[{"title":"Data for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","publisher":"Institute of Science and Technology Austria","oa":1,"datarep_id":"78","citation":{"mla":"Vicoso, Beatriz. <i>Data for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>.","apa":"Vicoso, B. (2017). Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:78\">https://doi.org/10.15479/AT:ISTA:78</a>","short":"B. Vicoso, (2017).","ama":"Vicoso B. Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>","chicago":"Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:78\">https://doi.org/10.15479/AT:ISTA:78</a>.","ista":"Vicoso B. 2017. Data for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>.","ieee":"B. Vicoso, “Data for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017."},"abstract":[{"lang":"eng","text":"This folder contains all the data used in each of the main figures of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. \r\n"}],"file_date_updated":"2020-07-14T12:47:04Z","doi":"10.15479/AT:ISTA:78","file":[{"relation":"main_file","access_level":"open_access","checksum":"4520eb2b8379417ee916995719158f16","file_name":"IST-2017-78-v1+1_Data.zip","content_type":"application/zip","file_size":143697895,"file_id":"5618","date_created":"2018-12-12T13:03:00Z","creator":"system","date_updated":"2020-07-14T12:47:04Z"}],"month":"11","date_updated":"2024-02-21T13:48:16Z","status":"public","ddc":["576"],"contributor":[{"contributor_type":"contact_person","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2017-11-06T00:00:00Z","_id":"5571","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_created":"2018-12-12T12:31:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","license":"https://creativecommons.org/publicdomain/zero/1.0/","department":[{"_id":"BeVi"}],"article_processing_charge":"No","year":"2017","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"research_paper","id":"542"}]},"author":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"type":"research_data","day":"06"},{"_id":"5572","date_published":"2017-11-06T00:00:00Z","ddc":["576"],"status":"public","date_updated":"2024-02-21T13:48:28Z","month":"11","file":[{"date_updated":"2020-07-14T12:47:05Z","creator":"system","date_created":"2018-12-12T13:05:15Z","file_id":"5643","file_size":49823,"content_type":"application/zip","file_name":"IST-2017-79-v1+1_Code.zip","checksum":"3e70a7bcd6ff0c38b79e4c8a7d137034","access_level":"open_access","relation":"main_file"}],"doi":"10.15479/AT:ISTA:79 ","citation":{"ista":"Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>.","ieee":"B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017.","mla":"Vicoso, Beatriz. <i>Code for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>.","apa":"Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">https://doi.org/10.15479/AT:ISTA:79 </a>","ama":"Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>","short":"B. Vicoso, (2017).","chicago":"Vicoso, Beatriz. “Code for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">https://doi.org/10.15479/AT:ISTA:79 </a>."},"file_date_updated":"2020-07-14T12:47:05Z","abstract":[{"text":"Code described in the Supplementary Methods of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.)","lang":"eng"}],"datarep_id":"79","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Code for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","type":"research_data","day":"06","author":[{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"542"}]},"has_accepted_license":"1","year":"2017","article_processing_charge":"No","department":[{"_id":"BeVi"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:36Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"}},{"publisher":"The Royal Society","abstract":[{"lang":"eng","text":"Immune specificity is the degree to which a host’s immune system discriminates among various pathogens or antigenic variants. Vertebrate immune memory is highly specific due to antibody responses. On the other hand, some invertebrates show immune priming, i.e. improved survival after secondary exposure to a previously encountered pathogen. Until now, specificity of priming has only been demonstrated via the septic infection route or when live pathogens were used for priming. Therefore, we tested for specificity in the oral priming route in the red flour beetle, Tribolium castaneum. For priming, we used pathogen-free supernatants derived from three different strains of the entomopathogen, Bacillus thuringiensis, which express different Cry toxin variants known for their toxicity against this beetle. Subsequent exposure to the infective spores showed that oral priming was specific for two naturally occurring strains, while a third engineered strain did not induce any priming effect. Our data demonstrate that oral immune priming with a non-infectious bacterial agent can be specific, but the priming effect is not universal across all bacterial strains."