[{"page":"177-189.e7","title":"Synaptic transmission optimization predicts expression loci of long-term plasticity","publisher":"Elsevier","article_type":"original","_id":"8016","ddc":["570"],"publication_status":"published","file_date_updated":"2020-07-14T12:48:08Z","pmid":1,"language":[{"iso":"eng"}],"author":[{"first_name":"Rui Ponte","last_name":"Costa","full_name":"Costa, Rui Ponte"},{"first_name":"Zahid","last_name":"Padamsey","full_name":"Padamsey, Zahid"},{"last_name":"D’Amour","full_name":"D’Amour, James A.","first_name":"James A."},{"last_name":"Emptage","full_name":"Emptage, Nigel J.","first_name":"Nigel J."},{"last_name":"Froemke","full_name":"Froemke, Robert C.","first_name":"Robert C."},{"orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","full_name":"Vogels, Tim P"}],"publication_identifier":{"issn":["0896-6273"]},"article_processing_charge":"No","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"cziletti","file_id":"8103","relation":"main_file","file_size":7140149,"date_created":"2020-07-09T09:42:49Z","file_name":"2017_Neuron_Costa.pdf","date_updated":"2020-07-14T12:48:08Z","checksum":"49fbca2821066c0965bd5678b32b6b48"}],"date_updated":"2021-01-12T08:16:32Z","abstract":[{"lang":"eng","text":"Long-term modifications of neuronal connections are critical for reliable memory storage in the brain. However, their locus of expression—pre- or postsynaptic—is highly variable. Here we introduce a theoretical framework in which long-term plasticity performs an optimization of the postsynaptic response statistics toward a given mean with minimal variance. Consequently, the state of the synapse at the time of plasticity induction determines the ratio of pre- and postsynaptic modifications. Our theory explains the experimentally observed expression loci of the hippocampal and neocortical synaptic potentiation studies we examined. Moreover, the theory predicts presynaptic expression of long-term depression, consistent with experimental observations. At inhibitory synapses, the theory suggests a statistically efficient excitatory-inhibitory balance in which changes in inhibitory postsynaptic response statistics specifically target the mean excitation. Our results provide a unifying theory for understanding the expression mechanisms and functions of long-term synaptic transmission plasticity."}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","volume":96,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"1","year":"2017","external_id":{"pmid":["28957667"]},"extern":"1","day":"27","oa":1,"doi":"10.1016/j.neuron.2017.09.021","date_published":"2017-09-27T00:00:00Z","intvolume":"        96","status":"public","month":"09","quality_controlled":"1","type":"journal_article","publication":"Neuron","citation":{"apa":"Costa, R. P., Padamsey, Z., D’Amour, J. A., Emptage, N. J., Froemke, R. C., &#38; Vogels, T. P. (2017). Synaptic transmission optimization predicts expression loci of long-term plasticity. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2017.09.021\">https://doi.org/10.1016/j.neuron.2017.09.021</a>","mla":"Costa, Rui Ponte, et al. “Synaptic Transmission Optimization Predicts Expression Loci of Long-Term Plasticity.” <i>Neuron</i>, vol. 96, no. 1, Elsevier, 2017, p. 177–189.e7, doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.09.021\">10.1016/j.neuron.2017.09.021</a>.","ama":"Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. Synaptic transmission optimization predicts expression loci of long-term plasticity. <i>Neuron</i>. 2017;96(1):177-189.e7. doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.09.021\">10.1016/j.neuron.2017.09.021</a>","ista":"Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. 2017. Synaptic transmission optimization predicts expression loci of long-term plasticity. Neuron. 96(1), 177–189.e7.","chicago":"Costa, Rui Ponte, Zahid Padamsey, James A. D’Amour, Nigel J. Emptage, Robert C. Froemke, and Tim P Vogels. “Synaptic Transmission Optimization Predicts Expression Loci of Long-Term Plasticity.” <i>Neuron</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.neuron.2017.09.021\">https://doi.org/10.1016/j.neuron.2017.09.021</a>.","short":"R.P. Costa, Z. Padamsey, J.A. D’Amour, N.J. Emptage, R.C. Froemke, T.P. Vogels, Neuron 96 (2017) 177–189.e7.","ieee":"R. P. Costa, Z. Padamsey, J. A. D’Amour, N. J. Emptage, R. C. Froemke, and T. P. Vogels, “Synaptic transmission optimization predicts expression loci of long-term plasticity,” <i>Neuron</i>, vol. 96, no. 1. Elsevier, p. 177–189.e7, 2017."},"oa_version":"Published Version","date_created":"2020-06-25T12:54:46Z"},{"article_type":"original","publisher":"Proceedings of the National Academy of Sciences","_id":"8018","publication_status":"published","page":"6666-6674","title":"Inhibitory engrams in perception and memory","volume":114,"year":"2017","issue":"26","language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"author":[{"first_name":"Helen C.","full_name":"Barron, Helen C.","last_name":"Barron"},{"full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181"},{"full_name":"Behrens, Timothy E.","last_name":"Behrens","first_name":"Timothy E."},{"first_name":"Mani","full_name":"Ramaswami, Mani","last_name":"Ramaswami"}],"date_updated":"2021-01-12T08:16:33Z","article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","abstract":[{"lang":"eng","text":"Nervous systems use excitatory cell assemblies to encode and represent sensory percepts. Similarly, synaptically connected cell assemblies or \"engrams\" are thought to represent memories of past experience. Multiple lines of recent evidence indicate that brain systems create and use inhibitory replicas of excitatory representations for important cognitive functions. Such matched \"inhibitory engrams\" can form through homeostatic potentiation of inhibition onto postsynaptic cells that show increased levels of excitation. Inhibitory engrams can reduce behavioral responses to familiar stimuli, thereby resulting in behavioral habituation. In addition, by preventing inappropriate activation of excitatory memory engrams, inhibitory engrams can make memories quiescent, stored in a latent form that