--- _id: '8225' abstract: - lang: eng text: Birch pollen allergy is among the most prevalent pollen allergies in Northern and Central Europe. This IgE-mediated disease can be treated with allergen immunotherapy (AIT), which typically gives rise to IgG antibodies inducing tolerance. Although the main mechanisms of allergen immunotherapy (AIT) are known, questions regarding possible Fc-mediated effects of IgG antibodies remain unanswered. This can mainly be attributed to the unavailability of appropriate tools, i.e., well-characterised recombinant antibodies (rAbs). We hereby aimed at providing human rAbs of several classes for mechanistic studies and as possible candidates for passive immunotherapy. We engineered IgE, IgG1, and IgG4 sharing the same variable region against the major birch pollen allergen Bet v 1 using Polymerase Incomplete Primer Extension (PIPE) cloning. We tested IgE functionality and IgG blocking capabilities using appropriate model cell lines. In vitro studies showed IgE engagement with FcεRI and CD23 and Bet v 1-dependent degranulation. Overall, we hereby present fully functional, human IgE, IgG1, and IgG4 sharing the same variable region against Bet v 1 and showcase possible applications in first mechanistic studies. Furthermore, our IgG antibodies might be useful candidates for passive immunotherapy of birch pollen allergy. article_number: '5693' article_processing_charge: No article_type: original author: - first_name: Verena K. full_name: Köhler, Verena K. last_name: Köhler orcid: 0000-0001-5581-398X - first_name: Silvia full_name: Crescioli, Silvia last_name: Crescioli orcid: 0000-0002-1909-5957 - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Heather J. full_name: Bax, Heather J. last_name: Bax orcid: 0000-0003-0432-4160 - first_name: Gerhard full_name: Hofer, Gerhard last_name: Hofer - first_name: Christina L. full_name: Pranger, Christina L. last_name: Pranger - first_name: Karin full_name: Hufnagl, Karin last_name: Hufnagl - first_name: Rodolfo full_name: Bianchini, Rodolfo last_name: Bianchini orcid: 0000-0003-0351-6937 - first_name: Sabine full_name: Flicker, Sabine last_name: Flicker orcid: 0000-0003-4768-8693 - first_name: Walter full_name: Keller, Walter last_name: Keller orcid: 0000-0002-2261-958X - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis orcid: 0000-0002-4100-7810 - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim orcid: 0000-0003-4019-5765 citation: ama: 'Köhler VK, Crescioli S, Singer J, et al. Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165693' apa: 'Köhler, V. K., Crescioli, S., Singer, J., Bax, H. J., Hofer, G., Pranger, C. L., … Jensen-Jarolim, E. (2020). Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165693' chicago: 'Köhler, Verena K., Silvia Crescioli, Judit Singer, Heather J. Bax, Gerhard Hofer, Christina L. Pranger, Karin Hufnagl, et al. “Filling the Antibody Pipeline in Allergy: PIPE Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen Allergen Bet v 1.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165693.' ieee: 'V. K. Köhler et al., “Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.' ista: 'Köhler VK, Crescioli S, Singer J, Bax HJ, Hofer G, Pranger CL, Hufnagl K, Bianchini R, Flicker S, Keller W, Karagiannis SN, Jensen-Jarolim E. 2020. Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. International Journal of Molecular Sciences. 21(16), 5693.' mla: 'Köhler, Verena K., et al. “Filling the Antibody Pipeline in Allergy: PIPE Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen Allergen Bet v 1.” International Journal of Molecular Sciences, vol. 21, no. 16, 5693, MDPI, 2020, doi:10.3390/ijms21165693.' short: V.K. Köhler, S. Crescioli, J. Singer, H.J. Bax, G. Hofer, C.L. Pranger, K. Hufnagl, R. Bianchini, S. Flicker, W. Keller, S.N. Karagiannis, E. Jensen-Jarolim, International Journal of Molecular Sciences 21 (2020). date_created: 2020-08-10T11:47:29Z date_published: 2020-08-08T00:00:00Z date_updated: 2021-01-12T08:17:34Z day: '08' ddc: - '570' doi: 10.3390/ijms21165693 extern: '1' external_id: pmid: - '32784509' file: - access_level: open_access checksum: dac7ccef7cdcea9be292664d8c488425 content_type: application/pdf creator: dernst date_created: 2020-09-10T07:06:22Z date_updated: 2020-09-10T07:06:22Z file_id: '8356' file_name: 2020_IntMolecSciences_Koehler.pdf file_size: 2680908 relation: main_file success: 1 file_date_updated: 2020-09-10T07:06:22Z has_accepted_license: '1' intvolume: ' 21' issue: '16' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: International Journal of Molecular Sciences publication_identifier: issn: - 1422-0067 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: 'Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2020' ... --- _id: '8226' article_processing_charge: No article_type: letter_note author: - first_name: Jelena full_name: Gotovina, Jelena last_name: Gotovina orcid: 0000-0003-1503-5276 - first_name: Rodolfo full_name: Bianchini, Rodolfo last_name: Bianchini orcid: 0000-0003-0351-6937 - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Ina full_name: Herrmann, Ina last_name: Herrmann orcid: 0000-0003-2772-9144 - first_name: Giulia full_name: Pellizzari, Giulia last_name: Pellizzari orcid: 0000-0003-0387-1912 - first_name: Ian D. full_name: Haidl, Ian D. last_name: Haidl orcid: 0000-0002-5301-0822 - first_name: Karin full_name: Hufnagl, Karin last_name: Hufnagl orcid: 0000-0002-2288-2468 - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis orcid: 0000-0002-4100-7810 - first_name: Jean S. full_name: Marshall, Jean S. last_name: Marshall orcid: 0000-0002-5642-1379 - first_name: Erika full_name: Jensen‐Jarolim, Erika last_name: Jensen‐Jarolim orcid: 0000-0003-4019-5765 citation: ama: Gotovina J, Bianchini R, Singer J, et al. Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. Allergy. 2020. doi:10.1111/all.14299 apa: Gotovina, J., Bianchini, R., Singer, J., Herrmann, I., Pellizzari, G., Haidl, I. D., … Jensen‐Jarolim, E. (2020). Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. Allergy. Wiley. https://doi.org/10.1111/all.14299 chicago: Gotovina, Jelena, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Giulia Pellizzari, Ian D. Haidl, Karin Hufnagl, Sophia N. Karagiannis, Jean S. Marshall, and Erika Jensen‐Jarolim. “Epinephrine Drives Human M2a Allergic Macrophages to a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” Allergy. Wiley, 2020. https://doi.org/10.1111/all.14299. ieee: J. Gotovina et al., “Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro,” Allergy. Wiley, 2020. ista: Gotovina J, Bianchini R, Singer J, Herrmann I, Pellizzari G, Haidl ID, Hufnagl K, Karagiannis SN, Marshall JS, Jensen‐Jarolim E. 2020. Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. Allergy. mla: Gotovina, Jelena, et al. “Epinephrine Drives Human M2a Allergic Macrophages to a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” Allergy, Wiley, 2020, doi:10.1111/all.14299. short: J. Gotovina, R. Bianchini, J. Singer, I. Herrmann, G. Pellizzari, I.D. Haidl, K. Hufnagl, S.N. Karagiannis, J.S. Marshall, E. Jensen‐Jarolim, Allergy (2020). date_created: 2020-08-10T11:50:30Z date_published: 2020-04-04T00:00:00Z date_updated: 2021-01-12T08:17:35Z day: '04' doi: 10.1111/all.14299 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/all.14299 month: '04' oa: 1 oa_version: Published Version publication: Allergy publication_identifier: issn: - 0105-4538 - 1398-9995 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' status: public title: Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8250' 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.' 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." article_number: '4013' article_processing_charge: No article_type: original author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17734-z chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z. ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013. mla: Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z. short: B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020). date_created: 2020-08-12T09:13:50Z date_published: 2020-08-11T00:00:00Z date_updated: 2024-03-25T23:30:05Z day: '11' ddc: - '570' department: - _id: GaTk doi: 10.1038/s41467-020-17734-z external_id: isi: - '000562769300008' file: - access_level: open_access checksum: 986bebb308850a55850028d3d2b5b664 content_type: application/pdf creator: dernst date_created: 2020-08-17T07:36:57Z date_updated: 2020-08-17T07:36:57Z file_id: '8275' file_name: 2020_NatureComm_Kavcic.pdf file_size: 1965672 relation: main_file success: 1 file_date_updated: 2020-08-17T07:36:57Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8657' relation: dissertation_contains status: public status: public title: Mechanisms of drug interactions between translation-inhibiting antibiotics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8254' 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." article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254 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. https://doi.org/10.15479/AT:ISTA:8254 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. https://doi.org/10.15479/AT:ISTA:8254. 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. ista: Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254. mla: Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254. short: L.S. Arathoon, (2020). contributor: - contributor_type: data_collector first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - contributor_type: project_member first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett date_created: 2020-08-12T12:49:23Z date_published: 2020-08-18T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '18' ddc: - '576' department: - _id: NiBa doi: 10.15479/AT:ISTA:8254 file: - access_level: open_access checksum: 4f1382ed4384751b6013398c11557bf6 content_type: application/x-zip-compressed creator: dernst date_created: 2020-08-18T08:03:23Z date_updated: 2020-08-18T08:03:23Z file_id: '8280' file_name: Data_Rcode_MathematicaNB.zip file_size: 5778420 relation: main_file success: 1 file_date_updated: 2020-08-18T08:03:23Z has_accepted_license: '1' month: '08' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11321' relation: later_version status: public - id: '9192' relation: later_version status: public status: public title: Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus) tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8261' 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. acknowledged_ssus: - _id: M-Shop - _id: ScienComp - _id: PreCl 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. article_processing_charge: No article_type: original author: - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006 apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006 chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006. ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020. 