[{"doi":"10.1101/2022.03.16.484431","publication":"bioRxiv","date_published":"2022-05-09T00:00:00Z","author":[{"first_name":"Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB91342-F248-11E8-B48F-1D18A9856A87","full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","last_name":"Miguel Villalba","first_name":"Eder"},{"last_name":"Michalska","orcid":"0000-0003-3862-1235","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M"},{"full_name":"Wei, Donglai","first_name":"Donglai","last_name":"Wei"},{"first_name":"Zudi","last_name":"Lin","full_name":"Lin, Zudi"},{"first_name":"Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"first_name":"Johanna","last_name":"Beyer","full_name":"Beyer, Johanna"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav","last_name":"Ben Simon","first_name":"Yoav"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr","orcid":"0000-0003-0201-2315","first_name":"Wiebke"},{"last_name":"Cenameri","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban"},{"full_name":"Broichhagen, Johannes","first_name":"Johannes","last_name":"Broichhagen"},{"last_name":"Grant","first_name":"Seth G. N.","full_name":"Grant, Seth G. N."},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"language":[{"iso":"eng"}],"_id":"11943","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."}],"date_created":"2022-08-23T11:07:59Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"13267"},{"status":"public","id":"12470","relation":"dissertation_contains"}]},"fulldoi":"https://doi.org/10.1101/2022.03.16.484431","title":"Saturated reconstruction of living brain tissue","article_processing_charge":"No","das_tickbox":"1","month":"05","date_updated":"2026-11-06T23:30:50Z","day":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.16.484431"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","publication_status":"draft","OA_place":"repository","citation":{"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>.","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>","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.).","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>.","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>. .","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>."},"oa":1,"status":"public","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"}],"corr_author":"1","type":"preprint","year":"2022"},{"date_updated":"2026-11-06T23:30:50Z","month":"08","article_processing_charge":"No","das_tickbox":"1","title":"Uncovering brain tissue architecture across scales with super-resolution light microscopy","fulldoi":"https://doi.org/10.1101/2022.08.17.504272","related_material":{"record":[{"relation":"dissertation_contains","id":"12470","status":"public"}]},"date_created":"2022-08-24T08:24:52Z","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"}],"language":[{"iso":"eng"}],"_id":"11950","author":[{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska","orcid":"0000-0003-3862-1235"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"last_name":"Korinkova","first_name":"Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","full_name":"Korinkova, Hana"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","orcid":"0000-0002-8698-3823","last_name":"Watson"},{"last_name":"Cenameri","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","first_name":"Alessandro"},{"full_name":"Roessler, Karl","last_name":"Roessler","first_name":"Karl"},{"full_name":"Czech, Thomas","last_name":"Czech","first_name":"Thomas"},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-08-18T00:00:00Z","publication":"bioRxiv","doi":"10.1101/2022.08.17.504272","year":"2022","type":"preprint","corr_author":"1","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"}],"status":"public","citation":{"ieee":"J. M. Michalska <i>et al.</i>, “Uncovering brain tissue architecture across scales with super-resolution light microscopy,” <i>bioRxiv</i>. .","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>","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>.","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.).","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>.","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>"},"oa":1,"publication_status":"draft","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2022.08.17.504272","open_access":"1"}],"day":"18"},{"publication_identifier":{"issn":["2691-3399"]},"doi":"10.1103/prxquantum.3.020365","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. "}],"isi":1,"language":[{"iso":"eng"}],"intvolume":"         3","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).","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17208"},{"id":"14622","relation":"dissertation_contains","status":"public"}]},"fulldoi":"https://doi.org/10.1103/prxquantum.3.020365","ddc":["530"],"volume":3,"oa_version":"Published Version","keyword":["General Medicine"],"external_id":{"isi":["000822564300001"],"arxiv":["2201.08194"]},"day":"29","citation":{"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>.","short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","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>","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>.","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.","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>","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365."},"issue":"2","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","date_published":"2022-06-29T00:00:00Z","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan"},{"full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869"},{"orcid":"0000-0002-8443-1064","last_name":"Michailidis","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"last_name":"Kueng","first_name":"Richard","full_name":"Kueng, Richard"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"publication":"PRX Quantum","file":[{"date_created":"2022-06-30T07:14:48Z","file_size":4231591,"file_id":"11472","success":1,"date_updated":"2022-06-30T07:14:48Z","creator":"dernst","file_name":"2022_PRXQuantum_Sack.pdf","checksum":"a7706b28d24a0e32a55ea04b82a2df43","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"_id":"11471","title":"Avoiding barren plateaus using classical shadows","article_type":"original","date_created":"2022-06-29T20:21:32Z","arxiv":1,"month":"06","date_updated":"2026-11-06T23:30:57Z","article_processing_charge":"No","publication_status":"published","publisher":"American Physical Society","file_date_updated":"2022-06-30T07:14:48Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","oa":1,"article_number":"020365","license":"https://creativecommons.org/licenses/by/4.0/","corr_author":"1","type":"journal_article","scopus_import":"1","year":"2022","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"department":[{"_id":"MaSe"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-01-30T08:59:58Z","publisher":"Oxford University Press","publication_status":"published","article_number":"iyac123","oa":1,"quality_controlled":"1","pmid":1,"department":[{"_id":"BeVi"}],"project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"scopus_import":"1","type":"journal_article","year":"2022","corr_author":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f79ff5383e882ea3f95f3da47a78029d","file_name":"2022_Genetics_Elkrewi.pdf","creator":"dernst","date_updated":"2023-01-30T08:59:58Z","success":1,"file_id":"12440","date_created":"2023-01-30T08:59:58Z","file_size":1347136}],"publication":"Genetics","author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","full_name":"Khauratovich, Uladzislava","last_name":"Khauratovich","first_name":"Uladzislava"},{"last_name":"Toups","orcid":"0000-0002-9752-7380","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K"},{"first_name":"Andrea","last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"first_name":"Luca","last_name":"Sax","full_name":"Sax, Luca","id":"701c5602-97d8-11ed-96b5-b52773c70189"},{"first_name":"Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hontoria, Francisco","first_name":"Francisco","last_name":"Hontoria"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"date_published":"2022-10-01T00:00:00Z","_id":"12248","ec_funded":1,"date_created":"2023-01-16T09:56:10Z","title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","article_type":"original","article_processing_charge":"No","month":"10","date_updated":"2026-11-06T23:30:58Z","day":"01","external_id":{"isi":["000850270300001"],"pmid":["35977389"]},"keyword":["Genetics"],"oa_version":"Published Version","issue":"2","citation":{"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>","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>.","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>","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).","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>.","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."