}],"citation":{"apa":"Futo, M., Sell, M., Kutzer, M., &#38; Kurtz, J. (2017). Specificity of oral immune priming in the red flour beetle Tribolium castaneum. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2017.0632\">https://doi.org/10.1098/rsbl.2017.0632</a>","mla":"Futo, Momir, et al. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” <i>Biology Letters</i>, vol. 13, no. 12, 0632, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0632\">10.1098/rsbl.2017.0632</a>.","chicago":"Futo, Momir, Marie Sell, Megan Kutzer, and Joachim Kurtz. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” <i>Biology Letters</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsbl.2017.0632\">https://doi.org/10.1098/rsbl.2017.0632</a>.","short":"M. Futo, M. Sell, M. Kutzer, J. Kurtz, Biology Letters 13 (2017).","ama":"Futo M, Sell M, Kutzer M, Kurtz J. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. <i>Biology Letters</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0632\">10.1098/rsbl.2017.0632</a>","ista":"Futo M, Sell M, Kutzer M, Kurtz J. 2017. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. 13(12), 0632.","ieee":"M. Futo, M. Sell, M. Kutzer, and J. Kurtz, “Specificity of oral immune priming in the red flour beetle Tribolium castaneum,” <i>Biology Letters</i>, vol. 13, no. 12. The Royal Society, 2017."},"month":"12","scopus_import":"1","date_updated":"2023-10-18T06:42:25Z","publist_id":"7255","date_published":"2017-12-01T00:00:00Z","_id":"558","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:10Z","publication_status":"published","pmid":1,"year":"2017","author":[{"full_name":"Futo, Momir","last_name":"Futo","first_name":"Momir"},{"first_name":"Marie","last_name":"Sell","full_name":"Sell, Marie"},{"full_name":"Kutzer, Megan","last_name":"Kutzer","orcid":"0000-0002-8696-6978","first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kurtz, Joachim","first_name":"Joachim","last_name":"Kurtz"}],"title":"Specificity of oral immune priming in the red flour beetle Tribolium castaneum","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1098/rsbl.2017.0632","intvolume":"        13","publication_identifier":{"issn":["1744-9561"]},"status":"public","publication":"Biology Letters","external_id":{"pmid":["29237813"]},"volume":13,"oa_version":"None","article_number":"0632","article_type":"original","department":[{"_id":"SyCr"}],"issue":"12","article_processing_charge":"No","day":"01","type":"journal_article"},{"year":"2017","author":[{"full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","last_name":"Abusalah"},{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F"},{"last_name":"Cohen","first_name":"Bram","full_name":"Cohen, Bram"},{"full_name":"Khilko, Danylo","last_name":"Khilko","first_name":"Danylo"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:10Z","publication_status":"published","month":"11","scopus_import":1,"date_updated":"2023-09-07T12:30:22Z","ec_funded":1,"publist_id":"7257","date_published":"2017-11-18T00:00:00Z","_id":"559","publisher":"Springer","abstract":[{"text":"Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).","lang":"eng"}],"citation":{"ieee":"H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L. Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.","ista":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625, 357–379.","chicago":"Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space,” 10625:357–79. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">https://doi.org/10.1007/978-3-319-70697-9_13</a>.","ama":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer; 2017:357-379. doi:<a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">10.1007/978-3-319-70697-9_13</a>","short":"H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379.","apa":"Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., &#38; Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China: Springer. <a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">https://doi.org/10.1007/978-3-319-70697-9_13</a>","mla":"Abusalah, Hamza M., et al. <i>Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space</i>. Vol. 10625, Springer, 2017, pp. 357–79, doi:<a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">10.1007/978-3-319-70697-9_13</a>."