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. mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006. short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225. date_created: 2020-08-14T09:36:05Z date_published: 2020-09-23T00:00:00Z date_updated: 2023-08-22T08:30:55Z day: '23' ddc: - '570' department: - _id: PeJo - _id: ScienComp doi: 10.1016/j.neuron.2020.07.006 ec_funded: 1 external_id: isi: - '000579698700009' pmid: - '32763145' file: - access_level: open_access checksum: 44a5960fc083a4cb3488d22224859fdc content_type: application/pdf creator: dernst date_created: 2020-12-04T09:29:21Z date_updated: 2020-12-04T09:29:21Z file_id: '8920' file_name: 2020_Neuron_Zhang.pdf file_size: 3011120 relation: main_file success: 1 file_date_updated: 2020-12-04T09:29:21Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version page: 1212-1225 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/ status: public title: Selective routing of spatial information flow from input to output in hippocampal granule cells tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2020' ... --- _id: '8268' abstract: - lang: eng 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.' 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Nezihe Merve full_name: Gurel, Nezihe Merve last_name: Gurel - first_name: Kaan full_name: Kara, Kaan last_name: Kara - first_name: Alen full_name: Stojanov, Alen last_name: Stojanov - first_name: Tyler full_name: Smith, Tyler last_name: Smith - first_name: Thomas full_name: Lemmin, Thomas last_name: Lemmin - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Markus full_name: Puschel, Markus last_name: Puschel - first_name: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355' 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. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355' 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.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.' ieee: 'N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.' 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.' mla: 'Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.' 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. date_created: 2020-08-16T22:00:56Z date_published: 2020-07-20T00:00:00Z date_updated: 2023-08-22T08:40:08Z day: '20' department: - _id: DaAl doi: 10.1109/TSP.2020.3010355 external_id: arxiv: - '1802.04907' isi: - '000562044500001' intvolume: ' 68' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.04907 month: '07' oa: 1 oa_version: Preprint page: 4268-4282 publication: IEEE Transactions on Signal Processing publication_identifier: eissn: - '19410476' issn: - 1053587X publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 68 year: '2020' ... --- _id: '8271' 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. article_processing_charge: No article_type: original author: - first_name: Peng full_name: He, Peng last_name: He - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Guanghui full_name: Xiao, Guanghui last_name: Xiao citation: ama: He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006 apa: He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.07.006 chicago: He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.07.006. ieee: P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020. 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. mla: He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:10.1016/j.molp.2020.07.006. short: P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240. date_created: 2020-08-16T22:00:57Z date_published: 2020-09-07T00:00:00Z date_updated: 2023-08-22T08:40:35Z day: '07' department: - _id: JiFr doi: 10.1016/j.molp.2020.07.006 external_id: isi: - '000566895400007' pmid: - '32688032' intvolume: ' 13' isi: 1 issue: '9' language: - iso: eng month: '09' oa_version: None page: 1238-1240 pmid: 1 publication: Molecular Plant publication_identifier: eissn: - '17529867' issn: - '16742052' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Origin of a subgenome and genome evolution of allotetraploid cotton species type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2020' ... --- _id: '8272' 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. alternative_title: - LNCS article_processing_charge: No arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler citation: ama: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21' apa: Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21 chicago: Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21. ieee: K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420. 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.' mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21. short: K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420. conference: name: 'CAV: Computer Aided Verification' date_created: 2020-08-16T22:00:58Z date_published: 2020-07-14T00:00:00Z date_updated: 2025-07-14T09:10:14Z day: '14' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-030-53291-8_21 ec_funded: 1 external_id: arxiv: - '2005.04018' isi: - '000695272500021' file: - access_level: open_access checksum: 093d4788d7d5b2ce0ffe64fbe7820043 content_type: application/pdf creator: dernst date_created: 2020-08-17T11:32:44Z date_updated: 2020-08-17T11:32:44Z file_id: '8276' file_name: 2020_LNCS_CAV_Chatterjee.pdf file_size: 625056 relation: main_file success: 1 file_date_updated: 2020-08-17T11:32:44Z has_accepted_license: '1' intvolume: ' 12225' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 398-420 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: International Conference on Computer Aided Verification publication_identifier: eissn: - '16113349' isbn: - '9783030532901' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '12738' relation: later_version status: public scopus_import: '1' status: public title: Stochastic games with lexicographic reachability-safety objectives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12225 year: '2020' ... --- _id: '8283' abstract: - lang: eng 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. ' acknowledgement: 'We would like to thank the reviewers for their helpful comments on the original manuscript. ' article_number: '5272' article_processing_charge: No article_type: original author: - first_name: Huihuang full_name: Chen, Huihuang last_name: Chen - first_name: Linyi full_name: Lai, Linyi last_name: Lai - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Liping full_name: Liu, Liping last_name: Liu - first_name: Bello Hassan full_name: Jakada, Bello Hassan last_name: Jakada - first_name: Youmei full_name: Huang, Youmei last_name: Huang - first_name: Qing full_name: He, Qing last_name: He - first_name: Mengnan full_name: Chai, Mengnan last_name: Chai - first_name: Xiaoping full_name: Niu, Xiaoping last_name: Niu - first_name: Yuan full_name: Qin, Yuan last_name: Qin citation: 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. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727 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. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727 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.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727. ieee: H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020. 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. mla: Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727. 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). date_created: 2020-08-24T06:24:03Z date_published: 2020-08-10T00:00:00Z date_updated: 2024-10-29T10:22:43Z day: '10' ddc: - '570' department: - _id: JiFr doi: 10.3390/ijms21165727 external_id: isi: - '000565090300001' pmid: - '32785037' file: - access_level: open_access checksum: 03b039244e6ae80580385fd9f577e2b2 content_type: application/pdf creator: cziletti date_created: 2020-08-25T09:53:50Z date_updated: 2020-08-25T09:53:50Z file_id: '8292' file_name: 2020_IntMolecSciences_Chen.pdf file_size: 5718755 relation: main_file success: 1 file_date_updated: 2020-08-25T09:53:50Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '16' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: International Journal of Molecular Sciences publication_identifier: eissn: - '14220067' issn: - '16616596' publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public scopus_import: '1' status: public title: AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '8284' abstract: - lang: eng 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. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc 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. article_number: e59407 article_processing_charge: No article_type: original author: - first_name: Julia full_name: Steiner, Julia id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87 last_name: Steiner orcid: 0000-0003-0493-3775 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407 apa: Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407 chicago: Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407. ieee: J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407. mla: Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407. short: J. Steiner, L.A. Sazanov, ELife 9 (2020). date_created: 2020-08-24T06:24:04Z date_published: 2020-07-31T00:00:00Z date_updated: 2023-09-07T13:14:08Z day: '31' ddc: - '570' department: - _id: LeSa doi: 10.7554/eLife.59407 external_id: isi: - '000562123600001' pmid: - '32735215' file: - access_level: open_access checksum: b3656d14d5ddbb9d26e3074eea2d0c15 content_type: application/pdf creator: cziletti date_created: 2020-08-24T13:31:53Z date_updated: 2020-08-24T13:31:53Z file_id: '8289' file_name: 2020_eLife_Steiner.pdf file_size: 7320493 relation: main_file success: 1 file_date_updated: 2020-08-24T13:31:53Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26169496-B435-11E9-9278-68D0E5697425 grant_number: '24741' name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/ record: - id: '8353' relation: dissertation_contains status: public scopus_import: '1' status: public title: Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '8285' abstract: - lang: eng 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. 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). article_number: '043202' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Benjamin K. full_name: Malia, Benjamin K. last_name: Malia - first_name: Julián full_name: Martínez-Rincón, Julián last_name: Martínez-Rincón - first_name: Yunfan full_name: Wu, Yunfan last_name: Wu - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Mark A. full_name: Kasevich, Mark A. last_name: Kasevich citation: 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. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202 apa: Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202 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.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202. 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,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020. 