},"status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/genetics/iyac123","publication_identifier":{"issn":["1943-2631"]},"language":[{"iso":"eng"}],"isi":1,"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 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."}],"fulldoi":"https://doi.org/10.1093/genetics/iyac123","related_material":{"record":[{"id":"11653","relation":"research_data","status":"public"},{"id":"19386","relation":"dissertation_contains","status":"public"}]},"intvolume":"       222","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.","volume":222,"acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"]},{"oa_version":"Published Version","external_id":{"isi":["000752812800012"],"pmid":["35135349"]},"day":"09","citation":{"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.","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>.","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>.","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985."},"issue":"1968","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","publication_identifier":{"eissn":["1471-2954"]},"doi":"10.1098/rspb.2021.1985","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."}],"isi":1,"language":[{"iso":"eng"}],"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. ","intvolume":"       289","related_material":{"record":[{"relation":"dissertation_contains","id":"19386","status":"public"},{"id":"17119","relation":"dissertation_contains","status":"public"}]},"fulldoi":"https://doi.org/10.1098/rspb.2021.1985","ddc":["570"],"volume":289,"publication_status":"published","publisher":"The Royal Society","file_date_updated":"2022-02-21T08:17:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"20211985","quality_controlled":"1","oa":1,"pmid":1,"corr_author":"1","type":"journal_article","year":"2022","scopus_import":"1","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"department":[{"_id":"BeVi"}],"date_published":"2022-02-09T00:00:00Z","author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","first_name":"Réka K"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","first_name":"Marwan N"},{"full_name":"Lindholm, Anna K.","last_name":"Lindholm","first_name":"Anna K."},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"file":[{"date_created":"2022-02-21T08:17:38Z","file_size":2366976,"file_id":"10779","success":1,"date_updated":"2022-02-21T08:17:38Z","creator":"dernst","file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","relation":"main_file","checksum":"27042a3706ae52a919fed1ac114bf7bb","access_level":"open_access","content_type":"application/pdf"}],"publication":"Proceedings of the Royal Society B: Biological Sciences","ec_funded":1,"_id":"10767","title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","article_type":"original","date_created":"2022-02-20T23:01:31Z","date_updated":"2026-11-06T23:31:01Z","month":"02","article_processing_charge":"No"},{"author":[{"full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","last_name":"Shevchenko"},{"full_name":"Kungurtsev, Vyacheslav","first_name":"Vyacheslav","last_name":"Kungurtsev"},{"last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"}],"date_published":"2022-04-01T00:00:00Z","file":[{"checksum":"d4ff5d1affb34848b5c5e4002483fc62","relation":"main_file","creator":"cchlebak","file_name":"21-1365.pdf","content_type":"application/pdf","access_level":"open_access","file_size":1521701,"date_created":"2022-05-30T08:22:55Z","date_updated":"2022-05-30T08:22:55Z","success":1,"file_id":"11422"}],"publication":"Journal of Machine Learning Research","_id":"11420","article_type":"original","title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","arxiv":1,"date_created":"2022-05-29T22:01:54Z","month":"04","date_updated":"2026-11-06T23:31:03Z","article_processing_charge":"No","publisher":"Journal of Machine Learning Research","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"1-55","file_date_updated":"2022-05-30T08:22:55Z","quality_controlled":"1","oa":1,"type":"journal_article","year":"2022","scopus_import":"1","corr_author":"1","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"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."}],"language":[{"iso":"eng"}],"intvolume":"        23","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","related_material":{"link":[{"relation":"other","url":"https://www.jmlr.org/papers/v23/21-1365.html"}],"record":[{"status":"public","relation":"dissertation_contains","id":"17465"}]},"ddc":["000"],"volume":23,"external_id":{"arxiv":["2111.02278"]},"oa_version":"Published Version","day":"01","citation":{"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.","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.","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.","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.","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.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55.","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."},"issue":"130","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1"},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"doi":"10.1038/s41586-022-05187-x","isi":1,"abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"language":[{"iso":"eng"}],"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","intvolume":"       609","fulldoi":"https://doi.org/10.1038/s41586-022-05187-x","related_material":{"record":[{"relation":"dissertation_contains","id":"19395","status":"public"},{"status":"public","id":"23145","relation":"dissertation_contains"},{"status":"public","id":"20364","relation":"dissertation_contains"}]},"ddc":["580"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"volume":609,"external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"oa_version":"Submitted Version","day":"15","citation":{"apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022."},"issue":"7927","status":"public","has_accepted_license":"1","author":[{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Gallei","orcid":"0000-0003-1286-7368","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana"},{"first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas"},{"first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuhn, Andre","first_name":"Andre","last_name":"Kuhn"},{"first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Randuch","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek"},{"last_name":"Rýdza","first_name":"Nikola","full_name":"Rýdza, Nikola"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","first_name":"Anastasiia","last_name":"Teplova"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"}],"date_published":"2022-09-15T00:00:00Z","publication":"Nature","file":[{"date_updated":"2023-11-02T17:12:37Z","success":1,"file_id":"14483","file_size":79774945,"date_created":"2023-11-02T17:12:37Z","content_type":"application/pdf","access_level":"open_access","checksum":"a6055c606aefb900bf62ae3e7d15f921","relation":"main_file","file_name":"Friml Nature 2022_merged.pdf","creator":"amally"}],"_id":"12291","ec_funded":1,"article_type":"original","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","date_created":"2023-01-16T10:04:48Z","month":"09","date_updated":"2026-11-06T23:31:12Z","article_processing_charge":"No","publisher":"Springer Nature","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"575-581","file_date_updated":"2023-11-02T17:12:37Z","quality_controlled":"1","oa":1,"pmid":1,"scopus_import":"1","type":"journal_article","year":"2022","corr_author":"1","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF"}]},{"isi":1,"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"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"doi":"10.1021/acs.chemmater.2c01967","ddc":["540"],"volume":34,"intvolume":"        34","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.","fulldoi":"https://doi.org/10.1021/acs.chemmater.2c01967","related_material":{"record":[{"status":"public","id":"12885","relation":"dissertation_contains"},{"id":"22017","relation":"dissertation_contains","status":"public"},{"id":"22626","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"20415","status":"public"}]},"citation":{"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.","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>","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.","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>.","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>","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>."