},"department":[{"_id":"KrPi"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"83"}]},"day":"18","type":"conference","conference":{"start_date":"2017-12-03","name":"ASIACRYPT: Theory and Applications of Cryptology and Information Security","end_date":"2017-12-07","location":"Hong Kong, China"},"volume":10625,"oa_version":"Submitted Version","project":[{"call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"publication_identifier":{"isbn":["978-331970696-2"]},"status":"public","title":"Beyond Hellman’s time-memory trade-offs with applications to proofs of space","quality_controlled":"1","page":"357 - 379","main_file_link":[{"url":"https://eprint.iacr.org/2017/893.pdf","open_access":"1"}],"oa":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-70697-9_13","intvolume":"     10625"},{"day":"01","type":"journal_article","issue":"2207","department":[{"_id":"JaMa"}],"oa_version":"Submitted Version","article_number":"0104","volume":473,"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","status":"public","publication_identifier":{"issn":["13645021"]},"project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"intvolume":"       473","language":[{"iso":"eng"}],"doi":"10.1098/rspa.2017.0104","main_file_link":[{"url":"https://arxiv.org/abs/1702.03229","open_access":"1"}],"oa":1,"title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","quality_controlled":"1","author":[{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","first_name":"Mate"},{"first_name":"Arnulf","last_name":"Jentzen","full_name":"Jentzen, Arnulf"},{"full_name":"Salimova, Diyora","last_name":"Salimova","first_name":"Diyora"}],"year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:47:11Z","_id":"560","ec_funded":1,"publist_id":"7256","date_published":"2017-11-01T00:00:00Z","month":"11","scopus_import":1,"date_updated":"2021-01-12T08:03:04Z","abstract":[{"text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.","lang":"eng"}],"citation":{"ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 473, no. 2207. Royal Society of London, 2017.","apa":"Gerencser, M., Jentzen, A., &#38; Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rspa.2017.0104\">https://doi.org/10.1098/rspa.2017.0104</a>","mla":"Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rspa.2017.0104\">10.1098/rspa.2017.0104</a>.","chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rspa.2017.0104\">https://doi.org/10.1098/rspa.2017.0104</a>.","short":"M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017).","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2017;473(2207). doi:<a href=\"https://doi.org/10.1098/rspa.2017.0104\">10.1098/rspa.2017.0104</a>"},"publisher":"Royal Society of London"},{"title":"Effects of mutations in phage restriction sites during escape from restriction–modification","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2017.0646"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsbl.2017.0646","intvolume":"        13","project":[{"grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)"},{"grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"status":"public","publication_identifier":{"issn":["1744-9561"]},"external_id":{"pmid":["29237814"]},"publication":"Biology Letters","volume":13,"oa_version":"Published Version","article_number":"20170646","article_type":"original","department":[{"_id":"CaGu"}],"article_processing_charge":"No","issue":"12","related_material":{"record":[{"relation":"research_data","id":"9847","status":"public"},{"relation":"dissertation_contains","id":"202","status":"public"}]},"day":"01","type":"journal_article","publisher":"The Royal Society","abstract":[{"lang":"eng","text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape."}],"citation":{"ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” <i>Biology Letters</i>, vol. 13, no. 12. The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>.","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>.","apa":"Pleska, M., &#38; Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>"},"acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","month":"12","date_updated":"2023-09-07T11:59:32Z","scopus_import":"1","publist_id":"7253","date_published":"2017-12-01T00:00:00Z","_id":"561","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:47:11Z","pmid":1,"year":"2017","author":[{"full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}]},{"publisher":"American Mathematical Society","citation":{"ieee":"L. Erdös and H. Yau, <i>A Dynamical Approach to Random Matrix Theory</i>, vol. 28. American Mathematical Society, 2017.","ista":"Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p.","chicago":"Erdös, László, and Horng Yau. <i>A Dynamical Approach to Random Matrix Theory</i>. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/cln/028\">https://doi.org/10.1090/cln/028</a>.","ama":"Erdös L, Yau H. <i>A Dynamical Approach to Random Matrix Theory</i>. Vol 28. American Mathematical Society; 2017. doi:<a href=\"https://doi.org/10.1090/cln/028\">10.1090/cln/028</a>","short":"L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017.","apa":"Erdös, L., &#38; Yau, H. (2017). <i>A Dynamical Approach to Random Matrix Theory</i> (Vol. 28). American Mathematical Society. <a href=\"https://doi.org/10.1090/cln/028\">https://doi.org/10.1090/cln/028</a>","mla":"Erdös, László, and Horng Yau. <i>A Dynamical Approach to Random Matrix Theory</i>. Vol. 28, American Mathematical Society, 2017, doi:<a href=\"https://doi.org/10.1090/cln/028\">10.1090/cln/028</a>."