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. mla: Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202. short: B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020). date_created: 2020-08-24T06:24:04Z date_published: 2020-07-24T00:00:00Z date_updated: 2023-10-18T08:38:35Z day: '24' department: - _id: OnHo doi: 10.1103/PhysRevLett.125.043202 external_id: arxiv: - '1912.10218' isi: - '000552227400008' pmid: - '32794788' intvolume: ' 125' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.10218 month: '07' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 125 year: '2020' ... --- _id: '8287' abstract: - lang: eng text: Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks. article_processing_charge: No arxiv: 1 author: - first_name: Sergiy full_name: Bogomolov, Sergiy last_name: Bogomolov - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Kostiantyn full_name: Potomkin, Kostiantyn last_name: Potomkin - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: Proceedings of the International Conference on Embedded Software. ; 2020.' apa: Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In Proceedings of the International Conference on Embedded Software. Virtual . chicago: Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In Proceedings of the International Conference on Embedded Software, 2020. ieee: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in Proceedings of the International Conference on Embedded Software, Virtual , 2020. ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.' mla: Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020. short: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020. conference: end_date: 2020-09-25 location: 'Virtual ' name: 'EMSOFT: International Conference on Embedded Software' start_date: 2020-09-20 date_created: 2020-08-24T12:56:20Z date_published: 2020-01-01T00:00:00Z date_updated: 2023-08-22T13:27:32Z ddc: - '000' department: - _id: ToHe ec_funded: 1 external_id: arxiv: - '1905.02458' file: - access_level: open_access checksum: d19e97d0f8a3a441dc078ec812297d75 content_type: application/pdf creator: cschilli date_created: 2020-08-24T12:53:15Z date_updated: 2020-08-24T12:53:15Z file_id: '8288' file_name: 2020EMSOFT.pdf file_size: 696384 relation: main_file success: 1 file_date_updated: 2020-08-24T12:53:15Z has_accepted_license: '1' keyword: - reachability - hybrid systems - decomposition language: - iso: eng oa: 1 oa_version: Preprint project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Proceedings of the International Conference on Embedded Software publication_status: published quality_controlled: '1' related_material: record: - id: '8790' relation: later_version status: public status: public title: Reachability analysis of linear hybrid systems via block decomposition tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8294' abstract: - lang: eng text: 'Automated root growth analysis and tracking of root tips. ' author: - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 citation: ama: Hauschild R. RGtracker. 2020. doi:10.15479/AT:ISTA:8294 apa: Hauschild, R. (2020). RGtracker. IST Austria. https://doi.org/10.15479/AT:ISTA:8294 chicago: Hauschild, Robert. “RGtracker.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8294. ieee: R. Hauschild, “RGtracker.” IST Austria, 2020. ista: Hauschild R. 2020. RGtracker, IST Austria, 10.15479/AT:ISTA:8294. mla: Hauschild, Robert. RGtracker. IST Austria, 2020, doi:10.15479/AT:ISTA:8294. short: R. Hauschild, (2020). date_created: 2020-08-25T12:52:48Z date_published: 2020-09-10T00:00:00Z date_updated: 2021-01-12T08:17:56Z day: '10' ddc: - '570' department: - _id: Bio doi: 10.15479/AT:ISTA:8294 file: - access_level: open_access checksum: 108352149987ac6f066e4925bd56e35e content_type: text/plain creator: rhauschild date_created: 2020-09-08T14:26:31Z date_updated: 2020-09-08T14:26:31Z file_id: '8346' file_name: readme.txt file_size: 882 relation: main_file success: 1 - access_level: open_access checksum: ffd6c643b28e0cc7c6d0060a18a7e8ea content_type: application/octet-stream creator: rhauschild date_created: 2020-09-08T14:26:33Z date_updated: 2020-09-08T14:26:33Z file_id: '8347' file_name: RGtracker.mlappinstall file_size: 246121 relation: main_file success: 1 file_date_updated: 2020-09-08T14:26:33Z has_accepted_license: '1' license: https://opensource.org/licenses/BSD-3-Clause month: '09' oa: 1 publisher: IST Austria status: public title: RGtracker tmp: legal_code_url: https://opensource.org/licenses/BSD-3-Clause name: The 3-Clause BSD License short: 3-Clause BSD type: software user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8307' abstract: - lang: eng text: "Classic Byzantine fault-tolerant consensus protocols forfeit liveness in the face of asynchrony in order to preserve safety, whereas most deployed blockchain protocols forfeit safety in order to remain live. In this work, we achieve the best of both worlds by proposing a novel abstractions called the finality gadget. A finality gadget allows for transactions to always optimistically commit but informs the clients that these transactions might be unsafe. As a result, a blockchain can execute transactions optimistically and only commit them after they have been sufficiently and provably audited. In\r\nthis work, we formally model the finality gadget abstraction, prove that it is impossible to solve it deterministically in full asynchrony (even though it is stronger than consensus) and provide a partially synchronous protocol which is currently securing