[{"article_processing_charge":"No","status":"public","year":"2021","language":[{"iso":"eng"}],"type":"preprint","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","related_material":{"record":[{"id":"12072","status":"public","relation":"dissertation_contains"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2104.06966"}],"author":[{"last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L","full_name":"Shute, Alec L","orcid":"0000-0002-1812-2810"}],"oa_version":"Preprint","external_id":{"arxiv":["2104.06966"]},"date_updated":"2023-02-21T16:37:30Z","abstract":[{"lang":"eng","text":"We find an asymptotic formula for the number of primitive vectors $(z_1,\\ldots,z_4)\\in (\\mathbb{Z}_{\\neq 0})^4$ such that $z_1,\\ldots, z_4$ are all squareful and bounded by $B$, and $z_1+\\cdots + z_4 = 0$. Our result agrees in the power of $B$ and $\\log B$ with the Campana-Manin conjecture of Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado."}],"article_number":"2104.06966","date_published":"2021-04-15T00:00:00Z","_id":"12076","oa":1,"title":"Sums of four squareful numbers","citation":{"ieee":"A. L. Shute, “Sums of four squareful numbers,” <i>arXiv</i>. .","ama":"Shute AL. Sums of four squareful numbers. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.06966\">10.48550/arXiv.2104.06966</a>","apa":"Shute, A. L. (n.d.). Sums of four squareful numbers. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.06966\">https://doi.org/10.48550/arXiv.2104.06966</a>","mla":"Shute, Alec L. “Sums of Four Squareful Numbers.” <i>ArXiv</i>, 2104.06966, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.06966\">10.48550/arXiv.2104.06966</a>.","chicago":"Shute, Alec L. “Sums of Four Squareful Numbers.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.06966\">https://doi.org/10.48550/arXiv.2104.06966</a>.","short":"A.L. Shute, ArXiv (n.d.).","ista":"Shute AL. Sums of four squareful numbers. arXiv, 2104.06966."},"publication_status":"submitted","date_created":"2022-09-09T10:42:51Z","doi":"10.48550/arXiv.2104.06966","department":[{"_id":"TiBr"}],"publication":"arXiv","arxiv":1},{"related_material":{"record":[{"status":"public","id":"12072","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0002-1812-2810","first_name":"Alec L","full_name":"Shute, Alec L","last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2104.14946"}],"acknowledgement":"The author would like to thank Damaris Schindler and Florian Wilsch for their helpful comments on the heights and Tamagawa measures used in Section 3, together with Marta Pieropan, Sho Tanimoto and Sam Streeter for providing valuable feedback on an earlier version of this paper, and Tim Browning for many useful comments and discussions during the development of this work. The author is also grateful to the anonymous referee for providing many valuable comments and suggestions that improved the quality of the paper.","date_updated":"2023-02-21T16:37:30Z","external_id":{"arxiv":["2104.14946"]},"abstract":[{"text":"We compare the Manin-type conjecture for Campana points recently formulated\r\nby Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado with an alternative\r\nprediction of Browning and Van Valckenborgh in the special case of the orbifold\r\n$(\\mathbb{P}^1,D)$, where $D =\\frac{1}{2}[0]+\\frac{1}{2}[1]+\\frac{1}{2}[\\infty]$. We find that the two predicted leading constants do not agree, and we discuss whether thin sets\r\ncould explain this discrepancy. Motivated by this, we provide a counterexample\r\nto the Manin-type conjecture for Campana points, by considering orbifolds\r\ncorresponding to squareful values of binary quadratic forms.","lang":"eng"}],"article_number":"2104.14946","language":[{"iso":"eng"}],"status":"public","year":"2021","type":"preprint","article_processing_charge":"No","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","department":[{"_id":"TiBr"}],"doi":"10.48550/arXiv.2104.14946","arxiv":1,"publication":"arXiv","date_published":"2021-04-30T00:00:00Z","_id":"12077","title":"On the leading constant in the Manin-type conjecture for Campana points","oa":1,"date_created":"2022-09-09T10:43:17Z","publication_status":"submitted","citation":{"short":"A.L. Shute, ArXiv (n.d.).","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>.","mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, 2104.14946, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>.","apa":"Shute, A. L. (n.d.). On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>","ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>arXiv</i>. .","ista":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. arXiv, 2104.14946."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"day":"27","article_processing_charge":"No","year":"2020","type":"research_data_reference","status":"public","month":"07","date_updated":"2024-09-10T12:23:51Z","abstract":[{"lang":"eng","text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". Additional raw data are available from the corresponding author on reasonable request."