},"abstract":[{"text":"This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n","lang":"eng"}],"series_title":"Courant Lecture Notes","month":"01","date_updated":"2022-05-24T06:57:28Z","_id":"567","ec_funded":1,"date_published":"2017-01-01T00:00:00Z","publist_id":"7247","publication_status":"published","date_created":"2018-12-11T11:47:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng"}],"year":"2017","page":"226","title":"A Dynamical Approach to Random Matrix Theory","quality_controlled":"1","intvolume":"        28","alternative_title":["Courant Lecture Notes"],"language":[{"iso":"eng"}],"doi":"10.1090/cln/028","status":"public","publication_identifier":{"isbn":["9-781-4704-3648-3"],"eisbn":["978-1-4704-4194-4"]},"project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"oa_version":"None","volume":28,"department":[{"_id":"LaEr"}],"day":"01","type":"book","article_processing_charge":"No"},{"publisher":"International Press","abstract":[{"text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z&lt; r(f) := (g-1(0): ||g - f|| &lt; r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z&lt; r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r &gt; 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).","lang":"eng"}],"citation":{"ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” <i>Homology, Homotopy and Applications</i>, vol. 19, no. 2. International Press, pp. 313–342, 2017.","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342.","chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” <i>Homology, Homotopy and Applications</i>. International Press, 2017. <a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">https://doi.org/10.4310/HHA.2017.v19.n2.a16</a>.","ama":"Franek P, Krcál M. Persistence of zero sets. <i>Homology, Homotopy and Applications</i>. 2017;19(2):313-342. doi:<a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">10.4310/HHA.2017.v19.n2.a16</a>","short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","apa":"Franek, P., &#38; Krcál, M. (2017). Persistence of zero sets. <i>Homology, Homotopy and Applications</i>. International Press. <a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">https://doi.org/10.4310/HHA.2017.v19.n2.a16</a>","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” <i>Homology, Homotopy and Applications</i>, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:<a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">10.4310/HHA.2017.v19.n2.a16</a>."},"scopus_import":1,"date_updated":"2021-01-12T08:03:12Z","month":"01","_id":"568","publist_id":"7246","date_published":"2017-01-01T00:00:00Z","ec_funded":1,"publication_status":"published","date_created":"2018-12-11T11:47:14Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek","first_name":"Peter"},{"full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Krcál"}],"year":"2017","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.04310"}],"oa":1,"page":"313 - 342","quality_controlled":"1","title":"Persistence of zero sets","intvolume":"        19","doi":"10.4310/HHA.2017.v19.n2.a16","language":[{"iso":"eng"}],"status":"public","publication_identifier":{"issn":["15320073"]},"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"701309","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"publication":"Homology, Homotopy and Applications","oa_version":"Submitted Version","volume":19,"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"day":"01","type":"journal_article","issue":"2"},{"date_updated":"2023-02-23T12:30:29Z","scopus_import":1,"month":"11","publist_id":"7245","date_published":"2017-11-06T00:00:00Z","_id":"569","publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:10Z","abstract":[{"text":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.","lang":"eng"}],"citation":{"apa":"Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.30867\">https://doi.org/10.7554/eLife.30867</a>","mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” <i>ELife</i>, vol. 6, e30867, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.30867\">10.7554/eLife.30867</a>.","chicago":"Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.30867\">https://doi.org/10.7554/eLife.30867</a>.","ama":"Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.30867\">10.7554/eLife.30867</a>","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).","ista":"Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867.","ieee":"F. Spira <i>et al.</i>, “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017."