kleinhanns"},{"full_name":"Garcia, Maria","id":"6e5c50b8-97dc-11ed-be98-b0a74c84cae0","first_name":"Maria","last_name":"Garcia"},{"last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"full_name":"Calcabrini, Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","first_name":"Mariano","last_name":"Calcabrini"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843"}],"file_date_updated":"2023-01-30T07:35:09Z","intvolume":"        34","oa":1,"publication_status":"published","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2023-01-30T07:35:09Z","file_size":10923495,"success":1,"file_id":"12434","date_created":"2023-01-30T07:35:09Z","file_name":"2022_ChemistryMaterials_Fiedler.pdf","access_level":"open_access","checksum":"f7143e44ab510519d1949099c3558532","creator":"dernst"}],"doi":"10.1021/acs.chemmater.2c01967","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"year":"2022","article_type":"original","date_created":"2023-01-16T09:51:26Z","day":"20","publication":"Chemistry of Materials","corr_author":"1","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"12237","ec_funded":1,"department":[{"_id":"MaIb"}],"issue":"19","tmp":{"short":"CC BY (4.0)","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"},"has_accepted_license":"1","page":"8471-8489","quality_controlled":"1","date_updated":"2026-08-07T10:54:20Z","external_id":{"pmid":["36248227"],"isi":["000917837600001"]},"month":"09","volume":34,"date_published":"2022-09-20T00:00:00Z","article_processing_charge":"Yes (via OA deal)","acknowledgement":"This work was financially supported by ISTA and the Werner Siemens Foundation. M.C. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385.","isi":1,"title":"Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇","related_material":{"record":[{"relation":"dissertation_contains","id":"20415","status":"public"},{"id":"12885","relation":"dissertation_contains","status":"public"},{"status":"public","id":"22017","relation":"dissertation_contains"},{"status":"for_moderation","id":"22626","relation":"dissertation_contains"}]},"status":"public","type":"journal_article","publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"abstract":[{"text":"Thermoelectric technology requires synthesizing complex materials where not only the crystal structure but also other structural features such as defects, grain size and orientation, and interfaces must be controlled. To date, conventional solid-state techniques are unable to provide this level of control. Herein, we present a synthetic approach in which dense inorganic thermoelectric materials are produced by the consolidation of well-defined nanoparticle powders. The idea is that controlling the characteristics of the powder allows the chemical transformations that take place during consolidation to be guided, ultimately yielding inorganic solids with targeted features. Different from conventional methods, syntheses in solution can produce particles with unprecedented control over their size, shape, crystal structure, composition, and surface chemistry. However, to date, most works have focused only on the low-cost benefits of this strategy. In this perspective, we first cover the opportunities that solution processing of the powder offers, emphasizing the potential structural features that can be controlled by precisely engineering the inorganic core of the particle, the surface, and the organization of the particles before consolidation. We then discuss the challenges of this synthetic approach and more practical matters related to solution processing. Finally, we suggest some good practices for adequate knowledge transfer and improving reproducibility among different laboratories.","lang":"eng"}],"citation":{"ama":"Fiedler C, Kleinhanns T, Garcia M, Lee S, Calcabrini M, Ibáñez M. Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇. <i>Chemistry of Materials</i>. 2022;34(19):8471-8489. doi:<a href=\"https://doi.org/10.1021/acs.chemmater.2c01967\">10.1021/acs.chemmater.2c01967</a>","ieee":"C. Fiedler, T. Kleinhanns, M. Garcia, S. Lee, M. Calcabrini, and M. Ibáñez, “Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇,” <i>Chemistry of Materials</i>, vol. 34, no. 19. American Chemical Society, pp. 8471–8489, 2022.","short":"C. Fiedler, T. Kleinhanns, M. Garcia, S. Lee, M. Calcabrini, M. Ibáñez, Chemistry of Materials 34 (2022) 8471–8489.","ista":"Fiedler C, Kleinhanns T, Garcia M, Lee S, Calcabrini M, Ibáñez M. 2022. Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇. Chemistry of Materials. 34(19), 8471–8489.","mla":"Fiedler, Christine, et al. “Solution-Processed Inorganic Thermoelectric Materials: Opportunities and Challenges ∇.” <i>Chemistry of Materials</i>, vol. 34, no. 19, American Chemical Society, 2022, pp. 8471–89, doi:<a href=\"https://doi.org/10.1021/acs.chemmater.2c01967\">10.1021/acs.chemmater.2c01967</a>.","chicago":"Fiedler, Christine, Tobias Kleinhanns, Maria Garcia, Seungho Lee, Mariano Calcabrini, and Maria Ibáñez. “Solution-Processed Inorganic Thermoelectric Materials: Opportunities and Challenges ∇.” <i>Chemistry of Materials</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.chemmater.2c01967\">https://doi.org/10.1021/acs.chemmater.2c01967</a>.","apa":"Fiedler, C., Kleinhanns, T., Garcia, M., Lee, S., Calcabrini, M., &#38; Ibáñez, M. (2022). Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇. <i>Chemistry of Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemmater.2c01967\">https://doi.org/10.1021/acs.chemmater.2c01967</a>"},"scopus_import":"1","keyword":["Materials Chemistry","General Chemical Engineering","General Chemistry"],"oa_version":"Published Version","publisher":"American Chemical Society"},{"main_file_link":[{"url":"https://arxiv.org/abs/2111.12968","open_access":"1"}],"das_tickbox":"1","publisher":"AIP Publishing","oa_version":"Preprint","scopus_import":"1","article_number":"074106","abstract":[{"text":"Titanium dioxide has been extensively studied in the rutile or anatase phase, while its high-pressure phases are less well-understood, despite that many are thought to have interesting optical, mechanical, and electrochemical properties. First-principles methods, such as density functional theory (DFT), are often used to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus, impractical for long time scale and large system-size simulations at finite temperatures. On the other hand, cheap empirical potentials fail to capture the relative stabilities of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure phases of TiO2, we design an empirical model as a baseline and then train a machine learning potential based on the difference between the DFT data and the empirical model. This so-called Δ-learning potential contains long-range electrostatic interactions and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range 0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition processes by compressing anatase at different temperatures. At 300 K, we predominantly observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic two-step mechanism with a highly ordered and collective atomic motion. At 2000 K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The pressures computed for these transitions show good agreement with experiments. Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases, and our method is generally applicable to other functional materials with multiple polymorphs.","lang":"eng"}],"citation":{"ieee":"J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential,” <i>The Journal of chemical physics</i>, vol. 156, no. 7. AIP Publishing, 2022.","ama":"Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of chemical physics</i>. 2022;156(7). doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>","chicago":"Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>.","apa":"Lee, J. G., Pickard, C. J., &#38; Cheng, B. (2022). High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>","ista":"Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7), 074106.","short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","mla":"Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 7, 074106, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>."},"status":"public","publication_identifier":{"eissn":["1089-7690"]},"type":"journal_article","supplementarymaterial":"yes","acknowledgement":"J.G.L. and B.C. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).","isi":1,"date_published":"2022-02-16T00:00:00Z","arxiv":1,"article_processing_charge":"No","title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","volume":156,"month":"02","date_updated":"2026-08-07T11:17:03Z","quality_controlled":"1","external_id":{"arxiv":["2111.12968"],"isi":["000796704500014"],"pmid":["35183078"]},"pmid":1,"issue":"7","department":[{"_id":"BiCh"}],"_id":"10827","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"The Journal of chemical physics","corr_author":"1","researchdata_availability":"yes","day":"16","article_type":"original","date_created":"2022-03-06T23:01:53Z","year":"2022","intvolume":"       156","doi":"10.1063/5.0079844","oa":1,"publication_status":"published","author":[{"first_name":"Jacob G.","last_name":"Lee","full_name":"Lee, Jacob G."},{"first_name":"Chris J.","last_name":"Pickard","full_name":"Pickard, Chris J."},{"first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"}],"language":[{"iso":"eng"}],"dataavailabilitystatement":"All original data generated for the study and the Δ-learning potential for TiO2 constructed in this study are in the SI repository at https://github.com/jacobglee1/tio2-mlp."},{"volume":3,"acknowledgement":"C P acknowledges funding from Astex through the Sustaining Innovation Program under the Milner Consortium. B C acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant EP/P020259/1. F A F acknowledges funding from the Swiss National Science Foundation (Grant No. P2BSP2_191736). ","isi":1,"date_published":"2022-11-17T00:00:00Z","article_processing_charge":"No","title":"BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale","date_updated":"2026-08-07T11:19:31Z","quality_controlled":"1","external_id":{"isi":["000886534000001"]},"month":"11","oa_version":"Published Version","keyword":["Artificial Intelligence","Human-Computer Interaction","Software"],"article_number":"040501","citation":{"chicago":"Poelking, Carl, Felix A Faber, and Bingqing Cheng. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” <i>Machine Learning: Science and Technology</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">https://doi.org/10.1088/2632-2153/ac4d11</a>.","apa":"Poelking, C., Faber, F. A., &#38; Cheng, B. (2022). BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. <i>Machine Learning: Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">https://doi.org/10.1088/2632-2153/ac4d11</a>","ista":"Poelking C, Faber FA, Cheng B. 2022. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. Machine Learning: Science and Technology. 3(4), 040501.","short":"C. Poelking, F.A. Faber, B. Cheng, Machine Learning: Science and Technology 3 (2022).","mla":"Poelking, Carl, et al. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” <i>Machine Learning: Science and Technology</i>, vol. 3, no. 4, 040501, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">10.1088/2632-2153/ac4d11</a>.","ieee":"C. Poelking, F. A. Faber, and B. Cheng, “BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale,” <i>Machine Learning: Science and Technology</i>, vol. 3, no. 4. IOP Publishing, 2022.","ama":"Poelking C, Faber FA, Cheng B. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. <i>Machine Learning: Science and Technology</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">10.1088/2632-2153/ac4d11</a>"},"scopus_import":"1","abstract":[{"text":"We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, in addition to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness.","lang":"eng"}],"das_tickbox":"1","publisher":"IOP Publishing","related_material":{"link":[{"relation":"software","url":"https://github.com/capoe/benchml"}]},"supplementarymaterial":"yes","status":"public","publication_identifier":{"issn":["2632-2153"]},"type":"journal_article","year":"2022","article_type":"original","date_created":"2023-01-12T12:02:21Z","author":[{"full_name":"Poelking, Carl","last_name":"Poelking","first_name":"Carl"},{"full_name":"Faber, Felix A","last_name":"Faber","first_name":"Felix A"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632"}],"ddc":["000"],"language":[{"iso":"eng"}],"dataavailabilitystatement":"The datasets used for this study are available at https://github.com/BingqingCheng/linear-regression-benchmarks. All data that support the findings of this study are included within the article (and any supplementary files).","file_date_updated":"2023-01-23T10:42:04Z","intvolume":"         3","doi":"10.1088/2632-2153/ac4d11","file":[{"file_size":13814559,"relation":"main_file","date_updated":"2023-01-23T10:42:04Z","content_type":"application/pdf","date_created":"2023-01-23T10:42:04Z","file_id":"12343","success":1,"creator":"dernst","checksum":"8930d4ad6ed9b47358c6f1a68666adb6","access_level":"open_access","file_name":"2022_MachLearning_Poelking.pdf"}],"oa":1,"publication_status":"published","department":[{"_id":"BiCh"}],"issue":"4","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"12128","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","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"},"researchdata_availability":"yes","day":"17","publication":"Machine Learning: Science and Technology","corr_author":"1"},{"oa_version":"Published Version","article_number":"121101","abstract":[{"text":"The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. ","lang":"eng"}],"citation":{"ieee":"B. Cheng, “Computing chemical potentials of solutions from structure factors,” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12. AIP Publishing, 2022.","ama":"Cheng B. Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. 2022;157(12). doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>","apa":"Cheng, B. (2022). Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>","chicago":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>.","mla":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12, 121101, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>.","ista":"Cheng B. 2022. Computing chemical potentials of solutions from structure factors. The Journal of Chemical Physics. 157(12), 121101.","short":"B. Cheng, The Journal of Chemical Physics 157 (2022)."},"scopus_import":"1","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"publisher":"AIP Publishing","das_tickbox":"1","related_material":{"link":[{"url":"https://github.com/ BingqingCheng/S0","relation":"software"}]},"supplementarymaterial":"yes","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"type":"journal_article","status":"public","volume":157,"title":"Computing chemical potentials of solutions from structure factors","acknowledgement":"I thank Daan Frenkel for providing feedback on an early draft and for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions on the manuscript.","isi":1,"article_processing_charge":"No","date_published":"2022-09-30T00:00:00Z","external_id":{"pmid":["36182422"],"isi":["000862856000003"]},"quality_controlled":"1","date_updated":"2026-08-07T11:22:29Z","month":"09","department":[{"_id":"BiCh"}],"issue":"12","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"12249","pmid":1,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","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"},"researchdata_availability":"yes","day":"30","corr_author":"1","publication":"The Journal of Chemical Physics","year":"2022","date_created":"2023-01-16T09:56:20Z","article_type":"original","dataavailabilitystatement":"All PYTHON scripts and simulation input files generated for the study are in the SI repository https://github.com/BingqingCheng/S0, Ref. 29.