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8529"}]},"author":[{"full_name":"Arnold, Georg M","first_name":"Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","orcid":"0000-0001-6613-1378","first_name":"Matthias","full_name":"Wulf, Matthias"},{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","orcid":"0000-0001-9868-2166","first_name":"William J","full_name":"Hease, William J"},{"first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3961562","open_access":"1"}],"citation":{"ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.3961561\">10.5281/ZENODO.3961561</a>.","mla":"Arnold, Georg M., et al. <i>Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.3961561\">10.5281/ZENODO.3961561</a>.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. <a href=\"https://doi.org/10.5281/ZENODO.3961561\">https://doi.org/10.5281/ZENODO.3961561</a>.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.3961561\">10.5281/ZENODO.3961561</a>","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.3961561\">https://doi.org/10.5281/ZENODO.3961561</a>"},"date_created":"2023-05-23T13:37:41Z","date_published":"2020-07-27T00:00:00Z","_id":"13056","oa":1,"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","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":"10.5281/ZENODO.3961561","publisher":"Zenodo","department":[{"_id":"JoFi"}]},{"author":[{"last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758"},{"full_name":"Stock, Miriam","first_name":"Miriam","last_name":"Stock","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger"},{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.crjdfn318"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7343"}]},"abstract":[{"lang":"eng","text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity ­– influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level."}],"date_updated":"2023-09-05T16:04:48Z","month":"12","article_processing_charge":"No","type":"research_data_reference","status":"public","year":"2020","day":"19","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","doi":"10.5061/DRYAD.CRJDFN318","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","oa":1,"title":"Social immunity modulates competition between coinfecting pathogens","date_published":"2020-12-19T00:00:00Z","_id":"13060","citation":{"mla":"Milutinovic, Barbara, et al. <i>Social Immunity Modulates Competition between Coinfecting Pathogens</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">10.5061/DRYAD.CRJDFN318</a>.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">https://doi.org/10.5061/DRYAD.CRJDFN318</a>.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">10.5061/DRYAD.CRJDFN318</a>","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., &#38; Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">https://doi.org/10.5061/DRYAD.CRJDFN318</a>","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.CRJDFN318\">10.5061/DRYAD.CRJDFN318</a>."},"date_created":"2023-05-23T16:11:22Z"},{"month":"10","article_processing_charge":"No","type":"research_data_reference","year":"2020","status":"public","day":"19","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"last_name":"Arnoux","first_name":"Stephanie","full_name":"Arnoux, Stephanie"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Sauvage, Christopher","first_name":"Christopher","last_name":"Sauvage"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"related_material":{"record":[{"relation":"used_in_publication","id":"8928","status":"public"}],"link":[{"relation":"software","url":"https://github.com/starnoux/arnoux_et_al_2019"}]},"abstract":[{"text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.","lang":"eng"}],"date_updated":"2023-08-04T11:19:26Z","oa":1,"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","date_published":"2020-10-19T00:00:00Z","_id":"13065","citation":{"apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","mla":"Arnoux, Stephanie, et al. <i>VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>.","chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>.","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>."},"date_created":"2023-05-23T16:30:20Z","doi":"10.5061/DRYAD.Q2BVQ83HD","publisher":"Dryad","department":[{"_id":"NiBa"}],"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"}},{"ddc":["530"],"day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","year":"2020","status":"public","type":"research_data_reference","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request."}],"date_updated":"2024-09-10T12:23:56Z","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4052883"}],"author":[{"last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea","full_name":"Trioni, Andrea"},{"first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"},{"first_name":"Martin","full_name":"Zemlicka, Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M"}],"related_material":{"record":[{"relation":"used_in_publication","id":"8755","status":"public"}]},"date_created":"2023-05-23T16:42:30Z","citation":{"short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","mla":"Peruzzo, Matilda, et al. <i>Surpassing the Resistance Quantum with a Geometric Superinductor</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>.","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. <a href=\"https://doi.org/10.5281/ZENODO.4052882\">https://doi.org/10.5281/ZENODO.4052882</a>.