is available for context-relevant activation. In neural networks with balanced excitatory and inhibitory engrams, the release of innate responses and recall of associative memories can occur through focused disinhibition. Understanding mechanisms that regulate the formation and expression of inhibitory engrams in vivo may help not only to explain key features of cognition but also to provide insight into transdiagnostic traits associated with psychiatric conditions such as autism, schizophrenia, and posttraumatic stress disorder. "}],"intvolume":"       114","date_published":"2017-06-27T00:00:00Z","doi":"10.1073/pnas.1701812114","status":"public","day":"27","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/","open_access":"1"}],"extern":"1","external_id":{"pmid":["28611219"]},"oa":1,"type":"journal_article","publication":"Proceedings of the National Academy of Sciences","date_created":"2020-06-25T12:56:58Z","citation":{"ama":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception and memory. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(26):6666-6674. doi:<a href=\"https://doi.org/10.1073/pnas.1701812114\">10.1073/pnas.1701812114</a>","mla":"Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 26, Proceedings of the National Academy of Sciences, 2017, pp. 6666–74, doi:<a href=\"https://doi.org/10.1073/pnas.1701812114\">10.1073/pnas.1701812114</a>.","apa":"Barron, H. C., Vogels, T. P., Behrens, T. E., &#38; Ramaswami, M. (2017). Inhibitory engrams in perception and memory. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1701812114\">https://doi.org/10.1073/pnas.1701812114</a>","ieee":"H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams in perception and memory,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674, 2017.","short":"H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the National Academy of Sciences 114 (2017) 6666–6674.","chicago":"Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami. “Inhibitory Engrams in Perception and Memory.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1701812114\">https://doi.org/10.1073/pnas.1701812114</a>.","ista":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. 114(26), 6666–6674."},"oa_version":"Published Version","month":"06","quality_controlled":"1"},{"day":"24","external_id":{"isi":["000408372400014"]},"oa":1,"status":"public","intvolume":"       170","date_published":"2017-08-24T00:00:00Z","doi":"10.1016/j.cell.2017.07.038","isi":1,"quality_controlled":"1","month":"08","publication":"Cell","date_created":"2018-12-11T11:48:35Z","citation":{"ama":"Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. 2017;170(5):956-972. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>","apa":"Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., &#38; Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>","mla":"Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>.","ieee":"M. Samwer <i>et al.</i>, “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” <i>Cell</i>, vol. 170, no. 5. Cell Press, pp. 956–972, 2017.","short":"M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972.","ista":"Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972.","chicago":"Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>."},"oa_version":"Published Version","type":"journal_article","department":[{"_id":"CaHe"}],"page":"956 - 972","title":"DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes","file_date_updated":"2020-07-14T12:48:08Z","ddc":["570"],"publication_status":"published","publist_id":"6848","publisher":"Cell Press","_id":"803","file":[{"checksum":"64897b0c5373f22273f598e4672c60ff","file_name":"2017_Cell_Samwer.pdf","date_updated":"2020-07-14T12:48:08Z","file_id":"5852","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_size":17666637,"date_created":"2019-01-18T13:45:40Z"}],"date_updated":"2023-09-27T10:59:14Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function."}],"language":[{"iso":"eng"}],"author":[{"first_name":"Matthias","last_name":"Samwer","full_name":"Samwer, Matthias"},{"full_name":"Schneider, Maximilian","last_name":"Schneider","first_name":"Maximilian"},{"first_name":"Rudolf","last_name":"Hoefler","full_name":"Hoefler, Rudolf"},{"orcid":"0000-0002-5795-0133","first_name":"Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","full_name":"Schmalhorst, Philipp S","last_name":"Schmalhorst"},{"first_name":"Julian","last_name":"Jude","full_name":"Jude, Julian"},{"first_name":"Johannes","last_name":"Zuber","full_name":"Zuber, Johannes"},{"full_name":"Gerlic, Daniel","last_name":"Gerlic","first_name":"Daniel"}],"publication_identifier":{"issn":["00928674"]},"year":"2017","issue":"5","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"}],"volume":170,"has_accepted_license":"1"},{"article_processing_charge":"No","date_updated":"2023-09-27T10:58:45Z","abstract":[{"lang":"eng","text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["15499618"]},"author":[{"full_name":"Schmalhorst, Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","first_name":"Philipp S","orcid":"0000-0002-5795-0133"},{"full_name":"Deluweit, Felix","last_name":"Deluweit","first_name":"Felix"},{"first_name":"Roger","full_name":"Scherrers, Roger","last_name":"Scherrers"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K"}],"issue":"10","scopus_import":"1","year":"2017","acknowledged_ssus":[{"_id":"ScienComp"}],"volume":13,"department":[{"_id":"CaHe"}],"page":"5039 - 5053","title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","publication_status":"published","publisher":"American Chemical Society","publist_id":"6847","_id":"804","quality_controlled":"1","acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the  Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","month":"10","publication":"Journal of Chemical Theory and Computation","citation":{"apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &#38; Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>","mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>.","ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. 