a major blockchain. This way we show that the protocol designer can decouple safety and liveness in order to speed up recovery from failures. We believe that there can be other types of finality gadgets that provide weaker safety (e.g., probabilistic) in order to gain more efficiency and this can depend on the probability that the network is not in synchrony." article_number: '2007.01560' article_processing_charge: No arxiv: 1 author: - first_name: Alistair full_name: Stewart, Alistair last_name: Stewart - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: 'Stewart A, Kokoris Kogias E. GRANDPA: A Byzantine finality gadget. arXiv.' apa: 'Stewart, A., & Kokoris Kogias, E. (n.d.). GRANDPA: A Byzantine finality gadget. arXiv.' chicago: 'Stewart, Alistair, and Eleftherios Kokoris Kogias. “GRANDPA: A Byzantine Finality Gadget.” ArXiv, n.d.' ieee: 'A. Stewart and E. Kokoris Kogias, “GRANDPA: A Byzantine finality gadget,” arXiv. .' ista: 'Stewart A, Kokoris Kogias E. GRANDPA: A Byzantine finality gadget. arXiv, 2007.01560.' mla: 'Stewart, Alistair, and Eleftherios Kokoris Kogias. “GRANDPA: A Byzantine Finality Gadget.” ArXiv, 2007.01560.' short: A. Stewart, E. Kokoris Kogias, ArXiv (n.d.). date_created: 2020-08-26T12:32:10Z date_published: 2020-07-03T00:00:00Z date_updated: 2021-01-12T08:18:02Z day: '03' extern: '1' external_id: arxiv: - '2007.01560' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.01560 month: '07' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'GRANDPA: A Byzantine finality gadget' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8308' abstract: - lang: eng text: 'Many-body localization provides a mechanism to avoid thermalization in isolated interacting quantum systems. The breakdown of thermalization may be complete, when all eigenstates in the many-body spectrum become localized, or partial, when the so-called many-body mobility edge separates localized and delocalized parts of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)] suggested a possible instability of the many-body mobility edge in energy density. The local ergodic regions—so-called “bubbles”—resonantly spread throughout the system, leading to delocalization. In order to study such instability mechanism, in this work we design a model featuring many-body mobility edge in particle density: the states at small particle density are localized, while increasing the density of particles leads to delocalization. Using numerical simulations with matrix product states, we demonstrate the stability of many-body localization with respect to small bubbles in large dilute systems for experimentally relevant timescales. In addition, we demonstrate that processes where the bubble spreads are favored over processes that lead to resonant tunneling, suggesting a possible mechanism behind the observed stability of many-body mobility edge. We conclude by proposing experiments to probe particle density mobility edge in the Bose-Hubbard model.' acknowledgement: 'Acknowledgments. We acknowledge useful discussions with W. De Roeck and A. Michailidis. P.B. was supported by the European Union''s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385. D.A. was supported by the Swiss National Science Foundation. M.S. was supported by European Research Council (ERC) under the European Union''s Horizon 2020 research and innovation program (Grant Agreement No. 850899). This work benefited from visits to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958 and from the program “Thermalization, Many Body Localization and Hydrodynamics” at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).' article_number: 060202(R) article_processing_charge: No article_type: original author: - first_name: Pietro full_name: Brighi, Pietro id: 4115AF5C-F248-11E8-B48F-1D18A9856A87 last_name: Brighi orcid: 0000-0002-7969-2729 - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting systems. Physical Review B. 2020;102(6). doi:10.1103/physrevb.102.060202 apa: Brighi, P., Abanin, D. A., & Serbyn, M. (2020). Stability of mobility edges in disordered interacting systems. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.060202 chicago: Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility Edges in Disordered Interacting Systems.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.060202. ieee: P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered interacting systems,” Physical Review B, vol. 102, no. 6. American Physical Society, 2020. ista: Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R). mla: Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting Systems.” Physical Review B, vol. 102, no. 6, 060202(R), American Physical Society, 2020, doi:10.1103/physrevb.102.060202. short: P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020). date_created: 2020-08-26T19:27:42Z date_published: 2020-08-26T00:00:00Z date_updated: 2023-08-24T14:20:21Z day: '26' ddc: - '530' department: - _id: MaSe doi: 10.1103/physrevb.102.060202 ec_funded: 1 external_id: isi: - '000562628300001' file: - access_level: open_access checksum: 716442fa7861323fcc80b93718ca009c content_type: application/pdf creator: mserbyn date_created: 2020-08-26T19:28:55Z date_updated: 2020-08-26T19:28:55Z file_id: '8309' file_name: PhysRevB.102.060202.pdf file_size: 488825 relation: main_file success: 1 - access_level: open_access checksum: be0abdc8f60fe065ea6dc92e08487122 content_type: application/pdf creator: mserbyn date_created: 2020-08-26T19:29:00Z date_updated: 2020-08-26T19:29:00Z