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., &#38; Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.4052882\">https://doi.org/10.5281/ZENODO.4052882</a>","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>."},"title":"Surpassing the resistance quantum with a geometric superinductor","oa":1,"date_published":"2020-09-27T00:00:00Z","_id":"13070","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"},"department":[{"_id":"JoFi"}],"publisher":"Zenodo","doi":"10.5281/ZENODO.4052882"},{"department":[{"_id":"JoFi"}],"doi":"10.5281/ZENODO.4266025","publisher":"Zenodo","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"},"title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","oa":1,"_id":"13071","date_published":"2020-11-10T00:00:00Z","date_created":"2023-05-23T16:44:11Z","citation":{"short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","mla":"Hease, William J., et al. <i>Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. <a href=\"https://doi.org/10.5281/ZENODO.4266025\">https://doi.org/10.5281/ZENODO.4266025</a>.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., &#38; Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.4266025\">https://doi.org/10.5281/ZENODO.4266025</a>","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>","ieee":"W. J. Hease <i>et al.</i>, “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>."},"author":[{"orcid":"0000-0001-9868-2166","full_name":"Hease, William J","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","first_name":"Rishabh","orcid":"0000-0001-6264-2162"},{"last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","first_name":"Matthias"},{"first_name":"Georg M","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold"},{"last_name":"Schwefel","full_name":"Schwefel, Harald","first_name":"Harald"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4266026"}],"oa_version":"Published Version","related_material":{"record":[{"id":"9114","status":"public","relation":"used_in_publication"}]},"abstract":[{"text":"This dataset comprises all data shown in the plots of the main part of the submitted article \"Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"date_updated":"2024-09-10T12:23:54Z","month":"11","status":"public","type":"research_data_reference","year":"2020","article_processing_charge":"No","ddc":["530"],"day":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"related_material":{"record":[{"relation":"used_in_publication","id":"8708","status":"public"}]},"oa_version":"Published Version","author":[{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"full_name":"El Ayari, Tahani","first_name":"Tahani","last_name":"El Ayari"},{"first_name":"Cathy","full_name":"Liautard-Haag, Cathy","last_name":"Liautard-Haag"},{"last_name":"Strelkov","full_name":"Strelkov, Petr","first_name":"Petr"},{"last_name":"Welch","full_name":"Welch, John","first_name":"John"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.r4xgxd29n","open_access":"1"}],"date_updated":"2023-08-04T11:04:11Z","abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"article_processing_charge":"No","year":"2020","status":"public","type":"research_data_reference","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"day":"22","doi":"10.5061/DRYAD.R4XGXD29N","publisher":"Dryad","department":[{"_id":"NiBa"}],"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"13073","date_published":"2020-09-22T00:00:00Z","oa":1,"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","citation":{"chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>.","mla":"Simon, Alexis, et al. <i>How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>","ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., &#38; Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>."},"date_created":"2023-05-23T16:48:27Z"},{"type":"journal_article","intvolume":"         9","publication_identifier":{"issn":["2542-4653"]},"ddc":["530"],"file_date_updated":"2020-08-06T08:56:06Z","author":[{"id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden","orcid":"0000-0001-6814-7541","full_name":"Gulden, Tobias","first_name":"Tobias"},{"last_name":"Berg","full_name":"Berg, Erez","first_name":"Erez"},{"last_name":"Rudner","full_name":"Rudner, Mark Spencer","first_name":"Mark Spencer"},{"first_name":"Netanel","full_name":"Lindner, Netanel","last_name":"Lindner"}],"acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","date_updated":"2023-08-22T08:28:24Z","article_number":"015","abstract":[{"text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.","lang":"eng"}],"article_type":"original","date_published":"2020-07-29T00:00:00Z","_id":"8199","title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","ec_funded":1,"publication_status":"published","citation":{"ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","apa":"Gulden, T., Berg, E., Rudner, M. S., &#38; Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. 2020;9. doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” <i>SciPost Physics</i>, vol. 9. SciPost Foundation, 2020.","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>. SciPost Foundation, 2020. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>.","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>, vol. 9, 015, SciPost Foundation, 2020, doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>."