[{"publication":"Scientific Reports","status":"public","acknowledgement":"We wish to thank CSC – IT Centre for Science (Espoo, Finland) for computational resources. For financial support, we wish to thank the Academy of Finland (TR, IV and PAP; Center of Excellence in Biomembrane Research (IV, TR)), the Finnish Doctoral Programme in Computational Sciences (KK), the Sigrid Juselius Foundation (IV), the Paulo Foundation (PAP), and the European Research Council (IV, TR; Advanced Grant project CROWDED-PRO-LIPIDS). AO acknowledges The Wellcome Trust International Senior Research Fellowship.","date_published":"2016-09-26T00:00:00Z","year":"2016","publist_id":"6040","ddc":["576"],"quality_controlled":"1","doi":"10.1038/srep33607","publisher":"Nature Publishing Group","date_updated":"2021-01-12T06:49:34Z","_id":"1276","type":"journal_article","oa":1,"pubrep_id":"691","language":[{"iso":"eng"}],"citation":{"apa":"Postila, P., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A., &#38; Róg, T. (2016). Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep33607\">https://doi.org/10.1038/srep33607</a>","mla":"Postila, Pekka, et al. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” <i>Scientific Reports</i>, vol. 6, 33607, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep33607\">10.1038/srep33607</a>.","chicago":"Postila, Pekka, Karol Kaszuba, Patryk Kuleta, Ilpo Vattulainen, Marcin Sarewicz, Artur Osyczka, and Tomasz Róg. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep33607\">https://doi.org/10.1038/srep33607</a>.","ista":"Postila P, Kaszuba K, Kuleta P, Vattulainen I, Sarewicz M, Osyczka A, Róg T. 2016. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 6, 33607.","ieee":"P. Postila <i>et al.</i>, “Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"P. Postila, K. Kaszuba, P. Kuleta, I. Vattulainen, M. Sarewicz, A. Osyczka, T. Róg, Scientific Reports 6 (2016).","ama":"Postila P, Kaszuba K, Kuleta P, et al. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep33607\">10.1038/srep33607</a>"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"09","department":[{"_id":"LeSa"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":1960563,"date_created":"2018-12-12T10:17:09Z","file_id":"5261","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-691-v1+1_srep33607.pdf","checksum":"07c591c1250ebef266333cbc3228b4dd","relation":"main_file"}],"article_number":"33607","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         6","abstract":[{"lang":"eng","text":"The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site."}],"publication_status":"published","file_date_updated":"2020-07-14T12:44:42Z","author":[{"first_name":"Pekka","last_name":"Postila","full_name":"Postila, Pekka"},{"id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","full_name":"Kaszuba, Karol","last_name":"Kaszuba","first_name":"Karol"},{"first_name":"Patryk","last_name":"Kuleta","full_name":"Kuleta, Patryk"},{"last_name":"Vattulainen","full_name":"Vattulainen, Ilpo","first_name":"Ilpo"},{"first_name":"Marcin","last_name":"Sarewicz","full_name":"Sarewicz, Marcin"},{"full_name":"Osyczka, Artur","last_name":"Osyczka","first_name":"Artur"},{"first_name":"Tomasz","last_name":"Róg","full_name":"Róg, Tomasz"}],"scopus_import":1,"day":"26","oa_version":"Published Version","title":"Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex","volume":6,"date_created":"2018-12-11T11:51:05Z"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. <i>PNAS</i>. 2016;113(39):11028-11033. doi:<a href=\"https://doi.org/10.1073/pnas.1605588113\">10.1073/pnas.1605588113</a>","ieee":"F. Ortiz Morea <i>et al.</i>, “Danger-associated peptide signaling in Arabidopsis requires clathrin,” <i>PNAS</i>, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016.","short":"F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.","ista":"Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033.","chicago":"Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1605588113\">https://doi.org/10.1073/pnas.1605588113</a>.","apa":"Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1605588113\">https://doi.org/10.1073/pnas.1605588113</a>","mla":"Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” <i>PNAS</i>, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:<a href=\"https://doi.org/10.1073/pnas.1605588113\">10.1073/pnas.1605588113</a>."},"issue":"39","month":"09","department":[{"_id":"JiFr"}],"intvolume":"       113","abstract":[{"lang":"eng","text":"The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n"}],"publication_status":"published","oa_version":"Preprint","title":"Danger-associated peptide signaling in Arabidopsis requires clathrin","scopus_import":1,"day":"27","author":[{"full_name":"Ortiz Morea, Fausto","last_name":"Ortiz Morea","first_name":"Fausto"},{"last_name":"Savatin","full_name":"Savatin, Daniel","first_name":"Daniel"},{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"full_name":"Kumar, Rahul","last_name":"Kumar","first_name":"Rahul"},{"full_name":"Luo, Yu","last_name":"Luo","first_name":"Yu"},{"orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jos","last_name":"Van Begin","full_name":"Van Begin, Jos"},{"first_name":"Keini","last_name":"Dressano","full_name":"Dressano, Keini"},{"first_name":"Guilherme","full_name":"De Oliveira, Guilherme","last_name":"De Oliveira"},{"first_name":"Xiuyang","full_name":"Zhao, Xiuyang","last_name":"Zhao"},{"full_name":"Lu, Qing","last_name":"Lu","first_name":"Qing"},{"full_name":"Madder, Annemieke","last_name":"Madder","first_name":"Annemieke"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"De Moura","full_name":"De Moura, Daniel","first_name":"Daniel"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"date_created":"2018-12-11T11:51:06Z","volume":113,"status":"public","publication":"PNAS","date_published":"2016-09-27T00:00:00Z","acknowledgement":"F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line.","year":"2016","publist_id":"6039","page":"11028 - 11033","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/"}],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1605588113","type":"journal_article","_id":"1277","date_updated":"2021-01-12T06:49:34Z"},{"publisher":"Public Library of Science","article_processing_charge":"No","doi":"10.1371/journal.pone.0164037","type":"journal_article","_id":"1278","date_updated":"2021-01-12T06:49:34Z","ddc":["570","571"],"quality_controlled":"1","year":"2016","publist_id":"6038","status":"public","publication":"PLoS