[{"doi":"10.7554/eLife.32035","date_published":"2018-03-09T00:00:00Z","date_created":"2018-12-11T11:46:23Z","has_accepted_license":"1","isi":1,"year":"2018","day":"09","publication":"eLife","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","author":[{"first_name":"Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","last_name":"Payne"},{"last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas","first_name":"Lukas"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"publist_id":"7400","external_id":{"isi":["000431035800001"]},"article_processing_charge":"No","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","citation":{"ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e32035","related_material":{"record":[{"relation":"research_data","status":"public","id":"9840"}]},"volume":7,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-17T10:36:07Z","file_name":"2018_eLife_Payne.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:25Z","file_size":3533881,"file_id":"5689","checksum":"447cf6e680bdc3c01062a8737d876569","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 7","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:25Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2023-09-11T12:49:17Z","ddc":["576"],"type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","_id":"423"},{"status":"public","conference":{"start_date":"2018-09-26","end_date":"2018-09-28","location":"Barcelona, Spain","name":"Graph Drawing and Network Visualization"},"type":"conference","_id":"5791","department":[{"_id":"UlWa"}],"date_updated":"2023-09-11T12:49:55Z","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07608"}],"alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths.","lang":"eng"}],"volume":"11282 ","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030044138"]},"title":"Crossing minimization in perturbed drawings","external_id":{"isi":["000672802500016"],"arxiv":["1808.07608"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"full_name":"Tóth, Csaba D.","last_name":"Tóth","first_name":"Csaba D."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16."},"oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-30T22:59:15Z","date_published":"2018-12-18T00:00:00Z","doi":"10.1007/978-3-030-04414-5_16","page":"229-241","day":"18","year":"2018","isi":1},{"_id":"291","type":"journal_article","status":"public","date_updated":"2023-09-11T12:45:44Z","department":[{"_id":"BjHo"}],"abstract":[{"text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01918"}],"month":"05","intvolume":" 3","publication_status":"published","language":[{"iso":"eng"}],"issue":"5","volume":3,"article_number":"054401","citation":{"mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401.","apa":"Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401","short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).","ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society, 2018.","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.054401.","ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7590","author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000433426200001"],"arxiv":["1802.01918"]},"article_processing_charge":"No","title":"Complexity of the laminar-turbulent boundary in pipe flow","quality_controlled":"1","publisher":"American Physical Society","oa":1,"isi":1,"year":"2018","day":"30","publication":"Physical Review Fluids","doi":"10.1103/PhysRevFluids.3.054401","date_published":"2018-05-30T00:00:00Z","date_created":"2018-12-11T11:45:39Z"},{"department":[{"_id":"HeEd"}],"date_updated":"2023-09-11T12:48:39Z","type":"journal_article","status":"public","_id":"58","issue":"3","volume":32,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1604.00960","open_access":"1"}],"month":"09","intvolume":" 32","abstract":[{"lang":"eng","text":"Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks."}],"oa_version":"Preprint","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"full_name":"Segal Halevi, Erel","last_name":"Segal Halevi","first_name":"Erel"}],"publist_id":"7996","external_id":{"isi":["000450810500036"],"arxiv":["1604.00960"]},"article_processing_charge":"No","title":"Counting blanks in polygonal arrangements","citation":{"chicago":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.","ista":"Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.","mla":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X.","short":"A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257.","ieee":"A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018.","apa":"Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X","ama":"Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"page":"2242 - 2257","doi":"10.1137/16M110407X","date_published":"2018-09-06T00:00:00Z","date_created":"2018-12-11T11:44:24Z","isi":1,"year":"2018","day":"06","publication":"SIAM Journal on Discrete Mathematics","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","oa":1},{"date_updated":"2023-09-11T12:49:17Z","citation":{"ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Payne","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","_id":"9840","type":"research_data_reference","status":"public","year":"2018","day":"12","related_material":{"record":[{"relation":"used_in_publication","id":"423","status":"public"}]},"date_published":"2018-03-12T00:00:00Z","doi":"10.5061/dryad.42n44","date_created":"2021-08-09T13:10:02Z","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"oa":1,"month":"03"}]