2017;13(10):5039-5053. doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>","ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053.","chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>.","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053.","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:48:35Z","type":"journal_article","external_id":{"isi":["000412965700036"]},"main_file_link":[{"url":"https://arxiv.org/abs/1704.03773","open_access":"1"}],"day":"10","oa":1,"status":"public","date_published":"2017-10-10T00:00:00Z","doi":"10.1021/acs.jctc.7b00374","intvolume":"        13","isi":1},{"publication_status":"published","ddc":["020"],"file_date_updated":"2020-07-14T12:48:09Z","publisher":"VÖB","publist_id":"6843","_id":"807","department":[{"_id":"E-Lib"}],"title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","page":"274 - 280","issue":"2","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"popular_science":"1","scopus_import":1,"year":"2017","volume":70,"has_accepted_license":"1","date_updated":"2021-01-12T08:16:45Z","file":[{"checksum":"558c18bcf5580d87dd371ec626d52075","file_name":"2017_VOEB_Andrae.pdf","date_updated":"2020-07-14T12:48:09Z","file_size":125065,"date_created":"2019-01-18T13:39:26Z","file_id":"5851","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group &quot;Springer Compact Evaluierung&quot; made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Magdalena","full_name":"Andrae, Magdalena","last_name":"Andrae"},{"first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","full_name":"Villányi, Márton","last_name":"Villányi","orcid":"0000-0001-8126-0426"}],"publication_identifier":{"issn":["10222588"]},"status":"public","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1898","intvolume":"        70","day":"01","oa":1,"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","oa_version":"Published Version","citation":{"ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2017;70(2):274-280. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>","apa":"Andrae, M., &#38; Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>.","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>."},"date_created":"2018-12-11T11:48:36Z","type":"journal_article","month":"08"},{"status":"public","intvolume":"         6","doi":"10.7554/elife.22152","date_published":"2017-03-06T00:00:00Z","article_number":"e22152","day":"06","external_id":{"pmid":["28267430"]},"extern":"1","oa":1,"publication":"eLife","date_created":"2020-06-30T13:32:18Z","oa_version":"Published Version","citation":{"ama":"Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. Mapping the function of neuronal ion channels in model and experiment. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.22152\">10.7554/elife.22152</a>","apa":"Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R., &#38; Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model and experiment. <i>ELife</i>. eLife Sciences Publications, Ltd. <a href=\"https://doi.org/10.7554/elife.22152\">https://doi.org/10.7554/elife.22152</a>","mla":"Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” <i>ELife</i>, vol. 6, e22152, eLife Sciences Publications, Ltd, 2017, doi:<a href=\"https://doi.org/10.7554/elife.22152\">10.7554/elife.22152</a>.","ieee":"W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,” <i>eLife</i>, vol. 6. eLife Sciences Publications, Ltd, 2017.","short":"W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P. Vogels, ELife 6 (2017).","ista":"Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. 2017. Mapping the function of neuronal ion channels in model and experiment. eLife. 6, e22152.","chicago":"Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck, Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” <i>ELife</i>. eLife Sciences Publications, Ltd, 2017. <a href=\"https://doi.org/10.7554/elife.22152\">https://doi.org/10.7554/elife.22152</a>."},"type":"journal_article","quality_controlled":"1","month":"03","file_date_updated":"2020-07-16T12:08:40Z","ddc":["570"],"publication_status":"published","article_type":"original","publisher":"eLife Sciences Publications, Ltd","_id":"8075","title":"Mapping the function of neuronal ion channels in model and experiment","year":"2017","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":6,"has_accepted_license":"1","file":[{"success":1,"checksum":"e5c5a33bcb3ac38ad62df1010ab29040","date_updated":"2020-07-16T12:08:40Z","file_name":"2017_elife_Podlaski.pdf","relation":"main_file","file_id":"8124","creator":"cziletti","access_level":"open_access","content_type":"application/pdf","date_created":"2020-07-16T12:08:40Z","file_size":16034505}],"date_updated":"2021-01-12T08:16:46Z","article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","abstract":[{"text":"Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling.","lang":"eng"}],"language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"issn":["2050-084X"]},"author":[{"first_name":"William F","last_name":"Podlaski","full_name":"Podlaski, William F"},{"last_name":"Seeholzer","full_name":"Seeholzer, Alexander","first_name":"Alexander"},{"last_name":"Groschner","full_name":"Groschner, Lukas N","first_name":"Lukas N"},{"first_name":"Gero","last_name":"Miesenböck","full_name":"Miesenböck, Gero"},{"first_name":"Rajnish","full_name":"Ranjan, Rajnish","last_name":"Ranjan"},{"last_name":"Vogels","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181"}]},{"page":"272-283","title":"Cortical microcircuits as gated-recurrent neural networks","publication_status":"published","publisher":"Neural Information Processing Systems Foundation","_id":"8129","article_processing_charge":"No","date_updated":"2021-01-12T08:17:03Z","abstract":[{"lang":"eng","text":"Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function.\r\nOverall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"end_date":"2017-12-09","location":"Long Beach, CA, United States","start_date":"2017-12-04","name":"NIPS: Neural Information Processing System"},"author":[{"first_name":"Rui Ponte","full_name":"Costa, Rui Ponte","last_name":"Costa"},{"first_name":"Yannis M.","last_name":"Assael","full_name":"Assael, Yannis M."