},"date_created":"2020-08-04T13:04:15Z","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"file":[{"access_level":"open_access","relation":"main_file","date_updated":"2020-08-06T08:56:06Z","file_id":"8202","file_size":531137,"success":1,"creator":"dernst","date_created":"2020-08-06T08:56:06Z","file_name":"2020_SciPostPhys_Gulden.pdf","content_type":"application/pdf"}],"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"},"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"year":"2020","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"29","scopus_import":"1","oa_version":"Published Version","external_id":{"isi":["000557362300008"]},"has_accepted_license":"1","quality_controlled":"1","oa":1,"volume":9,"doi":"10.21468/scipostphys.9.1.015","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"publication":"SciPost Physics"},{"publication":"Nano Letters","isi":1,"doi":"10.1021/acs.nanolett.0c01466","project":[{"grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa":1,"volume":20,"quality_controlled":"1","external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"has_accepted_license":"1","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7689","relation":"research_data"}]},"scopus_import":"1","day":"01","pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"06","article_processing_charge":"Yes (via OA deal)","status":"public","language":[{"iso":"eng"}],"year":"2020","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"},"file":[{"file_size":3308906,"success":1,"file_id":"8204","creator":"dernst","date_updated":"2020-08-06T09:35:37Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2020_NanoLetters_Katsaros.pdf","date_created":"2020-08-06T09:35:37Z"}],"publisher":"American Chemical Society","department":[{"_id":"GeKa"}],"citation":{"ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>.","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>","ieee":"G. Katsaros <i>et al.</i>, “Zero field splitting of heavy-hole states in quantum dots,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. 2020;20(7):5201-5206. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>"},"publication_status":"published","date_created":"2020-08-06T09:25:04Z","title":"Zero field splitting of heavy-hole states in quantum dots","ec_funded":1,"_id":"8203","date_published":"2020-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits."}],"page":"5201-5206","article_type":"original","date_updated":"2024-02-21T12:44:01Z","author":[{"orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"},{"last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","first_name":"Josip"},{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","first_name":"Lada","full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636"},{"first_name":"Hannes","full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gao","full_name":"Gao, Fei","first_name":"Fei"},{"orcid":"0000-0002-4619-9575","first_name":"Ting","full_name":"Wang, Ting","last_name":"Wang"},{"first_name":"Jian-Jun","full_name":"Zhang, Jian-Jun","last_name":"Zhang"},{"first_name":"Karsten","full_name":"Held, Karsten","last_name":"Held"}],"acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","issue":"7","file_date_updated":"2020-08-06T09:35:37Z","ddc":["530"],"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"type":"journal_article","intvolume":"        20"},{"day":"21","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","article_processing_charge":"No","year":"2020","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"oa":1,"volume":117,"publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"doi":"10.1073/pnas.1921205117","project":[{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020"}],"ddc":["570"],"publication_identifier":{"eissn":["10916490"]},"type":"journal_article","intvolume":"       117","abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}],"article_type":"original","page":"16969-16975","date_updated":"2023-08-22T08:29:30Z","author":[{"orcid":"0000-0001-9806-5643","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"},{"first_name":"Kasumi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi"},{"last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I.J.","first_name":"Saskia I.J."},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"full_name":"Van Rheenen, Jacco","first_name":"Jacco","last_name":"Van Rheenen"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","issue":"29","file_date_updated":"2020-08-10T06:50:28Z","citation":{"short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>.","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., &#38; Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(29):16969-16975. doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>","ieee":"B. Corominas-Murtra <i>et al.</i>, “Stem cell lineage survival as a noisy competition for niche access,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975."