},"has_accepted_license":"1","year":"2017","author":[{"first_name":"Felix","last_name":"Spira","full_name":"Spira, Felix"},{"full_name":"Cuylen Haering, Sara","last_name":"Cuylen Haering","first_name":"Sara"},{"first_name":"Shalin","last_name":"Mehta","full_name":"Mehta, Shalin"},{"last_name":"Samwer","first_name":"Matthias","full_name":"Samwer, Matthias"},{"last_name":"Reversat","orcid":"0000-0003-0666-8928","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne"},{"full_name":"Verma, Amitabh","first_name":"Amitabh","last_name":"Verma"},{"first_name":"Rudolf","last_name":"Oldenbourg","full_name":"Oldenbourg, Rudolf"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"last_name":"Gerlich","first_name":"Daniel","full_name":"Gerlich, Daniel"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:14Z","pubrep_id":"919","status":"public","publication_identifier":{"issn":["2050084X"]},"publication":"eLife","ddc":["570"],"quality_controlled":"1","title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments","oa":1,"doi":"10.7554/eLife.30867","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","file_size":9666973,"file_id":"4829","date_created":"2018-12-12T10:10:40Z","access_level":"open_access","relation":"main_file","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","checksum":"ba09c1451153d39e4f4b7cee013e314c","date_updated":"2020-07-14T12:47:10Z","creator":"system"},{"creator":"system","date_updated":"2020-07-14T12:47:10Z","access_level":"open_access","relation":"main_file","file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf","checksum":"01eb51f1d6ad679947415a51c988e137","content_type":"application/pdf","file_size":5951246,"date_created":"2018-12-12T10:10:41Z","file_id":"4830"}],"intvolume":"         6","department":[{"_id":"MiSi"}],"type":"journal_article","day":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":6,"license":"https://creativecommons.org/licenses/by/4.0/","article_number":"e30867","oa_version":"Published Version"},{"month":"11","date_updated":"2021-01-12T08:03:15Z","scopus_import":1,"ec_funded":1,"publist_id":"7244","date_published":"2017-11-13T00:00:00Z","_id":"570","publisher":"eLife Sciences Publications","citation":{"ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921.","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” <i>ELife</i>, vol. 6, e28921, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.28921\">10.7554/eLife.28921</a>.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., &#38; Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.28921\">https://doi.org/10.7554/eLife.28921</a>","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.28921\">10.7554/eLife.28921</a>","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.28921\">https://doi.org/10.7554/eLife.28921</a>."},"file_date_updated":"2020-07-14T12:47:10Z","abstract":[{"text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ","lang":"eng"}],"year":"2017","has_accepted_license":"1","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sarikas","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan"},{"id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","last_name":"Acar","first_name":"Hande","full_name":"Acar, Hande"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:47:14Z","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"},{"call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"pubrep_id":"918","status":"public","publication_identifier":{"issn":["2050084X"]},"ddc":["576"],"publication":"eLife","title":"Regulatory network structure determines patterns of intermolecular epistasis","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.28921","intvolume":"         6","file":[{"file_id":"5096","date_created":"2018-12-12T10:14:42Z","content_type":"application/pdf","file_size":8453470,"file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","checksum":"273ab17f33305e4eaafd911ff88e7c5b","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:10Z","creator":"system"},{"creator":"system","date_updated":"2020-07-14T12:47:10Z","checksum":"b433f90576c7be597cd43367946f8e7f","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","relation":"main_file","access_level":"open_access","file_id":"5097","date_created":"2018-12-12T10:14:43Z","content_type":"application/pdf","file_size":1953221}],"department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"type":"journal_article","day":"13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":6,"oa_version":"Published Version","article_number":"e28921"},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:15Z","year":"2017","author":[{"last_name":"Gärtner","orcid":"0000-0001-6120-3723","first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"},{"full_name":"Ahmad, Zerkah","last_name":"Ahmad","first_name":"Zerkah"},{"last_name":"Rosenberger","first_name":"Gerhild","full_name":"Rosenberger, Gerhild"},{"last_name":"Fan","first_name":"Shuxia","full_name":"Fan, Shuxia"},{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"full_name":"Busch, Benjamin","last_name":"Busch","first_name":"Benjamin"},{"first_name":"Gökce","last_name":"Yavuz","full_name":"Yavuz, Gökce"},{"full_name":"Luckner, Manja","first_name":"Manja","last_name":"Luckner"},{"last_name":"Ishikawa Ankerhold","first_name":"Hellen","full_name":"Ishikawa