One","acknowledgement":"This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112 to SN].","date_published":"2016-10-06T00:00:00Z","oa_version":"Published Version","title":"Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies","scopus_import":1,"day":"06","author":[{"last_name":"Matsuno","full_name":"Matsuno, Hitomi","first_name":"Hitomi"},{"last_name":"Kudoh","full_name":"Kudoh, Moeko","first_name":"Moeko"},{"last_name":"Watakabe","full_name":"Watakabe, Akiya","first_name":"Akiya"},{"last_name":"Yamamori","full_name":"Yamamori, Tetsuo","first_name":"Tetsuo"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Soichi","full_name":"Nagao, Soichi","last_name":"Nagao"}],"date_created":"2018-12-11T11:51:06Z","article_type":"original","volume":11,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        11","abstract":[{"text":"Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (&lt; 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:42Z","publication_status":"published","month":"10","article_number":"e0164037","file":[{"relation":"main_file","checksum":"7c0ba0ca6d79844059158059d2a38d25","file_name":"IST-2016-689-v1+1_journal.pone.0164037.PDF","access_level":"open_access","content_type":"application/pdf","file_id":"5269","date_created":"2018-12-12T10:17:16Z","file_size":3657084,"date_updated":"2020-07-14T12:44:42Z","creator":"system"}],"department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"pubrep_id":"689","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS One 11 (2016).","ieee":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao, “Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies,” <i>PLoS One</i>, vol. 11, no. 10. Public Library of Science, 2016.","ama":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. <i>PLoS One</i>. 2016;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pone.0164037\">10.1371/journal.pone.0164037</a>","mla":"Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” <i>PLoS One</i>, vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0164037\">10.1371/journal.pone.0164037</a>.","apa":"Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., &#38; Nagao, S. (2016). Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0164037\">https://doi.org/10.1371/journal.pone.0164037</a>","chicago":"Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0164037\">https://doi.org/10.1371/journal.pone.0164037</a>.","ista":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 11(10), e0164037."},"issue":"10"},{"publication":"PLoS One","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] via the IST FELLOWSHIP awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant (acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We thank Lauri Viljanto for technical help in building the ripple detector.","date_published":"2016-10-19T00:00:00Z","year":"2016","publist_id":"6037","ddc":["570","571"],"quality_controlled":"1","doi":"10.1371/journal.pone.0164675","publisher":"Public Library of Science","_id":"1279","date_updated":"2021-01-12T06:49:35Z","type":"journal_article","oa":1,"pubrep_id":"690","language":[{"iso":"eng"}],"citation":{"ama":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. <i>PLoS One</i>. 2016;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pone.0164675\">10.1371/journal.pone.0164675</a>","short":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero, J.L. Csicsvari, PLoS One 11 (2016).","ieee":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero, and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus,” <i>PLoS One</i>, vol. 11, no. 10. Public Library of Science, 2016.","chicago":"Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen, Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0164675\">https://doi.org/10.1371/journal.pone.0164675</a>.","ista":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 11(10), e0164675.","mla":"Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” <i>PLoS One</i>, vol. 11, no. 10, e0164675, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0164675\">10.1371/journal.pone.0164675</a>.","apa":"Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero, D. K., &#38; Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0164675\">https://doi.org/10.1371/journal.pone.0164675</a>"},"issue":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","department":[{"_id":"JoCs"}],"article_number":"e0164675","file":[{"relation":"main_file","checksum":"395895ecb2216e9c39135abaa56b28b3","file_name":"IST-2016-690-v1+1_journal.pone.0164675.PDF","content_type":"application/pdf","access_level":"open_access","file_id":"5009","file_size":4353592,"date_created":"2018-12-12T10:13:26Z","date_updated":"2020-07-14T12:44:42Z","creator":"system"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        11","file_date_updated":"2020-07-14T12:44:42Z","publication_status":"published","scopus_import":1,"day":"19","author":[{"first_name":"Krisztián","last_name":"Kovács","full_name":"Kovács, Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph"},{"first_name":"Philipp","last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp"},{"last_name":"Penttonen","full_name":"Penttonen, Markku","first_name":"Markku"},{"orcid":"0000-0002-8602-4374","first_name":"Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Rangel Guerrero, Dámaris K","last_name":"Rangel Guerrero"},{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","title":"Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus","volume":11,"date_created":"2018-12-11T11:51:06Z"},{"oa_version":"Preprint","title":"Fixed energy universality for generalized wigner matrices","scopus_import":1,"day":"01","author":[{"first_name":"Paul","full_name":"Bourgade, Paul","last_name":"Bourgade"},{"orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"},{"full_name":"Yau, Horngtzer","last_name":"Yau","first_name":"Horngtzer"},{"full_name":"Yin, Jun","last_name":"Yin","first_name":"Jun"}],"date_created":"2018-12-11T11:51:07Z","volume":69,"intvolume":"        69","abstract":[{"text":"We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics.","lang":"eng"}],"publication_status":"published","month":"10","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881.","chicago":"Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy Universality for Generalized Wigner Matrices.” <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/cpa.21624\">https://doi.org/10.1002/cpa.21624</a>.","apa":"Bourgade, P., Erdös, L., Yau, H., &#38; Yin, J. (2016). Fixed energy universality for generalized wigner matrices. <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cpa.21624\">https://doi.org/10.1002/cpa.21624</a>","mla":"Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.” <i>Communications on Pure and Applied Mathematics</i>, vol. 69, no. 10, Wiley-Blackwell, 2016, pp. 1815–81, doi:<a href=\"https://doi.org/10.1002/cpa.21624\">10.1002/cpa.21624</a>.","ama":"Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized wigner matrices. <i>Communications on Pure and Applied Mathematics</i>. 