},{"first_name":"Brendan","full_name":"Shillingford, Brendan","last_name":"Shillingford"},{"last_name":"Freitas","full_name":"Freitas, Nando de","first_name":"Nando de"},{"orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"}],"publication_identifier":{"issn":["10495258"]},"year":"2017","volume":30,"extern":"1","external_id":{"arxiv":["1711.02448"]},"day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1711.02448","open_access":"1"}],"oa":1,"status":"public","date_published":"2017-12-01T00:00:00Z","intvolume":"        30","quality_controlled":"1","arxiv":1,"month":"12","publication":"Advances in Neural Information Processing Systems","citation":{"chicago":"Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas, and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” In <i>Advances in Neural Information Processing Systems</i>, 30:272–83. Neural Information Processing Systems Foundation, 2017.","ista":"Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical microcircuits as gated-recurrent neural networks. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.","ieee":"R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels, “Cortical microcircuits as gated-recurrent neural networks,” in <i>Advances in Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017, vol. 30, pp. 272–283.","short":"R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2017, pp. 272–283.","mla":"Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” <i>Advances in Neural Information Processing Systems</i>, vol. 30, Neural Information Processing Systems Foundation, 2017, pp. 272–83.","apa":"Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, &#38; Vogels, T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In <i>Advances in Neural Information Processing Systems</i> (Vol. 30, pp. 272–283). Long Beach, CA, United States: Neural Information Processing Systems Foundation.","ama":"Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits as gated-recurrent neural networks. In: <i>Advances in Neural Information Processing Systems</i>. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283."},"oa_version":"Preprint","date_created":"2020-07-16T19:13:10Z","type":"conference"},{"month":"09","quality_controlled":"1","type":"journal_article","oa_version":"Published Version","citation":{"ama":"Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. <i>Journal of Structural Biology</i>. 2017;199(3):187-195. doi:<a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">10.1016/j.jsb.2017.07.007</a>","apa":"Turoňová, B., Schur, F. K., Wan, W., &#38; Briggs, J. (2017). Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. <i>Journal of Structural Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">https://doi.org/10.1016/j.jsb.2017.07.007</a>","mla":"Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” <i>Journal of Structural Biology</i>, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:<a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">10.1016/j.jsb.2017.07.007</a>.","short":"B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology 199 (2017) 187–195.","ieee":"B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å,” <i>Journal of Structural Biology</i>, vol. 199, no. 3. Academic Press, pp. 187–195, 2017.","chicago":"Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” <i>Journal of Structural Biology</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">https://doi.org/10.1016/j.jsb.2017.07.007</a>.","ista":"Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. 199(3), 187–195."},"date_created":"2018-12-11T11:48:40Z","publication":"Journal of Structural Biology","oa":1,"extern":"1","day":"01","doi":"10.1016/j.jsb.2017.07.007","date_published":"2017-09-01T00:00:00Z","intvolume":"       199","status":"public","author":[{"last_name":"Turoňová","full_name":"Turoňová, Beata","first_name":"Beata"},{"orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4. Å resolution structure determined by subtomogram averaging."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:17:16Z","file":[{"file_name":"2017_Elsevier_Turonova.pdf","date_updated":"2020-07-14T12:48:09Z","checksum":"7f2d4bbac767f9acc254d1a4114d181a","content_type":"application/pdf","access_level":"open_access","creator":"kschuh","file_id":"6168","relation":"main_file","file_size":1310009,"date_created":"2019-03-22T09:29:44Z"}],"has_accepted_license":"1","volume":199,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"3","year":"2017","title":"Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å","page":"187-195","_id":"817","publisher":"Academic Press","publist_id":"6832","file_date_updated":"2020-07-14T12:48:09Z","ddc":["570"],"publication_status":"published"},{"_id":"818","publist_id":"6831","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:48:09Z","publication_status":"published","ddc":["571","579"],"page":"113","title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","supervisor":[{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"department":[{"_id":"ToBo"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","year":"2017","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Karin","full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ","lang":"eng"}],"file":[{"date_created":"2019-04-05T08:48:51Z","file_size":6331071,"relation":"source_file","file_id":"6210","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"da3993c5f90f59a8e8623cc31ad501dd","date_updated":"2020-07-14T12:48:09Z","file_name":"Thesis_KarinMitosch.docx"},{"checksum":"24c3d9e51992f1b721f3df55aa13fcb8","file_name":"Thesis_KarinMitosch.pdf","date_updated":"2020-07-14T12:48:09Z","file_size":9289852,"date_created":"2019-04-05T08:48:51Z","file_id":"6211","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"date_updated":"2023-09-07T12:00:26Z","article_processing_charge":"No","date_published":"2017-09-27T00:00:00Z","doi":"10.15479/AT:ISTA:th_862","related_material":{"record":[{"relation":"part_of_dissertation","id":"2001","status":"public"},{"status":"public","id":"666","relation":"part_of_dissertation"}]},"status":"public","oa":1,"day":"27","type":"dissertation","date_created":"2018-12-11T11:48:40Z","oa_version":"Published Version","citation":{"apa":"Mitosch, K. (2017). <i>Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>","mla":"Mitosch, Karin. <i>Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>.","ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>.","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017."