Ankerhold, Hellen"},{"first_name":"Roman","last_name":"Hennel","full_name":"Hennel, Roman"},{"full_name":"Benechet, Alexandre","last_name":"Benechet","first_name":"Alexandre"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"first_name":"Sue","last_name":"Chandraratne","full_name":"Chandraratne, Sue"},{"last_name":"Schubert","first_name":"Irene","full_name":"Schubert, Irene"},{"full_name":"Helmer, Sebastian","last_name":"Helmer","first_name":"Sebastian"},{"full_name":"Striednig, Bianca","last_name":"Striednig","first_name":"Bianca"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"last_name":"Janko","first_name":"Marek","full_name":"Janko, Marek"},{"full_name":"Böttcher, Ralph","first_name":"Ralph","last_name":"Böttcher"},{"full_name":"Verschoor, Admar","last_name":"Verschoor","first_name":"Admar"},{"last_name":"Leon","first_name":"Catherine","full_name":"Leon, Catherine"},{"first_name":"Christian","last_name":"Gachet","full_name":"Gachet, Christian"},{"full_name":"Gudermann, Thomas","first_name":"Thomas","last_name":"Gudermann"},{"first_name":"Michael","last_name":"Mederos Y Schnitzler","full_name":"Mederos Y Schnitzler, Michael"},{"first_name":"Zachary","last_name":"Pincus","full_name":"Pincus, Zachary"},{"full_name":"Iannacone, Matteo","last_name":"Iannacone","first_name":"Matteo"},{"full_name":"Haas, Rainer","first_name":"Rainer","last_name":"Haas"},{"full_name":"Wanner, Gerhard","first_name":"Gerhard","last_name":"Wanner"},{"last_name":"Lauber","first_name":"Kirsten","full_name":"Lauber, Kirsten"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"}],"publisher":"Cell Press","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface.","lang":"eng"}],"citation":{"ista":"Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.","ieee":"F. R. Gärtner <i>et al.</i>, “Migrating platelets are mechano scavengers that collect and bundle bacteria,” <i>Cell Press</i>, vol. 171, no. 6. Cell Press, pp. 1368–1382, 2017.","mla":"Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” <i>Cell Press</i>, vol. 171, no. 6, Cell Press, 2017, pp. 1368–82, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">10.1016/j.cell.2017.11.001</a>.","apa":"Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B., … Massberg, S. (2017). Migrating platelets are mechano scavengers that collect and bundle bacteria. <i>Cell Press</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">https://doi.org/10.1016/j.cell.2017.11.001</a>","ama":"Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano scavengers that collect and bundle bacteria. <i>Cell Press</i>. 2017;171(6):1368-1382. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">10.1016/j.cell.2017.11.001</a>","short":"F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G. Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S. Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher, A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus, M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press 171 (2017) 1368–1382.","chicago":"Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” <i>Cell Press</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">https://doi.org/10.1016/j.cell.2017.11.001</a>."},"month":"11","scopus_import":1,"date_updated":"2021-01-12T08:03:15Z","ec_funded":1,"date_published":"2017-11-30T00:00:00Z","publist_id":"7243","_id":"571","volume":171,"oa_version":"None","department":[{"_id":"MiSi"}],"issue":"6","day":"30","type":"journal_article","title":"Migrating platelets are mechano scavengers that collect and bundle bacteria","quality_controlled":"1","page":"1368 - 1382","language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2017.11.001","intvolume":"       171","project":[{"call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"status":"public","publication_identifier":{"issn":["00928674"]},"publication":"Cell Press"},{"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:15Z","has_accepted_license":"1","year":"2017","author":[{"full_name":"Olatunji, Damilola","first_name":"Damilola","last_name":"Olatunji"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"}],"citation":{"ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” <i>International Journal of Molecular Sciences</i>, vol. 18, no. 12. MDPI, 2017.","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587.","chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” <i>International Journal of Molecular Sciences</i>. MDPI, 2017. <a href=\"https://doi.org/10.3390/ijms18122587\">https://doi.org/10.3390/ijms18122587</a>.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. <i>International Journal of Molecular Sciences</i>. 2017;18(12). doi:<a href=\"https://doi.org/10.3390/ijms18122587\">10.3390/ijms18122587</a>","apa":"Olatunji, D., Geelen, D., &#38; Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms18122587\">https://doi.org/10.3390/ijms18122587</a>","mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” <i>International Journal of Molecular Sciences</i>, vol. 18, no. 12, 2587, MDPI, 2017, doi:<a href=\"https://doi.org/10.3390/ijms18122587\">10.3390/ijms18122587</a>."