},"issue":"19","external_id":{"pmid":["36248227"],"isi":["000917837600001"]},"keyword":["Materials Chemistry","General Chemical Engineering","General Chemistry"],"oa_version":"Published Version","day":"20","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","_id":"12237","ec_funded":1,"author":[{"last_name":"Fiedler","first_name":"Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine"},{"first_name":"Tobias","last_name":"Kleinhanns","orcid":"0000-0003-1537-7436","full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"full_name":"Garcia, Maria","id":"6e5c50b8-97dc-11ed-be98-b0a74c84cae0","first_name":"Maria","last_name":"Garcia"},{"first_name":"Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Mariano","orcid":"0000-0003-4566-5877","last_name":"Calcabrini","full_name":"Calcabrini, Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"date_published":"2022-09-20T00:00:00Z","file":[{"content_type":"application/pdf","access_level":"open_access","checksum":"f7143e44ab510519d1949099c3558532","relation":"main_file","file_name":"2022_ChemistryMaterials_Fiedler.pdf","creator":"dernst","date_updated":"2023-01-30T07:35:09Z","success":1,"file_id":"12434","date_created":"2023-01-30T07:35:09Z","file_size":10923495}],"publication":"Chemistry of Materials","date_updated":"2026-11-06T23:31:17Z","month":"09","article_processing_charge":"Yes (via OA deal)","article_type":"original","title":"Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇","date_created":"2023-01-16T09:51:26Z","quality_controlled":"1","oa":1,"publisher":"American Chemical Society","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"8471-8489","file_date_updated":"2023-01-30T07:35:09Z","type":"journal_article","scopus_import":"1","year":"2022","corr_author":"1","department":[{"_id":"MaIb"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"pmid":1},{"pmid":1,"department":[{"_id":"MiSi"}],"scopus_import":"1","type":"journal_article","year":"2021","page":"2051-2064.e8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_created":"2022-03-08T07:51:04Z","article_type":"original","title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","article_processing_charge":"No","month":"05","date_updated":"2023-08-17T07:01:14Z","publication":"Current Biology","date_published":"2021-05-24T00:00:00Z","author":[{"full_name":"Stahnke, Stephanie","first_name":"Stephanie","last_name":"Stahnke"},{"full_name":"Döring, Hermann","first_name":"Hermann","last_name":"Döring"},{"full_name":"Kusch, Charly","last_name":"Kusch","first_name":"Charly"},{"last_name":"de Gorter","first_name":"David J.J.","full_name":"de Gorter, David J.J."},{"last_name":"Dütting","first_name":"Sebastian","full_name":"Dütting, Sebastian"},{"full_name":"Guledani, Aleks","last_name":"Guledani","first_name":"Aleks"},{"full_name":"Pleines, Irina","last_name":"Pleines","first_name":"Irina"},{"last_name":"Schnoor","first_name":"Michael","full_name":"Schnoor, Michael"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"full_name":"Geffers, Robert","first_name":"Robert","last_name":"Geffers"},{"first_name":"Manfred","last_name":"Rohde","full_name":"Rohde, Manfred"},{"first_name":"Mathias","last_name":"Müsken","full_name":"Müsken, Mathias"},{"full_name":"Kage, Frieda","first_name":"Frieda","last_name":"Kage"},{"last_name":"Steffen","first_name":"Anika","full_name":"Steffen, Anika"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"first_name":"Bernhard","last_name":"Nieswandt","full_name":"Nieswandt, Bernhard"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"},{"full_name":"Stradal, Theresia E.B.","last_name":"Stradal","first_name":"Theresia E.B."}],"_id":"10834","status":"public","day":"24","main_file_link":[{"url":"https://doi.org/10.1101/2020.03.24.005835","open_access":"1"}],"oa_version":"Preprint","external_id":{"pmid":["33711252"],"isi":["000654652200002"]},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"issue":"10","citation":{"ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8.","apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>","ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. 2021;31(10):2051-2064.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>","chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>.","short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8.","ieee":"S. Stahnke <i>et al.</i>, “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” <i>Current Biology</i>, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.","mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>."},"fulldoi":"https://doi.org/10.1016/j.cub.2021.02.043","intvolume":"        31","acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","volume":31,"doi":"10.1016/j.cub.2021.02.043","publication_identifier":{"issn":["0960-9822"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis."}],"isi":1},{"volume":76,"ddc":["570"],"fulldoi":"https://doi.org/10.1111/all.14604","intvolume":"        76","acknowledgement":"This  work  was  supported  by  the  Austrian  Science  Fund  (FWF)  grants  MCCA  W1248-B30  and  SFB  F4606-B28  to  EJJ.  CP  received  a  short-term research fellowship of the European Federation of Immunological Societies  (EFIS-IL)  for  a  research  visit  at  Biocruces  Bizkaia  Health  Research  Institute,  Barakaldo,  Spain.  VKK  received  an  EFIS-IL  short-term  research  fellowship  for  a  research  visit  at  King’s  College  London.  The research was funded by the National Institute for Health Research (NIHR) Biomedical Research Centre (BRC) based at Guy's and St Thomas' NHS Foundation Trust and King's College London (IS-BRC-1215-20006) (SNK).  The  authors  acknowledge  support  by  the  Medical  Research  Council (MR/L023091/1) (SNK); Breast Cancer Now (147; KCL-BCN-Q3)(SNK); Cancer Research UK (C30122/A11527; C30122/A15774) (SNK); Cancer  Research  UK  King's  Health  Partners  Centre  at  King's  College  London   (C604/A25135)   (SNK);   CRUK/NIHR   in   England/DoH   for   Scotland,  Wales  and  Northern  Ireland  Experimental  Cancer  Medicine  Centre  (C10355/A15587)  (SNK).  The  views  expressed  are  those  of  the  author(s)  and  not  necessarily  those  of  the  NHS,  the  NIHR  or  the  Department  of  Health.  Additionally,  this  work  was  funded  by  Instituto  de  Salud  Carlos  III  through  the  project  \"PI16/01223\"  (Co-funded  by  European Regional Development Fund; “A way to make Europe”) to FB and  by  the  Department  of  Health,  Basque  Government  through  the  project “2019111031” to OZ. OZ is recipient of a Sara Borrell 2017 post-doctoral contract “CD17/00128” funded by Instituto de Salud Carlos III (Co-funded by European Social Fund; “Investing in your future”).","language":[{"iso":"eng"}],"isi":1,"doi":"10.1111/all.14604","publication_identifier":{"eissn":["1398-9995"],"issn":["0105-4538"]},"has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"5","citation":{"apa":"Pranger, C. L., Singer, J., Köhler, V. K., Pali‐Schöll, I., Fiocchi, A., Karagiannis, S. N., … Jensen‐Jarolim, E. (2021). PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. <i>Allergy</i>. Wiley. <a href=\"https://doi.org/10.1111/all.14604\">https://doi.org/10.1111/all.14604</a>","ista":"Pranger CL, Singer J, Köhler VK, Pali‐Schöll I, Fiocchi A, Karagiannis SN, Zenarruzabeitia O, Borrego F, Jensen‐Jarolim E. 2021. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 76(5), 1553–1556.","mla":"Pranger, Christina L., et al. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” <i>Allergy</i>, vol. 76, no. 5, Wiley, 2021, pp. 1553–56, doi:<a href=\"https://doi.org/10.1111/all.14604\">10.1111/all.14604</a>.","short":"C.L. Pranger, J. Singer, V.K. Köhler, I. Pali‐Schöll, A. Fiocchi, S.N. Karagiannis, O. Zenarruzabeitia, F. Borrego, E. Jensen‐Jarolim, Allergy 76 (2021) 1553–1556.","ama":"Pranger CL, Singer J, Köhler VK, et al. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. <i>Allergy</i>. 2021;76(5):1553-1556. doi:<a href=\"https://doi.org/10.1111/all.14604\">10.1111/all.14604</a>","chicago":"Pranger, Christina L., Judit Singer, Verena K. Köhler, Isabella Pali‐Schöll, Alessandro Fiocchi, Sophia N. Karagiannis, Olatz Zenarruzabeitia, Francisco Borrego, and Erika Jensen‐Jarolim. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” <i>Allergy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/all.14604\">https://doi.org/10.1111/all.14604</a>.","ieee":"C. L. Pranger <i>et al.</i>, “PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance,” <i>Allergy</i>, vol. 76, no. 5. Wiley, pp. 1553–1556, 2021."},"day":"01","external_id":{"pmid":["32990982"],"isi":["000577708800001"]},"keyword":["Immunology","Immunology and Allergy"],"oa_version":"Published Version","article_processing_charge":"No","month":"05","date_updated":"2023-09-05T15:58:53Z","date_created":"2022-03-08T11:19:05Z","title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","article_type":"letter_note","_id":"10836","file":[{"file_id":"10837","success":1,"date_updated":"2022-03-08T11:23:16Z","date_created":"2022-03-08T11:23:16Z","file_size":626081,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_name":"2021_Allergy_Pranger.pdf","checksum":"9526f9554112fc027c9f7fa540c488cd","relation":"main_file"}],"publication":"Allergy","author":[{"full_name":"Pranger, Christina L.","first_name":"Christina L.","last_name":"Pranger"},{"first_name":"Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Köhler, Verena K.","first_name":"Verena K.","last_name":"Köhler"},{"full_name":"Pali‐Schöll, Isabella","first_name":"Isabella","last_name":"Pali‐Schöll"},{"full_name":"Fiocchi, Alessandro","last_name":"Fiocchi","first_name":"Alessandro"},{"last_name":"Karagiannis","first_name":"Sophia N.","full_name":"Karagiannis, Sophia N."},{"last_name":"Zenarruzabeitia","first_name":"Olatz","full_name":"Zenarruzabeitia, Olatz"},{"full_name":"Borrego, Francisco","last_name":"Borrego","first_name":"Francisco"},{"full_name":"Jensen‐Jarolim, Erika","first_name":"Erika","last_name":"Jensen‐Jarolim"}],"date_published":"2021-05-01T00:00:00Z","department":[{"_id":"Bio"}],"year":"2021","scopus_import":"1","type":"journal_article","pmid":1,"oa":1,"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1553-1556","file_date_updated":"2022-03-08T11:23:16Z","publisher":"Wiley","publication_status":"published"},{"citation":{"mla":"Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>, vol. 30, no. 15, Wiley, 2021, pp. 3797–814, doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>.","ieee":"A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid zones to understand the genomic basis of adaptive divergence,” <i>Molecular Ecology</i>, vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>.","ama":"Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. 2021;30(15):3797-3814. doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 3797–3814.","apa":"Westram, A. M., Faria, R., Johannesson, K., &#38; Butlin, R. (2021). Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>","ista":"Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 30(15), 3797–3814."},"issue":"15","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"external_id":{"pmid":["33638231"],"isi":["000669439700001"]},"oa_version":"Published Version","day":"01","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","isi":1,"abstract":[{"lang":"eng","text":"Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones."}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"doi":"10.1111/mec.15861","ddc":["570"],"volume":30,"acknowledgement":"We thank everyone who helped with fieldwork, snail processing and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark Ravinet for helpful discussions, and to three anonymous reviewers for their constructive comments. This work was supported by the Natural Environment Research Council (NE/K014021/1), the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628), and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017). A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno. 754411/797747 and no. 706376, respectively.","intvolume":"        30","fulldoi":"https://doi.org/10.1111/mec.15861","oa":1,"quality_controlled":"1","publisher":"Wiley","publication_status":"published","page":"3797-3814","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2022-03-08T11:31:30Z","scopus_import":"1","type":"journal_article","year":"2021","corr_author":"1","department":[{"_id":"BeVi"}],"pmid":1,"_id":"10838","author":[{"last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"date_published":"2021-08-01T00:00:00Z","publication":"Molecular Ecology","file":[{"file_id":"10839","success":1,"date_updated":"2022-03-08T11:31:30Z","file_size":1726548,"date_created":"2022-03-08T11:31:30Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_name":"2021_MolecularEcology_Westram.pdf","checksum":"d5611f243ceb63a0e091d6662ebd9cda","relation":"main_file"}],"month":"08","date_updated":"2024-10-09T21:01:47Z","article_processing_charge":"No","title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence","article_type":"original","date_created":"2022-03-08T11:28:32Z"},{"status":"public","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.24963/ijcai.2021/575","open_access":"1"}],"day":"01","citation":{"mla":"Tomášek, Petr, et al. “Solving Partially Observable Stochastic Shortest-Path Games.” <i>30th International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2021, pp. 4182–89, doi:<a href=\"https://doi.org/10.24963/ijcai.2021/575\">10.24963/ijcai.2021/575</a>.","ieee":"P. Tomášek, K. Horák, A. Aradhye, B. Bošanský, and K. Chatterjee, “Solving partially observable stochastic shortest-path games,” in <i>30th International Joint Conference on Artificial Intelligence</i>, Virtual, Online, 2021, pp. 4182–4189.","short":"P. Tomášek, K. Horák, A. Aradhye, B. Bošanský, K. Chatterjee, in:, 30th International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 4182–4189.","ama":"Tomášek P, Horák K, Aradhye A, Bošanský B, Chatterjee K. Solving partially observable stochastic shortest-path games. In: <i>30th International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2021:4182-4189. doi:<a href=\"https://doi.org/10.24963/ijcai.2021/575\">10.24963/ijcai.2021/575</a>","chicago":"Tomášek, Petr, Karel Horák, Aditya Aradhye, Branislav Bošanský, and Krishnendu Chatterjee. “Solving Partially Observable Stochastic Shortest-Path Games.” In <i>30th International Joint Conference on Artificial Intelligence</i>, 4182–89. International Joint Conferences on Artificial Intelligence, 2021. <a href=\"https://doi.org/10.24963/ijcai.2021/575\">https://doi.org/10.24963/ijcai.2021/575</a>.","apa":"Tomášek, P., Horák, K., Aradhye, A., Bošanský, B., &#38; Chatterjee, K. (2021). Solving partially observable stochastic shortest-path games. In <i>30th International Joint Conference on Artificial Intelligence</i> (pp. 4182–4189). Virtual, Online: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2021/575\">https://doi.org/10.24963/ijcai.2021/575</a>","ista":"Tomášek P, Horák K, Aradhye A, Bošanský B, Chatterjee K. 2021. Solving partially observable stochastic shortest-path games. 