file_id: '8310' file_name: Supplementary-mbme.pdf file_size: 711405 relation: main_file success: 1 file_date_updated: 2020-08-26T19:29:00Z has_accepted_license: '1' intvolume: ' 102' isi: 1 issue: '6' language: - iso: eng month: '08' oa: 1 oa_version: None project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '12732' relation: dissertation_contains status: public scopus_import: '1' status: public title: Stability of mobility edges in disordered interacting systems type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 102 year: '2020' ... --- _id: '8318' abstract: - lang: eng text: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I. acknowledgement: This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster. article_number: '4135' article_processing_charge: No article_type: original author: - first_name: Javier full_name: Gutierrez-Fernandez, Javier id: 3D9511BA-F248-11E8-B48F-1D18A9856A87 last_name: Gutierrez-Fernandez - first_name: Karol full_name: Kaszuba, Karol id: 3FDF9472-F248-11E8-B48F-1D18A9856A87 last_name: Kaszuba - first_name: Gurdeep S. full_name: Minhas, Gurdeep S. last_name: Minhas - first_name: Rozbeh full_name: Baradaran, Rozbeh last_name: Baradaran - first_name: Margherita full_name: Tambalo, Margherita id: 4187dfe4-ec23-11ea-ae46-f08ab378313a last_name: Tambalo - first_name: David T. full_name: Gallagher, David T. last_name: Gallagher - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0 apa: Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0 chicago: Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0. ieee: J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020. ista: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135. mla: Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0. short: J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020). date_created: 2020-08-30T22:01:10Z date_published: 2020-08-18T00:00:00Z date_updated: 2023-08-22T09:03:00Z day: '18' ddc: - '570' department: - _id: LeSa doi: 10.1038/s41467-020-17957-0 external_id: isi: - '000607072900001' pmid: - '32811817' file: - access_level: open_access checksum: 52b96f41d7d0db9728064c08da00d030 content_type: application/pdf creator: cziletti date_created: 2020-08-31T13:40:00Z date_updated: 2020-08-31T13:40:00Z file_id: '8326' file_name: 2020_NatComm_Gutierrez-Fernandez.pdf file_size: 7527373 relation: main_file success: 1 file_date_updated: 2020-08-31T13:40:00Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/ scopus_import: '1' status: public title: Key role of quinone in the mechanism of respiratory complex I tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8319' abstract: - lang: eng text: We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated. acknowledgement: We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech. article_number: '012224' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yunfan full_name: Wu, Yunfan last_name: Wu - first_name: Rajiv full_name: Krishnakumar, Rajiv last_name: Krishnakumar - first_name: Julián full_name: Martínez-Rincón, Julián last_name: Martínez-Rincón - first_name: Benjamin K. full_name: Malia, Benjamin K. last_name: Malia - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Mark A. full_name: Kasevich, Mark A. last_name: Kasevich citation: ama: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224 apa: Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224 chicago: Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224. ieee: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020. ista: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224. mla: Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224. short: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020). date_created: 2020-08-30T22:01:10Z date_published: 2020-07-30T00:00:00Z date_updated: 2024-02-28T13:11:28Z day: '30' department: - _id: OnHo doi: 10.1103/PhysRevA.102.012224 external_id: arxiv: - '1912.08334' isi: - '000555104200011' intvolume: ' 102' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.08334 month: '07' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - '24699934' issn: - '24699926' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Retrieval of cavity-generated atomic spin squeezing after free-space release type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 102 year: '2020' ... --- _id: '8320' abstract: - lang: eng text: The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. acknowledgement: We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay. article_processing_charge: No article_type: original author: - first_name: S. A. full_name: Mukba, S. A. last_name: Mukba - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: P. M. full_name: Kolosov, P. M. last_name: Kolosov - first_name: E. Y. full_name: Shuvalova, E. Y. last_name: Shuvalova - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111' apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111' chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.' ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.' ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.' mla: 'Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.' short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484. date_created: 2020-08-30T22:01:11Z date_published: 2020-08-19T00:00:00Z date_updated: 2023-08-22T09:01:03Z day: '19' department: - _id: FyKo doi: 10.1134/S0026893320040111 external_id: isi: - '000562110300001' intvolume: ' 54' isi: 1 issue: '4' language: - iso: eng month: '08' oa_version: None page: 475-484 publication: Molecular Biology publication_identifier: eissn: - '16083245' issn: - '00268933' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8321' relation: original status: public scopus_import: '1' status: public title: 'Expanding the genetic code: Unnatural base pairs in biological systems' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 54 year: '2020' ... --- _id: '8321' abstract: - lang: eng text: The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. article_processing_charge: No article_type: original author: - first_name: S. A. full_name: Mukba, S. A. last_name: Mukba - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: P. M. full_name: Kolosov, P. M. last_name: Kolosov - first_name: E. Y. full_name: Shuvalova, E. Y. last_name: Shuvalova - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126' apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126' chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.' ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.' ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.' mla: 'Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.' short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541. date_created: 2020-08-30T22:01:11Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T09:01:02Z day: '01' department: - _id: FyKo doi: 10.31857/S0026898420040126 external_id: pmid: - '32799218' intvolume: ' 54' issue: '4' language: - iso: rus month: '07' oa_version: None page: 531-541 pmid: 1 publication: Molekuliarnaia biologiia publication_identifier: issn: - '00268984' publication_status: published publisher: Russian Academy of Sciences quality_controlled: '1' related_material: record: - id: '8320' relation: translation status: public scopus_import: '1' status: public title: 'Expanding the genetic code: Unnatural base pairs in biological systems' type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 54 year: '2020' ... --- _id: '8322' abstract: - lang: eng text: "Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question.\r\nIn this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to \U0001D45B−1 parties, while the remaining parties are corrupt in a functionality-preserving way.\r\nOur core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001)." acknowledgement: We would like to thank the anonymous reviewers for their helpful comments and suggestions. The work was initiated while the first author was in IIT Madras, India. Part of this work was done while the author was visiting the University of Warsaw. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT) and from the Foundation for Polish Science under grant TEAM/2016-1/4 founded within the UE 2014–2020 Smart Growth Operational Program. The last author was supported by the Independent Research Fund Denmark project BETHE and the Concordium Blockchain Research Center, Aarhus University, Denmark. alternative_title: - LNCS article_processing_charge: No author: - first_name: Suvradip full_name: Chakraborty, Suvradip id: B9CD0494-D033-11E9-B219-A439E6697425 last_name: Chakraborty - first_name: Stefan full_name: Dziembowski, Stefan last_name: Dziembowski - first_name: Jesper Buus full_name: Nielsen, Jesper Buus last_name: Nielsen citation: ama: 'Chakraborty S, Dziembowski S, Nielsen JB. Reverse firewalls for actively secure MPCs. In: Advances in Cryptology – CRYPTO 2020. Vol 12171. Springer Nature; 2020:732-762. doi:10.1007/978-3-030-56880-1_26' apa: 'Chakraborty, S., Dziembowski, S., & Nielsen, J. B. (2020). Reverse firewalls for actively secure MPCs. In Advances in Cryptology – CRYPTO 2020 (Vol. 12171, pp. 732–762). Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-56880-1_26' chicago: Chakraborty, Suvradip, Stefan Dziembowski, and Jesper Buus Nielsen. “Reverse Firewalls for Actively Secure MPCs.” In Advances in Cryptology – CRYPTO 2020, 12171:732–62. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-56880-1_26. ieee: S. Chakraborty, S. Dziembowski, and J. B. Nielsen, “Reverse firewalls for actively secure MPCs,” in Advances in Cryptology – CRYPTO 2020, Santa Barbara, CA, United States, 2020, vol. 12171, pp. 732–762. ista: 'Chakraborty S, Dziembowski S, Nielsen JB. 2020. Reverse firewalls for actively secure MPCs. Advances in Cryptology – CRYPTO 2020. CRYPTO: Annual International Cryptology Conference, LNCS, vol. 12171, 732–762.' mla: Chakraborty, Suvradip, et al. “Reverse Firewalls for Actively Secure MPCs.” Advances in Cryptology – CRYPTO 2020, vol. 12171, Springer Nature, 2020, pp. 732–62, doi:10.1007/978-3-030-56880-1_26. short: S. Chakraborty, S. Dziembowski, J.B. Nielsen, in:, Advances in Cryptology – CRYPTO 2020, Springer Nature, 2020, pp. 732–762. conference: end_date: 2020-08-21 location: Santa Barbara, CA, United States name: 'CRYPTO: Annual International Cryptology Conference' start_date: 2020-08-17 date_created: 2020-08-30T22:01:12Z date_published: 2020-08-10T00:00:00Z date_updated: 2021-01-12T08:18:08Z day: '10' department: - _id: KrPi doi: 10.1007/978-3-030-56880-1_26 ec_funded: 1 intvolume: ' 12171' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/1317 month: '08' oa: 1 oa_version: Preprint page: 732-762 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Advances in Cryptology – CRYPTO 2020 publication_identifier: eissn: - '16113349' isbn: - '9783030568795' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Reverse firewalls for actively secure MPCs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12171 year: '2020' ...