2016;69(10):1815-1881. doi:<a href=\"https://doi.org/10.1002/cpa.21624\">10.1002/cpa.21624</a>","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for generalized wigner matrices,” <i>Communications on Pure and Applied Mathematics</i>, vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied Mathematics 69 (2016) 1815–1881."},"issue":"10","publisher":"Wiley-Blackwell","doi":"10.1002/cpa.21624","type":"journal_article","_id":"1280","date_updated":"2021-01-12T06:49:35Z","page":"1815 - 1881","main_file_link":[{"url":"https://arxiv.org/abs/1407.5606","open_access":"1"}],"year":"2016","publist_id":"6036","publication":"Communications on Pure and Applied Mathematics","status":"public","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"acknowledgement":"The work of P.B. was partially supported by National Sci-\r\nence Foundation Grant DMS-1208859.  The work of L.E. was partially supported\r\nby ERC Advanced Grant RANMAT 338804.  The work of H.-T. Y. was partially\r\nsupported by National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award.  The work of J.Y. was partially supported by National Science\r\nFoundation Grant DMS-1207961.  The major part of this research was conducted\r\nwhen all authors were visiting IAS and were also supported by National Science\r\nFoundation Grant DMS-1128255.","date_published":"2016-10-01T00:00:00Z","ec_funded":1},{"year":"2016","publist_id":"6035","publication":"Plant Physiology","status":"public","date_published":"2016-10-01T00:00:00Z","acknowledgement":"This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility.","doi":"10.1104/pp.16.01047","publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T06:49:36Z","_id":"1281","type":"journal_article","page":"1237 - 1248","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/","open_access":"1"}],"quality_controlled":"1","month":"10","department":[{"_id":"EvBe"}],"oa":1,"language":[{"iso":"eng"}],"issue":"2","citation":{"chicago":"Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1104/pp.16.01047\">https://doi.org/10.1104/pp.16.01047</a>.","ista":"Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248.","apa":"Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.16.01047\">https://doi.org/10.1104/pp.16.01047</a>","mla":"Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” <i>Plant Physiology</i>, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:<a href=\"https://doi.org/10.1104/pp.16.01047\">10.1104/pp.16.01047</a>.","ama":"Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. <i>Plant Physiology</i>. 2016;172(2):1237-1248. doi:<a href=\"https://doi.org/10.1104/pp.16.01047\">10.1104/pp.16.01047</a>","ieee":"E. Bouguyon <i>et al.</i>, “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” <i>Plant Physiology</i>, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.","short":"E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Eléonore","full_name":"Bouguyon, Eléonore","last_name":"Bouguyon"},{"last_name":"Perrine Walker","full_name":"Perrine Walker, Francine","first_name":"Francine"},{"first_name":"Marjorie","full_name":"Pervent, Marjorie","last_name":"Pervent"},{"first_name":"Juliette","full_name":"Rochette, Juliette","last_name":"Rochette"},{"last_name":"Cuesta","full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","orcid":"0000-0003-1923-2410"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"last_name":"Martinière","full_name":"Martinière, Alexandre","first_name":"Alexandre"},{"last_name":"Bach","full_name":"Bach, Lien","first_name":"Lien"},{"first_name":"Gabriel","full_name":"Krouk, Gabriel","last_name":"Krouk"},{"first_name":"Alain","last_name":"Gojon","full_name":"Gojon, Alain"},{"first_name":"Philippe","full_name":"Nacry, Philippe","last_name":"Nacry"}],"day":"01","scopus_import":1,"title":"Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor","oa_version":"Preprint","volume":172,"date_created":"2018-12-11T11:51:07Z","abstract":[{"lang":"eng","text":"Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue."}],"intvolume":"       172","publication_status":"published"},{"_id":"1282","volume":216,"date_updated":"2021-01-12T06:49:36Z","date_created":"2018-12-11T11:51:07Z","type":"journal_article","scopus_import":1,"day":"01","doi":"10.1007/s11856-016-1419-1","author":[{"first_name":"Anna","last_name":"Gundert","full_name":"Gundert, Anna"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"title":"On eigenvalues of random complexes","oa_version":"Preprint","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.4906"}],"quality_controlled":"1","publication_status":"published","page":"545 - 582","intvolume":"       216","abstract":[{"lang":"eng","text":"We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k."}],"department":[{"_id":"UlWa"}],"publist_id":"6034","year":"2016","month":"10","citation":{"ieee":"A. Gundert and U. Wagner, “On eigenvalues of random complexes,” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2. Springer, pp. 545–582, 2016.","short":"A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.","ama":"Gundert A, Wagner U. On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. 2016;216(2):545-582. doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>","apa":"Gundert, A., &#38; Wagner, U. (2016). On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>","mla":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>.","ista":"Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582.","chicago":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>."