30th International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conferences on Artificial Intelligence, 4182–4189."},"acknowledgement":"This research was supported by the Czech Science Foundation (no. 19-24384Y), by the OP VVV MEYS funded project CZ.02.1.01/0.0/0.0/16 019/0000765 “Research Center for Informatics”, by the ERC CoG 863818 (ForM-SMArt), and by the Combat Capabilities Development Command Army Research Laboratory and was accomplished under Cooperative\r\nAgreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). The views and conclusions contained in this document are those of the authors and should not be interpreted as\r\nrepresenting the official policies, either expressed or implied, of the Combat Capabilities Development Command Army Research Laboratory or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes not withstanding any copyright notation here on. ","fulldoi":"https://doi.org/10.24963/ijcai.2021/575","ddc":["000"],"publication_identifier":{"isbn":["9780999241196"],"issn":["1045-0823"]},"doi":"10.24963/ijcai.2021/575","abstract":[{"text":"We study the two-player zero-sum extension of the partially observable stochastic shortest-path problem where one agent has only partial information about the environment. We formulate this problem as a partially observable stochastic game (POSG): given a set of target states and negative rewards for each transition, the player with imperfect information maximizes the expected undiscounted total reward until a target state is reached. The second player with the perfect information aims for the opposite. We base our formalism on POSGs with one-sided observability (OS-POSGs) and give the following contributions: (1) we introduce a novel heuristic search value iteration algorithm that iteratively solves depth-limited variants of the game, (2) we derive the bound on the depth guaranteeing an arbitrary precision, (3) we propose a novel upper-bound estimation that allows early terminations, and (4) we experimentally evaluate the algorithm on a pursuit-evasion game.","lang":"eng"}],"language":[{"iso":"eng"}],"scopus_import":"1","year":"2021","type":"conference","department":[{"_id":"KrCh"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"publisher":"International Joint Conferences on Artificial Intelligence","publication_status":"published","page":"4182-4189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","title":"Solving partially observable stochastic shortest-path games","date_created":"2022-03-13T23:01:47Z","date_updated":"2026-06-18T10:41:02Z","month":"09","article_processing_charge":"No","author":[{"full_name":"Tomášek, Petr","last_name":"Tomášek","first_name":"Petr"},{"last_name":"Horák","first_name":"Karel","full_name":"Horák, Karel"},{"full_name":"Aradhye, Aditya","first_name":"Aditya","last_name":"Aradhye"},{"first_name":"Branislav","last_name":"Bošanský","full_name":"Bošanský, Branislav"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"date_published":"2021-09-01T00:00:00Z","publication":"30th International Joint Conference on Artificial Intelligence","_id":"10847","conference":{"end_date":"2021-08-27","start_date":"2021-08-19","name":"IJCAI: International Joint Conferences on Artificial Intelligence","location":"Virtual, Online"},"ec_funded":1},{"date_created":"2022-03-18T08:11:34Z","arxiv":1,"title":"The polaron at strong coupling","article_type":"original","article_processing_charge":"No","month":"02","date_updated":"2025-04-14T07:26:58Z","publication":"Reviews in Mathematical Physics","date_published":"2021-02-01T00:00:00Z","author":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"ec_funded":1,"_id":"10852","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"RoSe"}],"corr_author":"1","type":"journal_article","scopus_import":"1","year":"2021","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publisher":"World Scientific Publishing","oa":1,"article_number":"2060012","quality_controlled":"1","fulldoi":"https://doi.org/10.1142/s0129055x20600120","acknowledgement":"This work was supported by the European Research Council (ERC) under the Euro-pean Union’s Horizon 2020 research and innovation programme (grant agreementNo. 694227).","intvolume":"        33","volume":33,"doi":"10.1142/s0129055x20600120","publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":" We review old and new results on the Fröhlich polaron model. The discussion includes the validity of the (classical) Pekar approximation in the strong coupling limit, quantum corrections to this limit, as well as the divergence of the effective polaron mass."}],"isi":1,"status":"public","day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1912.12509","open_access":"1"}],"oa_version":"Preprint","external_id":{"isi":["000613313200013"],"arxiv":["1912.12509"]},"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"issue":"01","citation":{"short":"R. Seiringer, Reviews in Mathematical Physics 33 (2021).","ama":"Seiringer R. The polaron at strong coupling. <i>Reviews in Mathematical Physics</i>. 2021;33(01). doi:<a href=\"https://doi.org/10.1142/s0129055x20600120\">10.1142/s0129055x20600120</a>","chicago":"Seiringer, Robert. “The Polaron at Strong Coupling.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2021. <a href=\"https://doi.org/10.1142/s0129055x20600120\">https://doi.org/10.1142/s0129055x20600120</a>.","ieee":"R. Seiringer, “The polaron at strong coupling,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 01. World Scientific Publishing, 2021.","mla":"Seiringer, Robert. “The Polaron at Strong Coupling.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 01, 2060012, World Scientific Publishing, 2021, doi:<a href=\"https://doi.org/10.1142/s0129055x20600120\">10.1142/s0129055x20600120</a>.","ista":"Seiringer R. 2021. The polaron at strong coupling. Reviews in Mathematical Physics. 33(01), 2060012.","apa":"Seiringer, R. (2021). The polaron at strong coupling. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x20600120\">https://doi.org/10.1142/s0129055x20600120</a>"}},{"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2105.08098"}],"day":"01","external_id":{"arxiv":["2105.08098"]},"oa_version":"Preprint","citation":{"ama":"Fedorov A, Koval N, Alistarh D-A. A scalable concurrent algorithm for dynamic connectivity. In: <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2021:208-220. doi:<a href=\"https://doi.org/10.1145/3409964.3461810\">10.1145/3409964.3461810</a>","short":"A. Fedorov, N. Koval, D.-A. Alistarh, in:, Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2021, pp. 208–220.","chicago":"Fedorov, Alexander, Nikita Koval, and Dan-Adrian Alistarh. “A Scalable Concurrent Algorithm for Dynamic Connectivity.” In <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>, 208–20. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3409964.3461810\">https://doi.org/10.1145/3409964.3461810</a>.","ieee":"A. Fedorov, N. Koval, and D.-A. Alistarh, “A scalable concurrent algorithm for dynamic connectivity,” in <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>, Virtual, Online, 2021, pp. 208–220.","mla":"Fedorov, Alexander, et al. “A Scalable Concurrent Algorithm for Dynamic Connectivity.” <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2021, pp. 208–20, doi:<a href=\"https://doi.org/10.1145/3409964.3461810\">10.1145/3409964.3461810</a>.","ista":"Fedorov A, Koval N, Alistarh D-A. 2021. A scalable concurrent algorithm for dynamic connectivity. Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 208–220.","apa":"Fedorov, A., Koval, N., &#38; Alistarh, D.