},"abstract":[{"lang":"eng","text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture."}],"file_date_updated":"2020-07-14T12:47:10Z","publisher":"MDPI","date_published":"2017-12-01T00:00:00Z","publist_id":"7242","_id":"572","date_updated":"2021-01-12T08:03:16Z","scopus_import":"1","month":"12","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":18,"article_number":"2587","oa_version":"Published Version","issue":"12","article_processing_charge":"No","day":"01","type":"journal_article","department":[{"_id":"JiFr"}],"doi":"10.3390/ijms18122587","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:10Z","creator":"system","content_type":"application/pdf","file_size":920962,"date_created":"2018-12-12T10:08:55Z","file_id":"4718","access_level":"open_access","relation":"main_file","file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","checksum":"82d51f11e493f7eec02976d9a9a9805e"}],"intvolume":"        18","quality_controlled":"1","title":"Control of endogenous auxin levels in plant root development","oa":1,"publication":"International Journal of Molecular Sciences","ddc":["580"],"pubrep_id":"917","status":"public"},{"month":"01","date_updated":"2021-01-12T08:03:33Z","status":"public","publication_identifier":{"issn":["0166-218X"]},"date_published":"2017-01-10T00:00:00Z","publication":"Discrete Applied Mathematics","_id":"5799","title":"On the polyhedra of graceful spheres and circular geodesics","quality_controlled":"1","page":"362-375","publisher":"Elsevier","abstract":[{"lang":"eng","text":"We construct a polyhedral surface called a graceful surface, which provides best possible approximation to a given sphere regarding certain criteria. In digital geometry terms, the graceful surface is uniquely characterized by its minimality while guaranteeing the connectivity of certain discrete (polyhedral) curves defined on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva (1999) and shown to be useful for triangular mesh discretization through graceful planes and graceful lines. In this paper we extend the considerations to a nonlinear object such as a sphere. In particular, we investigate the properties of a discrete geodesic path between two voxels and show that discrete 3D circles, circular arcs, and Mobius triangles are all constructible on a graceful sphere, with guaranteed minimum thickness and the desired connectivity in the discrete topological space."}],"language":[{"iso":"eng"}],"citation":{"mla":"Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” <i>Discrete Applied Mathematics</i>, vol. 216, Elsevier, 2017, pp. 362–75, doi:<a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">10.1016/j.dam.2015.11.017</a>.","apa":"Biswas, R., Bhowmick, P., &#38; Brimkov, V. E. (2017). On the polyhedra of graceful spheres and circular geodesics. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">https://doi.org/10.1016/j.dam.2015.11.017</a>","ama":"Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and circular geodesics. <i>Discrete Applied Mathematics</i>. 2017;216:362-375. doi:<a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">10.1016/j.dam.2015.11.017</a>","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017) 362–375.","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” <i>Discrete Applied Mathematics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">https://doi.org/10.1016/j.dam.2015.11.017</a>.","ista":"Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 216, 362–375.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres and circular geodesics,” <i>Discrete Applied Mathematics</i>, vol. 216. Elsevier, pp. 362–375, 2017."},"doi":"10.1016/j.dam.2015.11.017","intvolume":"       216","year":"2017","author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","last_name":"Biswas","first_name":"Ranita"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"},{"full_name":"Brimkov, Valentin E.","last_name":"Brimkov","first_name":"Valentin E."}],"type":"journal_article","day":"10","volume":216,"date_created":"2019-01-08T20:41:12Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","extern":"1"},{"publication_identifier":{"issn":["09249907"]},"status":"public","date_updated":"2021-01-12T08:03:34Z","month":"09","_id":"5800","date_published":"2017-09-01T00:00:00Z","publication":"Journal of Mathematical Imaging and Vision","publisher":"Springer Nature","page":"69-83","quality_controlled":"1","title":"On the functionality and usefulness of Quadraginta octants of naive sphere","intvolume":"        59","doi":"10.1007/s10851-017-0718-4","citation":{"ista":"Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83.","ieee":"R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta octants of naive sphere,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 59, no. 1. Springer Nature, pp. 69–83, 2017.","apa":"Biswas, R., &#38; Bhowmick, P. (2017). On the functionality and usefulness of Quadraginta octants of naive sphere. <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10851-017-0718-4\">https://doi.org/10.1007/s10851-017-0718-4</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:<a href=\"https://doi.org/10.1007/s10851-017-0718-4\">10.1007/s10851-017-0718-4</a>.