},"publication_status":"published","date_created":"2020-08-09T22:00:52Z","title":"Stem cell lineage survival as a noisy competition for niche access","ec_funded":1,"date_published":"2020-07-21T00:00:00Z","_id":"8220","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"},"file":[{"relation":"main_file","access_level":"open_access","date_updated":"2020-08-10T06:50:28Z","creator":"dernst","success":1,"file_size":1111604,"file_id":"8223","date_created":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf","content_type":"application/pdf"}],"publisher":"National Academy of Sciences","department":[{"_id":"EdHa"}]},{"doi":"10.1038/s41467-020-17734-z","project":[{"grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"isi":1,"publication":"Nature Communications","oa":1,"volume":11,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8657"}]},"oa_version":"Published Version","external_id":{"isi":["000562769300008"]},"has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2020","status":"public","month":"08","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"11","publisher":"Springer Nature","department":[{"_id":"GaTk"}],"file":[{"checksum":"986bebb308850a55850028d3d2b5b664","date_updated":"2020-08-17T07:36:57Z","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"file_id":"8275","file_size":1965672,"file_name":"2020_NatureComm_Kavcic.pdf","date_created":"2020-08-17T07:36:57Z","content_type":"application/pdf"}],"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"},"date_published":"2020-08-11T00:00:00Z","_id":"8250","title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","citation":{"ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17734-z\">10.1038/s41467-020-17734-z</a>","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17734-z\">https://doi.org/10.1038/s41467-020-17734-z</a>","mla":"Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” <i>Nature Communications</i>, vol. 11, 4013, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17734-z\">10.1038/s41467-020-17734-z</a>.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17734-z\">https://doi.org/10.1038/s41467-020-17734-z</a>.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013."},"publication_status":"published","date_created":"2020-08-12T09:13:50Z","file_date_updated":"2020-08-17T07:36:57Z","author":[{"last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","first_name":"Bor","orcid":"0000-0001-6041-254X"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach"}],"acknowledgement":"We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL.","date_updated":"2024-03-25T23:30:05Z","abstract":[{"lang":"eng","text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology."}],"article_type":"original","article_number":"4013","intvolume":"        11","type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"ddc":["570"]},{"abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"has_accepted_license":"1","date_updated":"2024-02-21T12:41:09Z","author":[{"last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","full_name":"Arathoon, Louise S","first_name":"Louise S","orcid":"0000-0003-1771-714X"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","id":"11321","status":"public"},{"id":"9192","status":"public","relation":"later_version"}]},"file_date_updated":"2020-08-18T08:03:23Z","ddc":["576"],"day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","article_processing_charge":"No","year":"2020","type":"research_data","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"},"file":[{"content_type":"application/x-zip-compressed","file_name":"Data_Rcode_MathematicaNB.zip","date_created":"2020-08-18T08:03:23Z","creator":"dernst","file_size":5778420,"file_id":"8280","success":1,"date_updated":"2020-08-18T08:03:23Z","checksum":"4f1382ed4384751b6013398c11557bf6","relation":"main_file","access_level":"open_access"}],"contributor":[{"contributor_type":"data_collector","first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478"},{"contributor_type":"project_member","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","first_name":"Carina","contributor_type":"project_member"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:8254","department":[{"_id":"NiBa"}],"citation":{"apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","short":"L.S. Arathoon, (2020).","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>.","mla":"Arathoon, Louise S. <i>Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus)</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>."},"date_created":"2020-08-12T12:49:23Z","oa":1,"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","_id":"8254","date_published":"2020-08-18T00:00:00Z"},{"type":"journal_article","intvolume":"       107","ddc":["570"],"publication_identifier":{"issn":["0896-6273"]},"author":[{"full_name":"Zhang, Xiaomin","first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100","first_name":"Alois","full_name":"Schlögl, Alois"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","file_date_updated":"2020-12-04T09:29:21Z","issue":"6","article_type":"original","abstract":[{"lang":"eng","text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion."}],"page":"1212-1225","date_updated":"2023-08-22T08:30:55Z","ec_funded":1,"title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","date_published":"2020-09-23T00:00:00Z","_id":"8261","date_created":"2020-08-14T09:36:05Z","publication_status":"published","citation":{"chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” <i>Neuron</i>, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. 