},"issue":"2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-10-01T00:00:00Z","oa":1,"publication":"Israel Journal of Mathematics","status":"public","language":[{"iso":"eng"}]},{"month":"10","file":[{"checksum":"4d569977fad7a7f22b7e3424003d2ab1","relation":"main_file","content_type":"application/pdf","access_level":"local","file_name":"IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf","file_id":"4679","creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":229094,"date_created":"2018-12-12T10:08:19Z"}],"department":[{"_id":"EvBe"}],"language":[{"iso":"eng"}],"pubrep_id":"1018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","citation":{"ieee":"Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” <i>Trends in Plant Science</i>, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.","short":"Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811.","ama":"Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. 2016;21(10):809-811. doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>","apa":"Zhu, Q., &#38; Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>","mla":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>, vol. 21, no. 10, Cell Press, 2016, pp. 809–11, doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>.","ista":"Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 21(10), 809–811.","chicago":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>."},"oa_version":"Submitted Version","title":"Seedlings’ strategy to overcome a soil barrier","author":[{"first_name":"Qiang","full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"day":"01","scopus_import":1,"article_type":"original","date_created":"2018-12-11T11:51:08Z","volume":21,"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":"        21","abstract":[{"lang":"eng","text":"The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil."}],"has_accepted_license":"1","publication_status":"published","file_date_updated":"2020-07-14T12:44:42Z","year":"2016","publist_id":"6033","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development"}],"publication":"Trends in Plant Science","status":"public","acknowledgement":"This work was supported by the Austrian Science Fund (FWF01_I1774S) to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript.","date_published":"2016-10-01T00:00:00Z","publisher":"Cell Press","doi":"10.1016/j.tplants.2016.08.003","type":"journal_article","date_updated":"2021-01-12T06:49:36Z","_id":"1283","ddc":["575"],"page":"809 - 811","quality_controlled":"1"},{"ec_funded":1,"citation":{"apa":"Paluch, E., Aspalter, I., &#38; Sixt, M. K. (2016). Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>","mla":"Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32, Annual Reviews, 2016, pp. 469–90, doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>.","chicago":"Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>.","ista":"Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 32, 469–490.","ieee":"E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32. Annual Reviews, pp. 469–490, 2016.","short":"E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental Biology 32 (2016) 469–490.","ama":"Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. 2016;32:469-490. doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>"},"date_published":"2016-10-06T00:00:00Z","acknowledgement":"We would like to thank Dani Bodor for critical comments on the manuscript and Guillaume Salbreux for discussions. The authors are supported by the United Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian Science Foundation (M.S.).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","call_identifier":"FWF"}],"status":"public","publication":"Annual Review of Cell and Developmental Biology","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"publist_id":"6031","year":"2016","month":"10","publication_status":"published","quality_controlled":"1","page":"469 - 490","abstract":[{"text":"Cell migration is central to a multitude of physiological processes, including embryonic development, immune surveillance, and wound healing, and deregulated migration is key to cancer dissemination. Decades of investigations have uncovered many of the molecular and physical mechanisms underlying cell migration. Together with protrusion extension and cell body retraction, adhesion to the substrate via specific focal adhesion points has long been considered an essential step in cell migration. Although this is true for cells moving on two-dimensional substrates, recent studies have demonstrated that focal adhesions are not required for cells moving in three dimensions, in which confinement is sufficient to maintain a cell in contact with its substrate. Here, we review the investigations that have led to challenging the requirement of specific adhesions for migration, discuss the physical mechanisms proposed for cell body translocation during focal adhesion-independent migration, and highlight the remaining open questions for the future.","lang":"eng"}],"intvolume":"        32","date_updated":"2021-01-12T06:49:37Z","volume":32,"_id":"1285","type":"journal_article","date_created":"2018-12-11T11:51:08Z","author":[{"first_name":"Ewa","full_name":"Paluch, Ewa","last_name":"Paluch"},{"last_name":"Aspalter","full_name":"Aspalter, Irene","first_name":"Irene"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"doi":"10.1146/annurev-cellbio-111315-125341","day":"06","scopus_import":1,"publisher":"Annual Reviews","oa_version":"None","title":"Focal adhesion-independent cell migration"},{"publisher":"American Physical Society","doi":"10.1103/PhysRevA.94.041601","type":"journal_article","_id":"1286","date_updated":"2021-01-12T06:49:37Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.06092"}],"year":"2016","publist_id":"6030","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_published":"2016-10-13T00:00:00Z","acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.","ec_funded":1,"title":"Rotation of cold molecular ions inside a Bose-Einstein condensate","oa_version":"Preprint","day":"13","scopus_import":1,"author":[{"last_name":"Midya","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali","first_name":"Bikashkali"},{"last_name":"Tomza","full_name":"Tomza, Michał","first_name":"Michał"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"date_created":"2018-12-11T11:51:09Z","volume":94,"abstract":[{"text":"We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.","lang":"eng"}],"intvolume":"        94","publication_status":"published","month":"10","article_number":"041601","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Midya, B., Tomza, M., Schmidt, R., &#38; Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>","mla":"Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>.","ista":"Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 94(4), 041601.","chicago":"Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>.","ieee":"B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4. American Physical Society, 2016.","short":"B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 94 (2016).","ama":"Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;94(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>"},"issue":"4"},{"type":"journal_article","_id":"1287","date_updated":"2023-10-17T12:16:24Z","publisher":"Optica Publishing Group","article_processing_charge":"No","doi":"10.1364/OL.41.004621","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.02863"}],"page":"4621 - 4624","publist_id":"6029","year":"2016","acknowledgement":"The research of B.M. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant No. [291734].","date_published":"2016-10-15T00:00:00Z","ec_funded":1,"publication":"Optics Letters","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"date_created":"2018-12-11T11:51:09Z","volume":41,"oa_version":"Preprint","title":"Modes and exceptional points in waveguides with impedance boundary conditions","scopus_import":"1","day":"15","author":[{"id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali","last_name":"Midya","first_name":"Bikashkali"},{"last_name":"Konotop","full_name":"Konotop, Vladimir","first_name":"Vladimir"}],"publication_status":"published","abstract":[{"lang":"eng","text":"A planar waveguide with an impedance boundary, composed of nonperfect metallic plates, and with passive or active dielectric filling, is considered. We show the possibility of selective mode guiding and amplification when a homogeneous pump is added to the dielectric and analyze differences in TE and TM mode propagation. Such a non-conservative system is also shown to feature exceptional points for specific and experimentally tunable parameters, which are described for a particular case of transparent dielectric."}],"intvolume":"        41","department":[{"_id":"MiLe"}],"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” <i>Optics Letters</i>. Optica Publishing Group, 2016. <a href=\"https://doi.org/10.1364/OL.41.004621\">https://doi.org/10.1364/OL.41.004621</a>.","ista":"Midya B, Konotop V. 2016. Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. 41(20), 4621–4624.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” <i>Optics Letters</i>, vol. 41, no. 20, Optica Publishing Group, 2016, pp. 4621–24, doi:<a href=\"https://doi.org/10.1364/OL.41.004621\">10.1364/OL.41.004621</a>.","apa":"Midya, B., &#38; Konotop, V. (2016). Modes and exceptional points in waveguides with impedance boundary conditions. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.41.004621\">https://doi.org/10.1364/OL.41.004621</a>","ama":"Midya B, Konotop V. Modes and exceptional points in waveguides with impedance boundary conditions. <i>Optics Letters</i>. 2016;41(20):4621-4624. doi:<a href=\"https://doi.org/10.1364/OL.41.004621\">10.1364/OL.41.004621</a>","short":"B. Midya, V. Konotop, Optics Letters 41 (2016) 4621–4624.","ieee":"B. Midya and V. Konotop, “Modes and exceptional points in waveguides with impedance boundary conditions,” <i>Optics Letters</i>, vol. 41, no. 20. Optica Publishing Group, pp. 4621–4624, 2016."},"issue":"20","language":[{"iso":"eng"}],"oa":1},{"publist_id":"6028","department":[{"_id":"LeSa"}],"month":"11","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was funded by the UK Medical Research Council.","date_published":"2016-11-01T00:00:00Z","citation":{"short":"P. Holt, R. Efremov, E. Nakamaru Ogiso, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 1777–1785.","ieee":"P. Holt, R. Efremov, E. Nakamaru Ogiso, and L. A. Sazanov, “Reversible FMN dissociation from Escherichia coli respiratory complex I,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 11. Elsevier, pp. 1777–1785, 2016.","ama":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. Reversible FMN dissociation from Escherichia coli respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2016;1857(11):1777-1785. doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">10.1016/j.bbabio.2016.08.008</a>","mla":"Holt, Peter, et al. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 11, Elsevier, 2016, pp. 1777–85, doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">10.1016/j.bbabio.2016.08.008</a>.","apa":"Holt, P., Efremov, R., Nakamaru Ogiso, E., &#38; Sazanov, L. A. (2016). Reversible FMN dissociation from Escherichia coli respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">https://doi.org/10.1016/j.bbabio.2016.08.008</a>","ista":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. 2016. Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(11), 1777–1785.","chicago":"Holt, Peter, Rouslan Efremov, Eiko Nakamaru Ogiso, and Leonid A Sazanov. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">https://doi.org/10.1016/j.bbabio.2016.08.008</a>."},"issue":"11","language":[{"iso":"eng"}],"publication":"Biochimica et Biophysica Acta - Bioenergetics","status":"public","date_created":"2018-12-11T11:51:09Z","type":"journal_article","_id":"1288","volume":1857,"date_updated":"2021-01-12T06:49:38Z","publisher":"Elsevier","title":"Reversible FMN dissociation from Escherichia coli respiratory complex I","oa_version":"None","scopus_import":1,"day":"01","author":[{"last_name":"Holt","full_name":"Holt, Peter","first_name":"Peter"},{"first_name":"Rouslan","full_name":"Efremov, Rouslan","last_name":"Efremov"},{"first_name":"Eiko","last_name":"Nakamaru Ogiso","full_name":"Nakamaru Ogiso, Eiko"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"doi":"10.1016/j.bbabio.2016.08.008","publication_status":"published","quality_controlled":"1","intvolume":"      1857","abstract":[{"lang":"eng","text":"Respiratory complex I transfers electrons from NADH to quinone, utilizing the reaction energy to translocate protons across the membrane. It is a key enzyme of the respiratory chain of many prokaryotic and most eukaryotic organisms. The reversible NADH oxidation reaction is facilitated in complex I by non-covalently bound flavin mononucleotide (FMN). Here we report that the catalytic activity of E. coli complex I with artificial electron acceptors potassium ferricyanide (FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar range in oxidized complex I to the nanomolar range in the NADH reduced enzyme, with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex I, rather than that of FMN, proved critical to the dissociation. Such dissociation is not observed with the T. thermophilus enzyme and our analysis suggests that the difference may be due to the unusually high redox potential of Fe-S cluster N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo by releasing FMN under highly reducing conditions."