-A. (2021). A scalable concurrent algorithm for dynamic connectivity. In <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 208–220). Virtual, Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3409964.3461810\">https://doi.org/10.1145/3409964.3461810</a>"},"fulldoi":"https://doi.org/10.1145/3409964.3461810","doi":"10.1145/3409964.3461810","publication_identifier":{"isbn":["9781450380706"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Dynamic Connectivity is a fundamental algorithmic graph problem, motivated by a wide range of applications to social and communication networks and used as a building block in various other algorithms, such as the bi-connectivity and the dynamic minimal spanning tree problems. In brief, we wish to maintain the connected components of the graph under dynamic edge insertions and deletions. In the sequential case, the problem has been well-studied from both theoretical and practical perspectives. However, much less is known about efficient concurrent solutions to this problem. This is the gap we address in this paper. We start from one of the classic data structures used to solve this problem, the Euler Tour Tree. Our first contribution is a non-blocking single-writer implementation of it. We leverage this data structure to obtain the first truly concurrent generalization of dynamic connectivity, which preserves the time complexity of its sequential counterpart, but is also scalable in practice. To achieve this, we rely on three main techniques. The first is to ensure that connectivity queries, which usually dominate real-world workloads, are non-blocking. The second non-trivial technique expands the above idea by making all queries that do not change the connectivity structure non-blocking. The third ingredient is applying fine-grained locking for updating the connected components, which allows operations on disjoint components to occur in parallel. We evaluate the resulting algorithm on various workloads, executing on both real and synthetic graphs. The results show the efficiency of each of the proposed optimizations; the most efficient variant improves the performance of a coarse-grained based implementation on realistic scenarios up to 6x on average and up to 30x when connectivity queries dominate."}],"department":[{"_id":"DaAl"}],"year":"2021","scopus_import":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"208-220","publisher":"Association for Computing Machinery","publication_status":"published","quality_controlled":"1","oa":1,"arxiv":1,"date_created":"2022-03-18T08:21:47Z","title":"A scalable concurrent algorithm for dynamic connectivity","article_processing_charge":"No","month":"07","date_updated":"2022-03-18T08:45:46Z","publication":"Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures","author":[{"full_name":"Fedorov, Alexander","first_name":"Alexander","last_name":"Fedorov"},{"last_name":"Koval","first_name":"Nikita","full_name":"Koval, Nikita"},{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"date_published":"2021-07-01T00:00:00Z","_id":"10853","conference":{"start_date":"2021-07-06","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Virtual, Online","end_date":"2021-07-08"}},{"scopus_import":"1","year":"2021","type":"conference","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020"}],"department":[{"_id":"DaAl"}],"quality_controlled":"1","oa":1,"publication_status":"published","publisher":"Association for Computing Machinery","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"71-72","date_updated":"2025-04-14T13:52:09Z","month":"05","article_processing_charge":"No","title":"Input-dynamic distributed algorithms for communication networks","date_created":"2022-03-18T08:48:41Z","arxiv":1,"conference":{"end_date":"2021-06-18","name":"SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems","location":"Virtual, Online","start_date":"2021-06-14"},"ec_funded":1,"_id":"10854","date_published":"2021-05-01T00:00:00Z","author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"first_name":"Janne","last_name":"Korhonen","full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"first_name":"Ami","last_name":"Paz","full_name":"Paz, Ami"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","last_name":"Rybicki","orcid":"0000-0002-6432-6646","first_name":"Joel"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"publication":"Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems","status":"public","citation":{"ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems, 71–72.","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., &#38; Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. In <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i> (pp. 71–72). Virtual, Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3410220.3453923\">https://doi.org/10.1145/3410220.3453923</a>","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” in <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>, Virtual, Online, 2021, pp. 71–72.","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” In <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>, 71–72. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3410220.3453923\">https://doi.org/10.1145/3410220.3453923</a>.","short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, in:, Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2021, pp. 71–72.","ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. In: <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>. Association for Computing Machinery; 2021:71-72. doi:<a href=\"https://doi.org/10.1145/3410220.3453923\">10.1145/3410220.3453923</a>","mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>, Association for Computing Machinery, 2021, pp. 71–72, doi:<a href=\"https://doi.org/10.1145/3410220.3453923\">10.1145/3410220.3453923</a>."},"oa_version":"Preprint","external_id":{"arxiv":["2005.07637"]},"day":"01","main_file_link":[{"url":"https://arxiv.org/abs/2005.07637","open_access":"1"}],"acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili and the reviewers for their time and suggestions on how to improve the paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","related_material":{"record":[{"status":"public","id":"10855","relation":"extended_version"}]},"fulldoi":"https://doi.org/10.1145/3410220.3453923","abstract":[{"text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner?\r\nTo address this question, we define the batch dynamic CONGEST model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labelled graph under batch changes. We investigate, when a batch of alpha edge label changes arrive, - how much time as a function of alpha we need to update an existing solution, and - how much information the nodes have to keep in local memory between batches in order to update the solution quickly.\r\nOur work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. The diverse time complexity of our model spans from constant time, through time polynomial in alpha, and to alpha time, which we show to be enough for any task.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450380720"]},"doi":"10.1145/3410220.3453923"},{"type":"journal_article","year":"2021","scopus_import":"1","department":[{"_id":"DaAl"}],"project":[{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems"},{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"publisher":"Association for Computing Machinery","publication_status":"published","page":"1-33","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","article_type":"original","title":"Input-dynamic distributed algorithms for communication networks","arxiv":1,"date_created":"2022-03-18T09:10:27Z","date_updated":"2025-04-14T13:52:09Z","month":"03","article_processing_charge":"No","author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne","last_name":"Korhonen"},{"last_name":"Paz","first_name":"Ami","full_name":"Paz, Ami"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"date_published":"2021-03-01T00:00:00Z","publication":"Proceedings of the ACM on Measurement and Analysis of Computing Systems","_id":"10855","ec_funded":1,"status":"public","keyword":["Computer Networks and Communications","Hardware and Architecture","Safety","Risk","Reliability and Quality","Computer Science (miscellaneous)"],"external_id":{"arxiv":["2005.07637"]},"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.07637"}],"day":"01","citation":{"mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>, vol. 5, no. 1, Association for Computing Machinery, 2021, pp. 1–33, doi:<a href=\"https://doi.org/10.1145/3447384\">10.1145/3447384</a>.","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>, vol. 5, no. 1. Association for Computing Machinery, pp. 1–33, 2021.","ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>. 