},"degree_awarded":"PhD","month":"09","pubrep_id":"862","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. "},{"oa_version":"Published Version","citation":{"ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017.","short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017.","ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>.","ama":"Pull C. Disease defence in garden ants. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>","mla":"Pull, Christopher. <i>Disease Defence in Garden Ants</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>.","apa":"Pull, C. (2017). <i>Disease defence in garden ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>"},"date_created":"2018-12-11T11:48:40Z","degree_awarded":"PhD","type":"dissertation","acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","pubrep_id":"861","month":"09","related_material":{"record":[{"status":"public","id":"616","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"806","status":"public"},{"id":"734","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"732","relation":"part_of_dissertation"}]},"status":"public","date_published":"2017-09-26T00:00:00Z","doi":"10.15479/AT:ISTA:th_861","oa":1,"day":"26","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2017","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","file":[{"file_size":18580400,"date_created":"2019-04-05T07:53:04Z","file_id":"6199","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"dernst","checksum":"4993cdd5382295758ecc3ecbd2a9aaff","file_name":"2017_Thesis_Pull.docx","date_updated":"2020-07-14T12:48:09Z"},{"file_size":14400681,"date_created":"2019-04-05T07:53:04Z","file_id":"6200","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","checksum":"ee2e3ebb5b53c154c866f5b052b25153","file_name":"2017_Thesis_Pull.pdf","date_updated":"2020-07-14T12:48:09Z"}],"date_updated":"2023-09-28T11:31:32Z","author":[{"orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"publication_status":"published","file_date_updated":"2020-07-14T12:48:09Z","ddc":["576","577","578","579","590","592"],"_id":"819","publisher":"Institute of Science and Technology Austria","publist_id":"6830","alternative_title":["ISTA Thesis"],"department":[{"_id":"SyCr"}],"page":"122","title":"Disease defence in garden ants","supervisor":[{"first_name":"Sylvia M","last_name":"Cremer","full_name":"Cremer, Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}]},{"article_processing_charge":"Yes (via OA deal)","file":[{"checksum":"67afa85ff1e220cbc1f9f477a828513c","date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf","relation":"main_file","file_id":"4665","creator":"system","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:08:05Z","file_size":1615755}],"date_updated":"2023-09-20T09:42:12Z","abstract":[{"lang":"eng","text":"We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-3036-1475","first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","last_name":"Bao"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"}],"publication_identifier":{"issn":["01788051"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","issue":"3-4","year":"2017","volume":167,"has_accepted_license":"1","department":[{"_id":"LaEr"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804"}],"title":"Delocalization for a class of random block band matrices","page":"673 - 776","publication_status":"published","file_date_updated":"2020-07-14T12:45:00Z","ddc":["530"],"publisher":"Springer","publist_id":"5644","article_type":"original","ec_funded":1,"_id":"1528","quality_controlled":"1","acknowledgement":"Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization.","pubrep_id":"489","month":"04","publication":"Probability Theory and Related Fields","citation":{"ama":"Bao Z, Erdös L. Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. 2017;167(3-4):673-776. doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>","mla":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>.","apa":"Bao, Z., &#38; Erdös, L. (2017). Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>","ieee":"Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4. Springer, pp. 673–776, 2017.","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.","ista":"Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776.","chicago":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>."},"oa_version":"Published Version","date_created":"2018-12-11T11:52:32Z","type":"journal_article","external_id":{"isi":["000398842700004"]},"day":"01","oa":1,"status":"public","date_published":"2017-04-01T00:00:00Z","doi":"10.1007/s00440-015-0692-y","intvolume":"       167","isi":1},{"publisher":"Oxford University Press","date_published":"2017-06-19T00:00:00Z","doi":"10.1093/imrn/rnx116","publist_id":"7752","_id":"169","status":"public","publication_status":"published","external_id":{"arxiv":["1609.06097"]},"extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1609.06097","open_access":"1"}],"day":"19","oa":1,"title":"Twisted Linnik implies optimal covering exponent for S3","type":"journal_article","publication":"International Mathematics Research Notices","year":"2017","citation":{"ama":"Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering exponent for S3. <i>International Mathematics Research Notices</i>. 2017. doi:<a href=\"https://doi.org/10.1093/imrn/rnx116\">10.1093/imrn/rnx116</a>","mla":"Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent for S3.” <i>International Mathematics Research Notices</i>, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/imrn/rnx116\">10.1093/imrn/rnx116</a>.","apa":"Browning, T. D., Kumaraswamy, V., &#38; Steiner, R. (2017). Twisted Linnik implies optimal covering exponent for S3. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnx116\">https://doi.org/10.1093/imrn/rnx116</a>","short":"T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research Notices (2017).","ieee":"T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal covering exponent for S3,” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017.","ista":"Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices.","chicago":"Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik Implies Optimal Covering Exponent for S3.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/imrn/rnx116\">https://doi.org/10.1093/imrn/rnx116</a>."},"oa_version":"None","date_created":"2018-12-11T11:44:59Z","arxiv":1,"language":[{"iso":"eng"}],"month":"06","author":[{"orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning"},{"first_name":"Vinay","last_name":"Kumaraswamy","full_name":"Kumaraswamy, Vinay"},{"first_name":"Rapael","last_name":"Steiner","full_name":"Steiner, Rapael"}],"article_processing_charge":"No","date_updated":"2021-01-12T06:52:32Z","quality_controlled":"1","abstract":[{"text":"We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","year":"2017","publication":"International Mathematics Research Notices","date_created":"2018-12-11T11:45:00Z","citation":{"chicago":"Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/imrn/rnx252\">https://doi.org/10.1093/imrn/rnx252</a>.","ista":"Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices.","short":"T.D. Browning, D. Schindler, International Mathematics Research Notices (2017).","ieee":"T. D. Browning and D. Schindler, “Strong approximation and a conjecture of Harpaz and Wittenberg,” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017.","apa":"Browning, T. D., &#38; Schindler, D. (2017). Strong approximation and a conjecture of Harpaz and Wittenberg. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnx252\">https://doi.org/10.1093/imrn/rnx252</a>","mla":"Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” <i>International Mathematics Research Notices</i>, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/imrn/rnx252\">10.1093/imrn/rnx252</a>.","ama":"Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and Wittenberg. <i>International Mathematics Research Notices</i>. 2017. doi:<a href=\"https://doi.org/10.1093/imrn/rnx252\">10.1093/imrn/rnx252</a>"},"oa_version":"None","language":[{"iso":"eng"}],"arxiv":1,"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177"},{"last_name":"Schindler","full_name":"Schindler, Damaris","first_name":"Damaris"}],"month":"10","date_updated":"2021-01-12T06:52:45Z","quality_controlled":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg."}],"publist_id":"7749","date_published":"2017-10-30T00:00:00Z","doi":"10.1093/imrn/rnx252","publisher":"Oxford University Press","_id":"172","status":"public","publication_status":"published","day":"30","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.07744"}],"extern":"1","external_id":{"arxiv":["1509.07744"]},"oa":1,"title":"Strong approximation and a conjecture of Harpaz and Wittenberg"},{"year":"2017","scopus_import":"1","issue":"2","volume":44,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.","lang":"eng"}],"date_updated":"2023-09-19T15:13:27Z","article_processing_charge":"No","publication_identifier":{"issn":["03036898"]},"author":[{"first_name":"Abraham","last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez"},{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"}],"language":[{"iso":"eng"}],"publication_status":"published","_id":"2016","publist_id":"5060","publisher":"Wiley-Blackwell","department":[{"_id":"GaTk"}],"page":"285 - 306","title":"Exact goodness-of-fit testing for the Ising model","date_created":"2018-12-11T11:55:13Z","oa_version":"Preprint","citation":{"ieee":"A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","ista":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.","chicago":"Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>.","ama":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. 2017;44(2):285-306. doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>","mla":"Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>.","apa":"Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., &#38; Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>"},"publication":"Scandinavian Journal of Statistics","type":"journal_article","quality_controlled":"1","month":"06","arxiv":1,"related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"status":"public","isi":1,"intvolume":"        44","date_published":"2017-06-01T00:00:00Z","doi":"10.1111/sjos.12251","oa":1,"day":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.1242"}],"external_id":{"arxiv":["1410.1242"],"isi":["000400985000001"]}},{"degree_awarded":"PhD","citation":{"mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017."},"oa_version":"Published Version","date_created":"2018-12-11T11:45:10Z","type":"dissertation","acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","month":"10","pubrep_id":"916","status":"public","related_material":{"record":[{"id":"1243","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"561","status":"public"},{"status":"public","id":"457","relation":"part_of_dissertation"}]},"date_published":"2017-10-01T00:00:00Z","doi":"10.15479/AT:ISTA:th_916","day":"01","oa":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2017","has_accepted_license":"1","article_processing_charge":"No","date_updated":"2023-09-15T12:04:56Z","file":[{"date_updated":"2020-07-14T12:45:24Z","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","checksum":"33cfb59674e91f82e3738396d3fb3776","creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4710","date_created":"2018-12-12T10:08:48Z","file_size":18569590},{"checksum":"dcc239968decb233e7f98cf1083d8c26","file_name":"2017_Pleska_Maros_Thesis.docx","date_updated":"2020-07-14T12:45:24Z","file_id":"6204","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"dernst","file_size":2801649,"date_created":"2019-04-05T08:33:14Z"}],"abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-7460-7479","last_name":"Pleska","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2020-07-14T12:45:24Z","ddc":["576","579"],"publisher":"Institute of Science and Technology Austria","publist_id":"7711","_id":"202","alternative_title":["ISTA Thesis"],"department":[{"_id":"CaGu"}],"supervisor":[{"first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"project":[{"grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"page":"126","title":"Biology of restriction-modification systems at the single-cell and population level"},{"intvolume":"        78","date_published":"2017-06-01T00:00:00Z","doi":"10.1007/s00453-016-0212-1","isi":1,"status":"public","day":"01","external_id":{"isi":["000400379500013"]},"oa":1,"type":"journal_article","publication":"Algorithmica","date_created":"2018-12-11T11:51:27Z","oa_version":"Published Version","citation":{"ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>."