}],"page":"1777 - 1785"},{"date_published":"2016-11-01T00:00:00Z","publication":"Pattern Recognition Letters","status":"public","publist_id":"6027","year":"2016","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1568"}]},"quality_controlled":"1","page":"13 - 22","ddc":["004","514"],"_id":"1289","date_updated":"2023-02-23T10:04:40Z","type":"journal_article","article_processing_charge":"No","doi":"10.1016/j.patrec.2015.12.012","publisher":"Elsevier","citation":{"ieee":"O. Dunaeva <i>et al.</i>, “The classification of endoscopy images with persistent homology,” <i>Pattern Recognition Letters</i>, vol. 83, no. 1. Elsevier, pp. 13–22, 2016.","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev, S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy images with persistent homology. <i>Pattern Recognition Letters</i>. 2016;83(1):13-22. doi:<a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">10.1016/j.patrec.2015.12.012</a>","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev, R., &#38; Kashin, S. (2016). The classification of endoscopy images with persistent homology. <i>Pattern Recognition Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">https://doi.org/10.1016/j.patrec.2015.12.012</a>","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” <i>Pattern Recognition Letters</i>, vol. 83, no. 1, Elsevier, 2016, pp. 13–22, doi:<a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">10.1016/j.patrec.2015.12.012</a>.","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images with Persistent Homology.” <i>Pattern Recognition Letters</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">https://doi.org/10.1016/j.patrec.2015.12.012</a>.","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin S. 2016. The classification of endoscopy images with persistent homology. Pattern Recognition Letters. 83(1), 13–22."},"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"pubrep_id":"975","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:44:42Z","date_created":"2019-04-17T07:55:51Z","file_size":1921113,"file_id":"6334","content_type":"application/pdf","access_level":"open_access","file_name":"2016-Edelsbrunner_The_classification.pdf","checksum":"33458bbb8c32a339e1adeca6d5a1112d","relation":"main_file"}],"month":"11","file_date_updated":"2020-07-14T12:44:42Z","publication_status":"published","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":"        83","abstract":[{"text":"Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI) magnifying endoscopic (ME) images of the stomach, we combine methods from image processing, topology, geometry, and machine learning to classify patterns into three classes: oval, tubular and irregular. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.","lang":"eng"}],"volume":83,"date_created":"2018-12-11T11:51:10Z","day":"01","scopus_import":1,"author":[{"full_name":"Dunaeva, Olga","last_name":"Dunaeva","first_name":"Olga"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Anton","last_name":"Lukyanov","full_name":"Lukyanov, Anton"},{"first_name":"Michael","full_name":"Machin, Michael","last_name":"Machin"},{"first_name":"Daria","last_name":"Malkova","full_name":"Malkova, Daria"},{"first_name":"Roman","last_name":"Kuvaev","full_name":"Kuvaev, Roman"},{"first_name":"Sergey","full_name":"Kashin, Sergey","last_name":"Kashin"}],"oa_version":"Submitted Version","title":"The classification of endoscopy images with persistent homology"},{"publication_status":"published","intvolume":"        12","abstract":[{"text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.","lang":"eng"}],"date_created":"2018-12-11T11:51:10Z","volume":12,"oa_version":"Preprint","title":"Compounds that select against the tetracycline-resistance efflux pump","scopus_import":1,"day":"01","author":[{"full_name":"Stone, Laura","last_name":"Stone","first_name":"Laura"},{"full_name":"Baym, Michael","last_name":"Baym","first_name":"Michael"},{"first_name":"Tami","full_name":"Lieberman, Tami","last_name":"Lieberman"},{"first_name":"Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","last_name":"Chait"},{"last_name":"Clardy","full_name":"Clardy, Jon","first_name":"Jon"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” <i>Nature Chemical Biology</i>, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. 2016;12(11):902-904. doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>.","apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., &#38; Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>.","ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904."},"issue":"11","language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"month":"11","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"page":"902 - 904","type":"journal_article","_id":"1290","date_updated":"2021-01-12T06:49:39Z","publisher":"Nature Publishing Group","doi":"10.1038/nchembio.2176","date_published":"2016-11-01T00:00:00Z","acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","publication":"Nature Chemical Biology","status":"public","publist_id":"6026","year":"2016"},{"year":"2016","month":"02","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file":[{"file_id":"12968","creator":"dernst","date_updated":"2023-05-16T07:03:56Z","file_size":1073523,"date_created":"2023-05-16T07:03:56Z","checksum":"4a7b00362e81358d568f5e216fa03c3e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2016_AHPC_Schloegl.pdf"}],"oa":1,"language":[{"iso":"eng"}],"status":"public","publication":"AHPC16 - Austrian HPC Meeting 2016","citation":{"mla":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” <i>AHPC16 - Austrian HPC Meeting 2016</i>, VSC - Vienna Scientific Cluster, 2016, p. 37.","apa":"Schlögl, A., &#38; Stadlbauer, S. (2016). High performance computing at IST Austria: Modelling the human hippocampus. In <i>AHPC16 - Austrian HPC Meeting 2016</i> (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster.","chicago":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” In <i>AHPC16 - Austrian HPC Meeting 2016</i>, 37. VSC - Vienna Scientific Cluster, 2016.","ista":"Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria: Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian HPC Meeting, 37.","short":"A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC - Vienna Scientific Cluster, 2016, p. 37.","ieee":"A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria: Modelling the human hippocampus,” in <i>AHPC16 - Austrian HPC Meeting 2016</i>, Grundlsee, Austria, 2016, p. 37.","ama":"Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling the human hippocampus. In: <i>AHPC16 - Austrian HPC Meeting 2016</i>. VSC - Vienna Scientific Cluster; 2016:37."