2021;5(1):1-33. doi:<a href=\"https://doi.org/10.1145/3447384\">10.1145/3447384</a>","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3447384\">https://doi.org/10.1145/3447384</a>.","short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, Proceedings of the ACM on Measurement and Analysis of Computing Systems 5 (2021) 1–33.","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., &#38; Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3447384\">https://doi.org/10.1145/3447384</a>","ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. 5(1), 1–33."},"issue":"1","acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili\r\nand the reviewers for their time and suggestions on how to improve the paper. This project\r\nhas received funding from the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","intvolume":"         5","fulldoi":"https://doi.org/10.1145/3447384","related_material":{"record":[{"relation":"shorter_version","id":"10854","status":"public"}]},"volume":5,"publication_identifier":{"issn":["2476-1249"]},"doi":"10.1145/3447384","abstract":[{"text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner? To address this question, we define the batch dynamic \\congest model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labeled graph under batch changes. We investigate, when a batch of α edge label changes arrive, \\beginitemize \\item how much time as a function of α we need to update an existing solution, and \\item how much information the nodes have to keep in local memory between batches in order to update the solution quickly. \\enditemize Our work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. In particular, we derive non-trivial upper bounds for two selected, contrasting problems: maintaining a minimum spanning tree and detecting cliques.","lang":"eng"}],"language":[{"iso":"eng"}]},{"fulldoi":"https://doi.org/10.1515/agms-2020-0103","intvolume":"         9","acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-\r\n2019-1926. G.I.was supported also by the SwissNational Science Foundation grant 200021-179133. The authors are very grateful to the anonymous reviewer for valuable remarks.","volume":9,"ddc":["510"],"doi":"10.1515/agms-2020-0103","publication_identifier":{"issn":["2299-3274"]},"language":[{"iso":"eng"}],"abstract":[{"text":"We study the properties of the maximal volume k-dimensional sections of the n-dimensional cube [−1, 1]n. We obtain a first order necessary condition for a k-dimensional subspace to be a local maximizer of the volume of such sections, which we formulate in a geometric way. We estimate the length of the projection of a vector of the standard basis of Rn onto a k-dimensional subspace that maximizes the volume of the intersection. We \u001cnd the optimal upper bound on the volume of a planar section of the cube [−1, 1]n , n ≥ 2.","lang":"eng"}],"isi":1,"has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"29","oa_version":"Published Version","keyword":["Applied Mathematics","Geometry and Topology","Analysis"],"external_id":{"isi":["000734286800001"],"arxiv":["2004.02674"]},"issue":"1","citation":{"mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” <i>Analysis and Geometry in Metric Spaces</i>, vol. 9, no. 1, De Gruyter, 2021, pp. 1–18, doi:<a href=\"https://doi.org/10.1515/agms-2020-0103\">10.1515/agms-2020-0103</a>.","ieee":"G. Ivanov and I. Tsiutsiurupa, “On the volume of sections of the cube,” <i>Analysis and Geometry in Metric Spaces</i>, vol. 9, no. 1. De Gruyter, pp. 1–18, 2021.","ama":"Ivanov G, Tsiutsiurupa I. On the volume of sections of the cube. <i>Analysis and Geometry in Metric Spaces</i>. 2021;9(1):1-18. doi:<a href=\"https://doi.org/10.1515/agms-2020-0103\">10.1515/agms-2020-0103</a>","short":"G. Ivanov, I. Tsiutsiurupa, Analysis and Geometry in Metric Spaces 9 (2021) 1–18.","chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” <i>Analysis and Geometry in Metric Spaces</i>. De Gruyter, 2021. <a href=\"https://doi.org/10.1515/agms-2020-0103\">https://doi.org/10.1515/agms-2020-0103</a>.","apa":"Ivanov, G., &#38; Tsiutsiurupa, I. (2021). On the volume of sections of the cube. <i>Analysis and Geometry in Metric Spaces</i>. De Gruyter. <a href=\"https://doi.org/10.1515/agms-2020-0103\">https://doi.org/10.1515/agms-2020-0103</a>","ista":"Ivanov G, Tsiutsiurupa I. 2021. On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. 9(1), 1–18."},"date_created":"2022-03-18T09:25:14Z","arxiv":1,"title":"On the volume of sections of the cube","article_type":"original","article_processing_charge":"No","month":"01","date_updated":"2023-08-17T07:07:58Z","publication":"Analysis and Geometry in Metric Spaces","file":[{"date_updated":"2022-03-18T09:31:59Z","file_id":"10857","success":1,"file_size":789801,"date_created":"2022-03-18T09:31:59Z","access_level":"open_access","content_type":"application/pdf","file_name":"2021_AnalysisMetricSpaces_Ivanov.pdf","creator":"dernst","checksum":"7e615ac8489f5eae580b6517debfdc53","relation":"main_file"}],"date_published":"2021-01-29T00:00:00Z","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory","last_name":"Ivanov","first_name":"Grigory"},{"full_name":"Tsiutsiurupa, Igor","last_name":"Tsiutsiurupa","first_name":"Igor"}],"_id":"10856","department":[{"_id":"UlWa"}],"type":"journal_article","scopus_import":"1","year":"2021","file_date_updated":"2022-03-18T09:31:59Z","page":"1-18","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"De Gruyter","quality_controlled":"1","oa":1},{"publication_identifier":{"issn":["2079-4991"]},"doi":"10.3390/nano11071827","abstract":[{"text":"The cost-effective conversion of low-grade heat into electricity using thermoelectric devices requires developing alternative materials and material processing technologies able to reduce the currently high device manufacturing costs. In this direction, thermoelectric materials that do not rely on rare or toxic elements such as tellurium or lead need to be produced using high-throughput technologies not involving high temperatures and long processes. Bi2Se3 is an obvious possible Te-free alternative to Bi2Te3 for ambient temperature thermoelectric applications, but its performance is still low for practical applications, and additional efforts toward finding proper dopants are required. Here, we report a scalable method to produce Bi2Se3 nanosheets at low synthesis temperatures. We studied the influence of different dopants on the thermoelectric properties of this material. Among the elements tested, we demonstrated that Sn doping resulted in the best performance. Sn incorporation resulted in a significant improvement to the Bi2Se3 Seebeck coefficient and a reduction in the thermal conductivity in the direction of the hot-press axis, resulting in an overall 60% improvement in the thermoelectric figure of merit of Bi2Se3.","lang":"eng"}],"isi":1,"language":[{"iso":"eng"}],"intvolume":"        11","acknowledgement":"M.L., Y.Z., T.Z. and K.X. thank the China Scholarship Council for their scholarship\r\nsupport. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and\r\ninnovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. thanks the ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and G.C. 2017 SGR 128. ICN2 acknowledges funding from the Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO ENE2017-85087-C3.","fulldoi":"https://doi.org/10.3390/nano11071827","ddc":["540"],"volume":11,"oa_version":"Published Version","keyword":["General Materials Science","General Chemical Engineering"],"external_id":{"pmid":["34361214"],"isi":["000676570000001"]},"day":"14","citation":{"ista":"Li M, Zhang Y, Zhang T, Zuo Y, Xiao K, Arbiol J, Llorca J, Liu Y, Cabot A. 2021. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. 11(7), 1827.","apa":"Li, M., Zhang, Y., Zhang, T., Zuo, Y., Xiao, K., Arbiol, J., … Cabot, A. (2021). Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. <i>Nanomaterials</i>. MDPI. <a href=\"https://doi.org/10.3390/nano11071827\">https://doi.org/10.3390/nano11071827</a>","chicago":"Li, Mengyao, Yu Zhang, Ting Zhang, Yong Zuo, Ke Xiao, Jordi Arbiol, Jordi Llorca, Yu Liu, and Andreu Cabot. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” <i>Nanomaterials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/nano11071827\">https://doi.org/10.3390/nano11071827</a>.","short":"M. Li, Y. Zhang, T. Zhang, Y. Zuo, K. Xiao, J. Arbiol, J. Llorca, Y. Liu, A. Cabot, Nanomaterials 11 (2021).","ama":"Li M, Zhang Y, Zhang T, et al. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. <i>Nanomaterials</i>. 2021;11(7). doi:<a href=\"https://doi.org/10.3390/nano11071827\">10.3390/nano11071827</a>","ieee":"M. Li <i>et al.</i>, “Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping,” <i>Nanomaterials</i>, vol. 11, no. 7. MDPI, 2021.","mla":"Li, Mengyao, et al. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” <i>Nanomaterials</i>, vol. 11, no. 7, 1827, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/nano11071827\">10.3390/nano11071827</a>."},"issue":"7","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public","date_published":"2021-07-14T00:00:00Z","author":[{"full_name":"Li, Mengyao","last_name":"Li","first_name":"Mengyao"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"full_name":"Zhang, Ting","last_name":"Zhang","first_name":"Ting"},{"full_name":"Zuo, Yong","last_name":"Zuo","first_name":"Yong"},{"first_name":"Ke","last_name":"Xiao","full_name":"Xiao, Ke"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"orcid":"0000-0001-7313-6740","last_name":"Liu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"file":[{"creator":"dernst","file_name":"2021_Nanomaterials_Li.pdf","checksum":"f28a8b5cf80f5605828359bb398463b0","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_created":"2022-03-18T09:53:15Z","file_size":4867547,"date_updated":"2022-03-18T09:53:15Z","file_id":"10859","success":1}],"publication":"Nanomaterials","ec_funded":1,"_id":"10858","title":"Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping","article_type":"original","date_created":"2022-03-18T09:45:02Z","date_updated":"2025-06-12T06:42:18Z","month":"07","article_processing_charge":"No","publication_status":"published","publisher":"MDPI","file_date_updated":"2022-03-18T09:53:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_number":"1827","oa":1,"pmid":1,"corr_author":"1","year":"2021","scopus_import":"1","type":"journal_article","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"department":[{"_id":"MaIb"}]},{"page":"942-963","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Canadian Mathematical Society","publication_status":"published","oa":1,"quality_controlled":"1","department":[{"_id":"UlWa"}],"type":"journal_article","scopus_import":"1","year":"2021","corr_author":"1","publication":"Canadian Mathematical Bulletin","author":[{"first_name":"Grigory","last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"}],"date_published":"2021-12-18T00:00:00Z","_id":"10860","arxiv":1,"date_created":"2022-03-18T09:55:59Z","title":"Tight frames and related geometric problems","article_type":"original","article_processing_charge":"No","month":"12","date_updated":"2024-10-09T21:01:50Z","main_file_link":[{"url":"https://arxiv.org/abs/1804.10055","open_access":"1"}],"day":"18","keyword":["General Mathematics","Tight frame","Grassmannian","zonotope"],"external_id":{"arxiv":["1804.10055"],"isi":["000730165300021"]},"oa_version":"Preprint","issue":"4","citation":{"ista":"Ivanov G. 2021. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 64(4), 942–963.","apa":"Ivanov, G. (2021). Tight frames and related geometric problems. <i>Canadian Mathematical Bulletin</i>. Canadian Mathematical Society. <a href=\"https://doi.org/10.4153/s000843952000096x\">https://doi.org/10.4153/s000843952000096x</a>","ieee":"G. Ivanov, “Tight frames and related geometric problems,” <i>Canadian Mathematical Bulletin</i>, vol. 64, no. 4. Canadian Mathematical Society, pp. 942–963, 2021.","short":"G. Ivanov, Canadian Mathematical Bulletin 64 (2021) 942–963.","ama":"Ivanov G. Tight frames and related geometric problems. <i>Canadian Mathematical Bulletin</i>. 2021;64(4):942-963. doi:<a href=\"https://doi.org/10.4153/s000843952000096x\">10.4153/s000843952000096x</a>","chicago":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” <i>Canadian Mathematical Bulletin</i>. Canadian Mathematical Society, 2021. <a href=\"https://doi.org/10.4153/s000843952000096x\">https://doi.org/10.4153/s000843952000096x</a>.","mla":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” <i>Canadian Mathematical Bulletin</i>, vol. 64, no. 4, Canadian Mathematical Society, 2021, pp. 942–63, doi:<a href=\"https://doi.org/10.4153/s000843952000096x\">10.4153/s000843952000096x</a>."},"status":"public","doi":"10.4153/s000843952000096x","publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"language":[{"iso":"eng"}],"isi":1,"abstract":[{"lang":"eng","text":"A tight frame is the orthogonal projection of some orthonormal basis of Rn onto Rk. We show that a set of vectors is a tight frame if and only if the set of all cross products of these vectors is a tight frame. We reformulate a range of problems on the volume of projections (or sections) of regular polytopes in terms of tight frames and write a first-order necessary condition for local extrema of these problems. As applications, we prove new results for the problem of maximization of the volume of zonotopes."}],"fulldoi":"https://doi.org/10.4153/s000843952000096x","intvolume":"        64","acknowledgement":"The author was supported by the Swiss National Science Foundation grant 200021_179133. The author acknowledges the financial support from the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no. 075-15-2019-1926.","volume":64},{"status":"public","citation":{"apa":"Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., &#38; Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>","ista":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. 2021. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.","mla":"Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>.","ieee":"S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman, and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain,” <i>Developmental Cell</i>, vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021.","short":"S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman, M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.","chicago":"Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra, Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>.","ama":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. 2021;56(21):P2952-2965.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>"},"issue":"21","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"external_id":{"pmid":["34715012"]},"oa_version":"None","day":"08","volume":56,"intvolume":"        56","fulldoi":"https://doi.org/10.1016/j.devcel.2021.10.008","abstract":[{"lang":"eng","text":"In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function."}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1534-5807"]},"doi":"10.1016/j.devcel.2021.10.008","scopus_import":"1","year":"2021","type":"journal_article","department":[{"_id":"MaHe"}],"extern":"1","pmid":1,"quality_controlled":"1","publisher":"Elsevier","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"P2952-2965.e9","month":"11","date_updated":"2025-12-15T10:01:56Z","article_processing_charge":"No","title":"Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain","article_type":"original","date_created":"2022-04-07T07:43:14Z","_id":"11052","author":[{"first_name":"Shefali","last_name":"Krishna","full_name":"Krishna, Shefali"},{"full_name":"Arrojo e Drigo, Rafael","first_name":"Rafael","last_name":"Arrojo e Drigo"},{"full_name":"Capitanio, Juliana S.","first_name":"Juliana S.","last_name":"Capitanio"},{"last_name":"Ramachandra","first_name":"Ranjan","full_name":"Ramachandra, Ranjan"},{"full_name":"Ellisman, Mark","last_name":"Ellisman","first_name":"Mark"},{"first_name":"Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"date_published":"2021-11-08T00:00:00Z","publication":"Developmental Cell"}]