2020;107(6):1212-1225. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>","apa":"Zhang, X., Schlögl, A., &#38; Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225."},"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"relation":"main_file","access_level":"open_access","date_updated":"2020-12-04T09:29:21Z","checksum":"44a5960fc083a4cb3488d22224859fdc","creator":"dernst","success":1,"file_size":3011120,"file_id":"8920","date_created":"2020-12-04T09:29:21Z","file_name":"2020_Neuron_Zhang.pdf","content_type":"application/pdf"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"09","year":"2020","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","pmid":1,"day":"23","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","description":"News on IST Website","relation":"press_release"}]},"quality_controlled":"1","has_accepted_license":"1","external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"volume":107,"oa":1,"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312"}],"doi":"10.1016/j.neuron.2020.07.006","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"publication":"Neuron","isi":1},{"doi":"10.1109/TSP.2020.3010355","isi":1,"arxiv":1,"publication":"IEEE Transactions on Signal Processing","volume":68,"oa":1,"scopus_import":"1","oa_version":"Preprint","external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2020","status":"public","article_processing_charge":"No","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"20","department":[{"_id":"DaAl"}],"publisher":"IEEE","_id":"8268","date_published":"2020-07-20T00:00:00Z","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","date_created":"2020-08-16T22:00:56Z","citation":{"apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. IEEE. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>","ieee":"N. M. Gurel <i>et al.</i>, “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” <i>IEEE Transactions on Signal Processing</i>, vol. 68. IEEE, pp. 4268–4282, 2020.","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. 2020;68:4268-4282. doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.","chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>.","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>, vol. 68, IEEE, 2020, pp. 4268–82, doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>.","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282."},"publication_status":"published","acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","author":[{"last_name":"Gurel","full_name":"Gurel, Nezihe Merve","first_name":"Nezihe Merve"},{"first_name":"Kaan","full_name":"Kara, Kaan","last_name":"Kara"},{"last_name":"Stojanov","full_name":"Stojanov, Alen","first_name":"Alen"},{"first_name":"Tyler","full_name":"Smith, Tyler","last_name":"Smith"},{"first_name":"Thomas","full_name":"Lemmin, Thomas","last_name":"Lemmin"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"},{"first_name":"Markus","full_name":"Puschel, Markus","last_name":"Puschel"},{"last_name":"Zhang","first_name":"Ce","full_name":"Zhang, Ce"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.04907"}],"date_updated":"2023-08-22T08:40:08Z","page":"4268-4282","abstract":[{"text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.","lang":"eng"}],"article_type":"original","intvolume":"        68","type":"journal_article","publication_identifier":{"eissn":["19410476"],"issn":["1053587X"]}},{"quality_controlled":"1","external_id":{"pmid":["32688032"],"isi":["000566895400007"]},"oa_version":"None","scopus_import":"1","day":"07","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","article_processing_charge":"No","year":"2020","language":[{"iso":"eng"}],"status":"public","publication":"Molecular Plant","isi":1,"doi":"10.1016/j.molp.2020.07.006","volume":13,"page":"1238-1240","article_type":"original","date_updated":"2023-08-22T08:40:35Z","acknowledgement":"We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared.","author":[{"last_name":"He","full_name":"He, Peng","first_name":"Peng"},{"orcid":"0000-0003-2627-6956","first_name":"Yuzhou","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang"},{"first_name":"Guanghui","full_name":"Xiao, Guanghui","last_name":"Xiao"}],"issue":"9","publication_identifier":{"eissn":["17529867"],"issn":["16742052"]},"type":"journal_article","intvolume":"        13","publisher":"Elsevier","department":[{"_id":"JiFr"}],"citation":{"ista":"He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","mla":"He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>.","chicago":"He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>.","apa":"He, P., Zhang, Y., &#38; Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>","ieee":"P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” <i>Molecular Plant</i>, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020.","ama":"He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. 2020;13(9):1238-1240. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>"},"publication_status":"published","date_created":"2020-08-16T22:00:57Z","title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","_id":"8271","date_published":"2020-09-07T00:00:00Z"},{"doi":"10.1007/978-3-030-53291-8_21","project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"isi":1,"publication":"International Conference on Computer Aided Verification","arxiv":1,"oa":1,"volume":12225,"related_material":{"record":[{"relation":"later_version","status":"public","id":"12738"}]},"scopus_import":"1","oa_version":"Published Version","external_id":{"arxiv":["2005.04018"],"isi":["000695272500021"]},"has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","year":"2020","language":[{"iso":"eng"}],"status":"public","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","alternative_title":["LNCS"],"day":"14","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"file":[{"file_name":"2020_LNCS_CAV_Chatterjee.pdf","date_created":"2020-08-17T11:32:44Z","content_type":"application/pdf","date_updated":"2020-08-17T11:32:44Z","checksum":"093d4788d7d5b2ce0ffe64fbe7820043","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"file_id":"8276","file_size":625056}],"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"},"date_published":"2020-07-14T00:00:00Z","_id":"8272","title":"Stochastic games with lexicographic reachability-safety objectives","ec_funded":1,"citation":{"ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 12225:398–420. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">https://doi.org/10.1007/978-3-030-53291-8_21</a>.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:<a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">10.1007/978-3-030-53291-8_21</a>.","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., &#38; Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 12225, pp. 398–420). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">https://doi.org/10.1007/978-3-030-53291-8_21</a>","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in <i>International Conference on Computer Aided Verification</i>, 2020, vol. 12225, pp. 398–420.","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 12225. Springer Nature; 2020:398-420. doi:<a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">10.1007/978-3-030-53291-8_21</a>"},"publication_status":"published","date_created":"2020-08-16T22:00:58Z","file_date_updated":"2020-08-17T11:32:44Z","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Katoen, Joost P","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"},{"last_name":"Winkler","first_name":"Tobias","full_name":"Winkler, Tobias"}],"date_updated":"2025-07-14T09:10:14Z","conference":{"name":"CAV: Computer Aided Verification"},"page":"398-420","abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in   NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is   PSPACE -hard and can be solved in   NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies."}],"intvolume":"     12225","type":"conference","publication_identifier":{"eissn":["16113349"],"issn":["03029743"],"isbn":["9783030532901"]},"ddc":["000"]},{"date_published":"2020-08-10T00:00:00Z","_id":"8283","title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","date_created":"2020-08-24T06:24:03Z","publication_status":"published","citation":{"apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21165727\">https://doi.org/10.3390/ijms21165727</a>","ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. <i>International Journal of Molecular Sciences</i>. 2020;21(16). doi:<a href=\"https://doi.org/10.3390/ijms21165727\">10.3390/ijms21165727</a>","ieee":"H. Chen <i>et al.</i>, “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16. MDPI, 2020.","short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16, 5272, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21165727\">10.3390/ijms21165727</a>.","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21165727\">https://doi.org/10.3390/ijms21165727</a>.","ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272."},"department":[{"_id":"JiFr"}],"publisher":"MDPI","file":[{"file_name":"2020_IntMolecSciences_Chen.pdf","date_created":"2020-08-25T09:53:50Z","content_type":"application/pdf","date_updated":"2020-08-25T09:53:50Z","checksum":"03b039244e6ae80580385fd9f577e2b2","access_level":"open_access","relation":"main_file","file_id":"8292","file_size":5718755,"success":1,"creator":"cziletti"}],"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"},"intvolume":"        21","type":"journal_article","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"ddc":["570"],"file_date_updated":"2020-08-25T09:53:50Z","issue":"16","author":[{"last_name":"Chen","first_name":"Huihuang","full_name":"Chen, Huihuang"},{"last_name":"Lai","full_name":"Lai, Linyi","first_name":"Linyi"},{"full_name":"Li, Lanxin","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"last_name":"Liu","full_name":"Liu, Liping","first_name":"Liping"},{"full_name":"Jakada, Bello Hassan","first_name":"Bello