},"conference":{"location":"Grundlsee, Austria","start_date":"2016-02-22","end_date":"2016-02-24","name":"AHPC: Austrian HPC Meeting"},"date_published":"2016-02-24T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","first_name":"Stephan"}],"day":"24","article_processing_charge":"No","title":"High performance computing at IST Austria: Modelling the human hippocampus","publisher":"VSC - Vienna Scientific Cluster","oa_version":"Published Version","date_updated":"2023-05-16T07:15:14Z","_id":"12903","type":"conference_abstract","date_created":"2023-05-05T12:54:47Z","page":"37","has_accepted_license":"1","ddc":["000"],"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2023-05-16T07:03:56Z"},{"publication":"Communications in Mathematical Physics","status":"public","project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"date_published":"2016-11-01T00:00:00Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The\r\nresearch leading to these results has received funding from the European Research Council under the European\r\nUnion’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN National Grant Geometric and analytic theory of Hamiltonian systems in finite and infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27. Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems, random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully acknowledged.","year":"2016","publist_id":"6025","ddc":["510","530"],"page":"983 - 1007","quality_controlled":"1","publisher":"Springer","doi":"10.1007/s00220-016-2665-0","type":"journal_article","_id":"1291","date_updated":"2021-01-12T06:49:40Z","language":[{"iso":"eng"}],"pubrep_id":"688","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models with competing interactions,” <i>Communications in Mathematical Physics</i>, vol. 347, no. 3. Springer, pp. 983–1007, 2016.","short":"A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016) 983–1007.","ama":"Giuliani A, Seiringer R. Periodic striped ground states in Ising models with competing interactions. <i>Communications in Mathematical Physics</i>. 2016;347(3):983-1007. doi:<a href=\"https://doi.org/10.1007/s00220-016-2665-0\">10.1007/s00220-016-2665-0</a>","apa":"Giuliani, A., &#38; Seiringer, R. (2016). Periodic striped ground states in Ising models with competing interactions. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-016-2665-0\">https://doi.org/10.1007/s00220-016-2665-0</a>","mla":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” <i>Communications in Mathematical Physics</i>, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:<a href=\"https://doi.org/10.1007/s00220-016-2665-0\">10.1007/s00220-016-2665-0</a>.","chicago":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” <i>Communications in Mathematical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00220-016-2665-0\">https://doi.org/10.1007/s00220-016-2665-0</a>.","ista":"Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007."},"issue":"3","month":"11","file":[{"file_name":"IST-2016-688-v1+1_s00220-016-2665-0.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3c6e08c048fc462e312788be72874bb1","file_size":794983,"date_created":"2018-12-12T10:09:02Z","date_updated":"2020-07-14T12:44:42Z","creator":"system","file_id":"4725"}],"department":[{"_id":"RoSe"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       347","abstract":[{"lang":"eng","text":"We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p &gt; 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity."}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:42Z","publication_status":"published","title":"Periodic striped ground states in Ising models with competing interactions","oa_version":"Published Version","day":"01","scopus_import":1,"author":[{"first_name":"Alessandro","full_name":"Giuliani, Alessandro","last_name":"Giuliani"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"date_created":"2018-12-11T11:51:11Z","volume":347},{"oa_version":"Preprint","title":"Computing the Thurston–Bennequin invariant in open books","author":[{"first_name":"Sebastian","last_name":"Durst","full_name":"Durst, Sebastian"},{"full_name":"Kegel, Marc","last_name":"Kegel","first_name":"Marc"},{"last_name":"Klukas","id":"34927512-F248-11E8-B48F-1D18A9856A87","full_name":"Klukas, Mirko D","first_name":"Mirko D"}],"day":"01","scopus_import":1,"date_created":"2018-12-11T11:51:11Z","volume":150,"abstract":[{"lang":"eng","text":"We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds."}],"intvolume":"       150","publication_status":"published","month":"12","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"2","citation":{"mla":"Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open Books.” <i>Acta Mathematica Hungarica</i>, vol. 150, no. 2, Springer, 2016, pp. 441–55, doi:<a href=\"https://doi.org/10.1007/s10474-016-0648-4\">10.1007/s10474-016-0648-4</a>.","apa":"Durst, S., Kegel, M., &#38; Klukas, M. D. (2016). Computing the Thurston–Bennequin invariant in open books. <i>Acta Mathematica Hungarica</i>. Springer. <a href=\"https://doi.org/10.1007/s10474-016-0648-4\">https://doi.org/10.1007/s10474-016-0648-4</a>","ista":"Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 150(2), 441–455.","chicago":"Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin Invariant in Open Books.” <i>Acta Mathematica Hungarica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s10474-016-0648-4\">https://doi.org/10.1007/s10474-016-0648-4</a>.","short":"S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455.","ieee":"S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant in open books,” <i>Acta Mathematica Hungarica</i>, vol. 150, no. 2. Springer, pp. 441–455, 2016.","ama":"Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in open books. <i>Acta Mathematica Hungarica</i>. 