},"month":"06","pubrep_id":"658","quality_controlled":"1","publist_id":"5931","publisher":"Springer","_id":"1336","ec_funded":1,"file_date_updated":"2020-07-14T12:44:44Z","ddc":["576"],"publication_status":"published","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"title":"Towards a runtime comparison of natural and artificial evolution","page":"681 - 713","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"volume":78,"has_accepted_license":"1","year":"2017","issue":"2","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["01784617"]},"author":[{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"file":[{"checksum":"7873f665a0c598ac747c908f34cb14b9","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","date_created":"2018-12-12T10:10:19Z","file_size":710206,"relation":"main_file","file_id":"4805","creator":"system","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2023-09-20T11:14:42Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}]},{"file_date_updated":"2020-07-14T12:44:44Z","publication_status":"published","ddc":["510","530"],"publisher":"Springer","publist_id":"5930","ec_funded":1,"_id":"1337","department":[{"_id":"LaEr"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"page":"667 - 727","title":"Universality for general Wigner-type matrices","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","issue":"3-4","year":"2017","volume":169,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file":[{"file_size":988843,"date_created":"2018-12-12T10:08:25Z","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"4686","relation":"main_file","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","date_updated":"2020-07-14T12:44:44Z","checksum":"29f5a72c3f91e408aeb9e78344973803"}],"date_updated":"2023-09-20T11:14:17Z","abstract":[{"lang":"eng","text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["01788051"]},"author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","last_name":"Ajanki","full_name":"Ajanki, Oskari H","first_name":"Oskari H"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H"}],"status":"public","date_published":"2017-12-01T00:00:00Z","doi":"10.1007/s00440-016-0740-2","intvolume":"       169","isi":1,"external_id":{"isi":["000414358400002"]},"day":"01","oa":1,"publication":"Probability Theory and Related Fields","citation":{"chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727.","mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2017). Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>","ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. 2017;169(3-4):667-727. doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>"},"oa_version":"Published Version","date_created":"2018-12-11T11:51:27Z","type":"journal_article","quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).  ","month":"12","pubrep_id":"657"},{"day":"01","external_id":{"isi":["000399888900001"]},"oa":1,"status":"public","related_material":{"record":[{"relation":"earlier_version","id":"1729","status":"public"}]},"intvolume":"        50","date_published":"2017-06-01T00:00:00Z","doi":"10.1007/s10703-016-0256-5","isi":1,"quality_controlled":"1","month":"06","pubrep_id":"656","publication":"Formal Methods in System Design","date_created":"2018-12-11T11:51:27Z","oa_version":"Published Version","citation":{"ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. 2017;50(2-3):97-139. doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>","mla":"Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>.","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3. Springer, pp. 97–139, 2017.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139."},"type":"journal_article","department":[{"_id":"ToHe"}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","page":"97 - 139","publication_status":"published","file_date_updated":"2020-07-14T12:44:44Z","ddc":["000"],"publist_id":"5929","publisher":"Springer","_id":"1338","ec_funded":1,"file":[{"creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4985","date_created":"2018-12-12T10:13:05Z","file_size":1416170,"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf","checksum":"1163dfd997e8212c789525d4178b1653"}],"date_updated":"2023-09-20T11:13:51Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively."}],"language":[{"iso":"eng"}],"author":[{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol"},{"first_name":"Edmund","last_name":"Clarke","full_name":"Clarke, Edmund"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"},{"first_name":"Leonid","full_name":"Ryzhyk, Leonid","last_name":"Ryzhyk"},{"first_name":"Roopsha","last_name":"Samanta","full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4409-8487","first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","last_name":"Tarrach"}],"year":"2017","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","issue":"2-3","volume":50,"has_accepted_license":"1"},{"language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"author":[{"first_name":"Thumu","full_name":"Udayabhaskararao, Thumu","last_name":"Udayabhaskararao"},{"last_name":"Altantzis","full_name":"Altantzis, Thomas","first_name":"Thomas"},{"first_name":"Lothar","full_name":"Houben, Lothar","last_name":"Houben"},{"full_name":"Coronado-Puchau, Marc","last_name":"Coronado-Puchau","first_name":"Marc"},{"first_name":"Judith","full_name":"Langer, Judith","last_name":"Langer"},{"full_name":"Popovitz-Biro, Ronit","last_name":"Popovitz-Biro","first_name":"Ronit"},{"first_name":"Luis M.","full_name":"Liz-Marzán, Luis