\r\n29. B. Cheng, https://github.com/BingqingCheng/S0 “Data repository for the S0 method” (2020).","file_date_updated":"2023-01-30T09:07:00Z","author":[{"full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng"}],"language":[{"iso":"eng"}],"ddc":["530","540"],"doi":"10.1063/5.0107059","file":[{"relation":"main_file","date_updated":"2023-01-30T09:07:00Z","content_type":"application/pdf","file_size":4402384,"access_level":"open_access","file_name":"2022_JourChemPhysics_Cheng.pdf","creator":"dernst","checksum":"b0915b706568a663a9a372fca24adf35","file_id":"12441","success":1,"date_created":"2023-01-30T09:07:00Z"}],"oa":1,"publication_status":"published","intvolume":"       157"},{"title":"Thermodynamics of high-pressure ice phases explored with atomistic simulations","date_published":"2022-08-10T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"We thank Chris Pickard for providing the initial structures of high-pressure ice phases and for useful advice. A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. M.B. was supported by the European Union within the Marie Skłodowska-Curie actions (xICE grant 894725) and acknowledges computational resources at North-German Supercomputing Alliance (HLRN) facilities. S.H. and M.M. acknowledge support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge programme. F.C. acknowledges support from the US DOE Office of Science, Office of Fusion Energy Sciences. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.","volume":13,"month":"08","external_id":{"isi":["000838655300022"],"pmid":["35948550"]},"quality_controlled":"1","date_updated":"2026-08-07T11:18:25Z","publisher":"Springer Nature","das_tickbox":"1","article_number":"4707","abstract":[{"lang":"eng","text":"Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII′ and X are the same thermodynamic phase under different conditions, whereas superionic ice VII″ has a first-order phase boundary with ice VII′. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems."}],"scopus_import":"1","citation":{"ieee":"A. Reinhardt, M. Bethkenhagen, F. Coppari, M. Millot, S. Hamel, and B. Cheng, “Thermodynamics of high-pressure ice phases explored with atomistic simulations,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Reinhardt A, Bethkenhagen M, Coppari F, Millot M, Hamel S, Cheng B. Thermodynamics of high-pressure ice phases explored with atomistic simulations. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32374-1\">10.1038/s41467-022-32374-1</a>","apa":"Reinhardt, A., Bethkenhagen, M., Coppari, F., Millot, M., Hamel, S., &#38; Cheng, B. (2022). Thermodynamics of high-pressure ice phases explored with atomistic simulations. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32374-1\">https://doi.org/10.1038/s41467-022-32374-1</a>","chicago":"Reinhardt, Aleks, Mandy Bethkenhagen, Federica Coppari, Marius Millot, Sebastien Hamel, and Bingqing Cheng. “Thermodynamics of High-Pressure Ice Phases Explored with Atomistic Simulations.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32374-1\">https://doi.org/10.1038/s41467-022-32374-1</a>.","mla":"Reinhardt, Aleks, et al. “Thermodynamics of High-Pressure Ice Phases Explored with Atomistic Simulations.” <i>Nature Communications</i>, vol. 13, 4707, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32374-1\">10.1038/s41467-022-32374-1</a>.","ista":"Reinhardt A, Bethkenhagen M, Coppari F, Millot M, Hamel S, Cheng B. 2022. Thermodynamics of high-pressure ice phases explored with atomistic simulations. Nature Communications. 13, 4707.","short":"A. Reinhardt, M. Bethkenhagen, F. Coppari, M. Millot, S. Hamel, B. Cheng, Nature Communications 13 (2022)."},"oa_version":"Published Version","type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"status":"public","supplementarymaterial":"yes","date_created":"2022-08-21T22:01:55Z","article_type":"original","year":"2022","publication_status":"published","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2022-08-22T06:33:02Z","relation":"main_file","file_size":1767206,"file_name":"2022_NatureCommunications_Reinhardt.pdf","access_level":"open_access","checksum":"8ff9b689cde59fd3a9959a9f01929dea","creator":"dernst","success":1,"file_id":"11939","date_created":"2022-08-22T06:33:02Z"}],"doi":"10.1038/s41467-022-32374-1","intvolume":"        13","dataavailabilitystatement":"All original data generated for the study are in the SI repository https://github.com/BingqingCheng/highP-ice.","file_date_updated":"2022-08-22T06:33:02Z","language":[{"iso":"eng"}],"ddc":["540"],"author":[{"full_name":"Reinhardt, Aleks","first_name":"Aleks","last_name":"Reinhardt"},{"full_name":"Bethkenhagen, Mandy","first_name":"Mandy","last_name":"Bethkenhagen"},{"full_name":"Coppari, Federica","first_name":"Federica","last_name":"Coppari"},{"first_name":"Marius","last_name":"Millot","full_name":"Millot, Marius"},{"full_name":"Hamel, Sebastien","first_name":"Sebastien","last_name":"Hamel"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632"}],"tmp":{"short":"CC BY (4.0)","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"},"has_accepted_license":"1","_id":"11937","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"BiCh"}],"pmid":1,"corr_author":"1","publication":"Nature Communications","day":"10","researchdata_availability":"yes"}]