2016;150(2):441-455. doi:<a href=\"https://doi.org/10.1007/s10474-016-0648-4\">10.1007/s10474-016-0648-4</a>"},"publisher":"Springer","doi":"10.1007/s10474-016-0648-4","type":"journal_article","date_updated":"2021-01-12T06:49:40Z","_id":"1292","page":"441 - 455","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.00794"}],"year":"2016","publist_id":"6023","publication":"Acta Mathematica Hungarica","status":"public","acknowledgement":"The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful discussions and advice and Christian Evers for helpful remarks on a draft version.","date_published":"2016-12-01T00:00:00Z"},{"publist_id":"6024","year":"2016","acknowledgement":"We wish to thank Alexander Engström and Bernd Sturmfels for various valuable discussions and insights. We also thank the two anonymous referees for their thoughtful feedback on the paper. CU was partially supported by the Austrian Science Fund (FWF) Y 903-N35.","date_published":"2016-11-15T00:00:00Z","status":"public","publication":"Linear Algebra and Its Applications","project":[{"_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 903-N35","name":"Gaussian Graphical Models: Theory and Applications"}],"type":"journal_article","_id":"1293","date_updated":"2021-01-12T06:49:40Z","publisher":"Elsevier","doi":"10.1016/j.laa.2016.07.026","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/pdf/1506.06702.pdf","open_access":"1"}],"page":"247 - 275","department":[{"_id":"CaUh"}],"month":"11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. <i>Linear Algebra and Its Applications</i>. 2016;509:247-275. doi:<a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">10.1016/j.laa.2016.07.026</a>","short":"L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509 (2016) 247–275.","ieee":"L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors,” <i>Linear Algebra and Its Applications</i>, vol. 509. Elsevier, pp. 247–275, 2016.","chicago":"Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">https://doi.org/10.1016/j.laa.2016.07.026</a>.","ista":"Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 509, 247–275.","mla":"Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” <i>Linear Algebra and Its Applications</i>, vol. 509, Elsevier, 2016, pp. 247–75, doi:<a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">10.1016/j.laa.2016.07.026</a>.","apa":"Solus, L. T., Uhler, C., &#38; Yoshida, R. (2016). Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">https://doi.org/10.1016/j.laa.2016.07.026</a>"},"language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:51:11Z","volume":509,"title":"Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors","oa_version":"Preprint","day":"15","scopus_import":1,"author":[{"first_name":"Liam T","last_name":"Solus","id":"2AADA620-F248-11E8-B48F-1D18A9856A87","full_name":"Solus, Liam T"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","first_name":"Caroline"},{"full_name":"Yoshida, Ruriko","last_name":"Yoshida","first_name":"Ruriko"}],"publication_status":"published","abstract":[{"text":"For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.","lang":"eng"}],"intvolume":"       509"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-10-01T00:00:00Z","acknowledgement":"This work is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.","ec_funded":1,"citation":{"short":"H. Edelsbrunner, M. Iglesias Ham, Electronic Notes in Discrete Mathematics 54 (2016) 169–174.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls II: Weighted averages,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 54. Elsevier, pp. 169–174, 2016.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls II: Weighted averages. <i>Electronic Notes in Discrete Mathematics</i>. 2016;54:169-174. doi:<a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">10.1016/j.endm.2016.09.030</a>","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 54, Elsevier, 2016, pp. 169–74, doi:<a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">10.1016/j.endm.2016.09.030</a>.","apa":"Edelsbrunner, H., &#38; Iglesias Ham, M. (2016). Multiple covers with balls II: Weighted averages. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">https://doi.org/10.1016/j.endm.2016.09.030</a>","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">https://doi.org/10.1016/j.endm.2016.09.030</a>.","ista":"Edelsbrunner H, Iglesias Ham M. 2016. Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. 54, 169–174."},"language":[{"iso":"eng"}],"status":"public","publication":"Electronic Notes in Discrete Mathematics","project":[{"call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"publist_id":"5976","department":[{"_id":"HeEd"}],"month":"10","year":"2016","publication_status":"published","quality_controlled":"1","abstract":[{"text":"Voronoi diagrams and Delaunay triangulations have been extensively used to represent and compute geometric features of point configurations. We introduce a generalization to poset diagrams and poset complexes, which contain order-k and degree-k Voronoi diagrams and their duals as special cases. Extending a result of Aurenhammer from 1990, we show how to construct poset diagrams as weighted Voronoi diagrams of average balls.","lang":"eng"}],"intvolume":"        54","page":"169 - 174","date_created":"2018-12-11T11:51:12Z","type":"journal_article","_id":"1295","volume":54,"date_updated":"2021-01-12T06:49:41Z","title":"Multiple covers with balls II: Weighted averages","publisher":"Elsevier","oa_version":"None","scopus_import":1,"day":"01","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham","first_name":"Mabel"}],"doi":"10.1016/j.endm.2016.09.030"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"abstract":[{"text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.","lang":"eng"}],"_id":"9704","date_updated":"2023-02-21T16:54:31Z","date_created":"2021-07-23T08:30:38Z","type":"research_data_reference","article_processing_charge":"No","day":"06","author":[{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"last_name":"Doublet","full_name":"Doublet, Vincent","first_name":"Vincent"},{"orcid":"0000-0002-3712-925X","first_name":"Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias"},{"first_name":"Silvio","last_name":"Weging","full_name":"Weging, Silvio"},{"full_name":"Brown, Mark","last_name":"Brown","first_name":"Mark"},{"last_name":"Gogol Döring","full_name":"Gogol Döring, Andreas","first_name":"Andreas"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"doi":"10.5061/dryad.cq7t1","publisher":"Dryad","oa_version":"Published Version","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","citation":{"apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2016-05-06T00:00:00Z","oa":1,"status":"public","department":[{"_id":"SyCr"}],"year":"2016","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1262"}]},"month":"05"}]