Hassan","last_name":"Jakada"},{"full_name":"Huang, Youmei","first_name":"Youmei","last_name":"Huang"},{"last_name":"He","first_name":"Qing","full_name":"He, Qing"},{"last_name":"Chai","first_name":"Mengnan","full_name":"Chai, Mengnan"},{"first_name":"Xiaoping","full_name":"Niu, Xiaoping","last_name":"Niu"},{"first_name":"Yuan","full_name":"Qin, Yuan","last_name":"Qin"}],"acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","date_updated":"2024-10-29T10:22:43Z","abstract":[{"text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. ","lang":"eng"}],"article_number":"5272","article_type":"original","volume":21,"oa":1,"doi":"10.3390/ijms21165727","isi":1,"publication":"International Journal of Molecular Sciences","status":"public","year":"2020","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"08","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"day":"10","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"oa_version":"Published Version","has_accepted_license":"1","external_id":{"pmid":["32785037"],"isi":["000565090300001"]},"quality_controlled":"1"},{"file":[{"content_type":"application/pdf","date_created":"2020-08-24T13:31:53Z","file_name":"2020_eLife_Steiner.pdf","creator":"cziletti","file_id":"8289","success":1,"file_size":7320493,"relation":"main_file","access_level":"open_access","date_updated":"2020-08-24T13:31:53Z","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15"}],"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"},"department":[{"_id":"LeSa"}],"publisher":"eLife Sciences Publications","date_created":"2020-08-24T06:24:04Z","publication_status":"published","citation":{"chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>.","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>, vol. 9, e59407, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>.","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Steiner, J., &#38; Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407."},"date_published":"2020-07-31T00:00:00Z","_id":"8284","title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","date_updated":"2023-09-07T13:14:08Z","abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"article_type":"original","article_number":"e59407","file_date_updated":"2020-08-24T13:31:53Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","author":[{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","last_name":"Steiner","orcid":"0000-0003-0493-3775","first_name":"Julia","full_name":"Steiner, Julia"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"eissn":["2050084X"]},"ddc":["570"],"type":"journal_article","intvolume":"         9","isi":1,"publication":"eLife","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741"}],"doi":"10.7554/eLife.59407","volume":9,"oa":1,"has_accepted_license":"1","external_id":{"pmid":["32735215"],"isi":["000562123600001"]},"quality_controlled":"1","scopus_import":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/"}],"record":[{"relation":"dissertation_contains","id":"8353","status":"public"}]},"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"day":"31","status":"public","year":"2020","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"07"},{"arxiv":1,"publication":"Physical Review Letters","isi":1,"doi":"10.1103/PhysRevLett.125.043202","volume":125,"oa":1,"quality_controlled":"1","external_id":{"isi":["000552227400008"],"arxiv":["1912.10218"],"pmid":["32794788"]},"oa_version":"Preprint","scopus_import":"1","pmid":1,"day":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","language":[{"iso":"eng"}],"year":"2020","status":"public","article_processing_charge":"No","department":[{"_id":"OnHo"}],"publisher":"American Physical Society","date_created":"2020-08-24T06:24:04Z","citation":{"ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">https://doi.org/10.1103/PhysRevLett.125.043202</a>.","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” <i>Physical Review Letters</i>, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">10.1103/PhysRevLett.125.043202</a>.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” <i>Physical Review Letters</i>, vol. 125, no. 4. American Physical Society, 2020.","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. <i>Physical Review Letters</i>. 2020;125(4). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">10.1103/PhysRevLett.125.043202</a>","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., &#38; Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">https://doi.org/10.1103/PhysRevLett.125.043202</a>"},"publication_status":"published","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","date_published":"2020-07-24T00:00:00Z","_id":"8285","abstract":[{"text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200  μm radius and falls roughly 300  μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively.","lang":"eng"}],"article_type":"original","article_number":"043202","date_updated":"2023-10-18T08:38:35Z","author":[{"full_name":"Malia, Benjamin K.","first_name":"Benjamin K.","last_name":"Malia"},{"first_name":"Julián","full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón"},{"full_name":"Wu, Yunfan","first_name":"Yunfan","last_name":"Wu"},{"orcid":"0000-0002-2031-204X","first_name":"Onur","full_name":"Hosten, Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark A.","full_name":"Kasevich, Mark A.","last_name":"Kasevich"}],"acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"issue":"4","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"type":"journal_article","intvolume":"       125"}]