M.","last_name":"Liz-Marzán"},{"full_name":"Vuković, Lela","last_name":"Vuković","first_name":"Lela"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"full_name":"Bals, Sara","last_name":"Bals","first_name":"Sara"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"date_updated":"2023-08-07T11:25:00Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Self-assembly of inorganic nanoparticles has been used to prepare hundreds of different colloidal crystals, but almost invariably with the restriction that the particles must be densely packed. Here, we show that non–close-packed nanoparticle arrays can be fabricated through the selective removal of one of two components comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle superlattices were prepared at the liquid-air interface, including several arrangements that were previously unknown. Molecular dynamics simulations revealed the particular role of the liquid in templating the formation of superlattices not achievable through self-assembly in bulk solution. Second, upon stabilization, all of these binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous materials having the same chemical composition but differing in their nanoscale architectures."}],"volume":358,"year":"2017","issue":"6362","scopus_import":"1","page":"514-518","title":"Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices","article_type":"original","publisher":"American Association for the Advancement of Science","_id":"13381","publication_status":"published","month":"10","quality_controlled":"1","type":"journal_article","publication":"Science","date_created":"2023-08-01T09:41:16Z","citation":{"apa":"Udayabhaskararao, T., Altantzis, T., Houben, L., Coronado-Puchau, M., Langer, J., Popovitz-Biro, R., … Klajn, R. (2017). Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aan6046\">https://doi.org/10.1126/science.aan6046</a>","mla":"Udayabhaskararao, Thumu, et al. “Tunable Porous Nanoallotropes Prepared by Post-Assembly Etching of Binary Nanoparticle Superlattices.” <i>Science</i>, vol. 358, no. 6362, American Association for the Advancement of Science, 2017, pp. 514–18, doi:<a href=\"https://doi.org/10.1126/science.aan6046\">10.1126/science.aan6046</a>.","ama":"Udayabhaskararao T, Altantzis T, Houben L, et al. Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices. <i>Science</i>. 2017;358(6362):514-518. doi:<a href=\"https://doi.org/10.1126/science.aan6046\">10.1126/science.aan6046</a>","ista":"Udayabhaskararao T, Altantzis T, Houben L, Coronado-Puchau M, Langer J, Popovitz-Biro R, Liz-Marzán LM, Vuković L, Král P, Bals S, Klajn R. 2017. Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices. Science. 358(6362), 514–518.","chicago":"Udayabhaskararao, Thumu, Thomas Altantzis, Lothar Houben, Marc Coronado-Puchau, Judith Langer, Ronit Popovitz-Biro, Luis M. Liz-Marzán, et al. “Tunable Porous Nanoallotropes Prepared by Post-Assembly Etching of Binary Nanoparticle Superlattices.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aan6046\">https://doi.org/10.1126/science.aan6046</a>.","ieee":"T. Udayabhaskararao <i>et al.</i>, “Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices,” <i>Science</i>, vol. 358, no. 6362. American Association for the Advancement of Science, pp. 514–518, 2017.","short":"T. Udayabhaskararao, T. Altantzis, L. Houben, M. Coronado-Puchau, J. Langer, R. Popovitz-Biro, L.M. Liz-Marzán, L. Vuković, P. Král, S. Bals, R. Klajn, Science 358 (2017) 514–518."},"oa_version":"Submitted Version","day":"27","main_file_link":[{"url":"https://repository.uantwerpen.be/docman/irua/8d722e/147242_2018_06_07.pdf","open_access":"1"}],"extern":"1","external_id":{"pmid":["29074773"]},"oa":1,"keyword":["Multidisciplinary"],"intvolume":"       358","date_published":"2017-10-27T00:00:00Z","doi":"10.1126/science.aan6046","status":"public"},{"page":"5474-5475","title":"Chemical systems out of equilibrium","_id":"13382","publisher":"Royal Society of Chemistry","article_type":"letter_note","publication_status":"published","publication_identifier":{"issn":["0306-0012"],"eissn":["1460-4744"]},"author":[{"first_name":"Jan H.","last_name":"van Esch","full_name":"van Esch, Jan H."},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"},{"first_name":"Sijbren","last_name":"Otto","full_name":"Otto, Sijbren"}],"pmid":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2023-08-07T11:27:42Z","volume":46,"issue":"18","scopus_import":"1","year":"2017","oa":1,"external_id":{"pmid":["28884760"]},"extern":"1","main_file_link":[{"url":"https://doi.org/10.1039/c7cs90088k","open_access":"1"}],"day":"08","keyword":["General Chemistry"],"doi":"10.1039/c7cs90088k","date_published":"2017-09-08T00:00:00Z","intvolume":"        46","status":"public","month":"09","quality_controlled":"1","type":"journal_article","citation":{"ieee":"J. H. van Esch, R. Klajn, and S. Otto, “Chemical systems out of equilibrium,” <i>Chemical Society Reviews</i>, vol. 46, no. 18. Royal Society of Chemistry, pp. 5474–5475, 2017.","short":"J.H. van Esch, R. Klajn, S. Otto, Chemical Society Reviews 46 (2017) 5474–5475.","ista":"van Esch JH, Klajn R, Otto S. 2017. Chemical systems out of equilibrium. Chemical Society Reviews. 46(18), 5474–5475.","chicago":"Esch, Jan H. van, Rafal Klajn, and Sijbren Otto. “Chemical Systems out of Equilibrium.” <i>Chemical Society Reviews</i>. Royal Society of Chemistry, 2017. <a href=\"https://doi.org/10.1039/c7cs90088k\">https://doi.org/10.1039/c7cs90088k</a>.","ama":"van Esch JH, Klajn R, Otto S. Chemical systems out of equilibrium. <i>Chemical Society Reviews</i>. 2017;46(18):5474-5475. doi:<a href=\"https://doi.org/10.1039/c7cs90088k\">10.1039/c7cs90088k</a>","apa":"van Esch, J. H., Klajn, R., &#38; Otto, S. (2017). Chemical systems out of equilibrium. <i>Chemical Society Reviews</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c7cs90088k\">https://doi.org/10.1039/c7cs90088k</a>","mla":"van Esch, Jan H., et al. “Chemical Systems out of Equilibrium.” <i>Chemical Society Reviews</i>, vol. 46, no. 18, Royal Society of Chemistry, 2017, pp. 5474–75, doi:<a href=\"https://doi.org/10.1039/c7cs90088k\">10.1039/c7cs90088k</a>."},"oa_version":"Published Version","date_created":"2023-08-01T09:41:30Z","publication":"Chemical Society Reviews"}]