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10851-017-0718-4\">https://doi.org/10.1007/s10851-017-0718-4</a>.","short":"R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017) 69–83.","ama":"Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants of naive sphere. <i>Journal of Mathematical Imaging and Vision</i>. 2017;59(1):69-83. doi:<a href=\"https://doi.org/10.1007/s10851-017-0718-4\">10.1007/s10851-017-0718-4</a>"},"language":[{"iso":"eng"}],"abstract":[{"text":"This paper presents a novel study on the functional gradation of coordinate planes in connection with the thinnest and tunnel-free (i.e., naive) discretization of sphere in the integer space. For each of the 48-symmetric quadraginta octants of naive sphere with integer radius and integer center, we show that the corresponding voxel set forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as its functional plane. We use this fundamental property to prove several other theoretical results for naive sphere. First, the quadraginta octants form symmetry groups and subgroups with certain equivalent topological properties. Second, a naive sphere is always unique and consists of fewest voxels. Third, it is efficiently constructible from its functional-plane projection. And finally, a special class of 4-symmetric discrete 3D circles can be constructed on a naive sphere based on back projection from the functional plane.","lang":"eng"}],"day":"01","type":"journal_article","author":[{"first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"year":"2017","issue":"1","oa_version":"None","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-01-08T20:42:08Z","volume":59,"extern":"1"},{"status":"public","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-319-66271-8"],"eissn":["1611-3349"],"eisbn":["978-3-319-66272-5"]},"month":"08","date_updated":"2022-01-27T15:34:25Z","_id":"5801","date_published":"2017-08-22T00:00:00Z","publication":"20th IAPR International Conference","page":"347-359","publisher":"Springer Nature","place":"Cham","title":"Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space","quality_controlled":"1","intvolume":"     10502","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Space filling circles and spheres have various applications in mathematical imaging and physical modeling. In this paper, we first show how the thinnest (i.e., 2-minimal) model of digital sphere can be augmented to a space filling model by fixing certain “simple voxels” and “filler voxels” associated with it. Based on elementary number-theoretic properties of such voxels, we design an efficient incremental algorithm for generation of these space filling spheres with successively increasing radius. The novelty of the proposed technique is established further through circular space filling on 3D digital plane. As evident from a preliminary set of experimental result, this can particularly be useful for parallel computing of 3D Voronoi diagrams in the digital space."}],"citation":{"ista":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 347–359.","ieee":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space,” in <i>20th IAPR International Conference</i>, Vienna, Austria, 2017, vol. 10502, pp. 347–359.","apa":"Dwivedi, S., Gupta, A., Roy, S., Biswas, R., &#38; Bhowmick, P. (2017). Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In <i>20th IAPR International Conference</i> (Vol. 10502, pp. 347–359). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">https://doi.org/10.1007/978-3-319-66272-5_28</a>","mla":"Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” <i>20th IAPR International Conference</i>, vol. 10502, Springer Nature, 2017, pp. 347–59, doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">10.1007/978-3-319-66272-5_28</a>.","chicago":"Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” In <i>20th IAPR International Conference</i>, 10502:347–59. Cham: Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">https://doi.org/10.1007/978-3-319-66272-5_28</a>.","ama":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In: <i>20th IAPR International Conference</i>. Vol 10502. Cham: Springer Nature; 2017:347-359. doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">10.1007/978-3-319-66272-5_28</a>","short":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 347–359."},"doi":"10.1007/978-3-319-66272-5_28","author":[{"last_name":"Dwivedi","first_name":"Shivam","full_name":"Dwivedi, Shivam"},{"full_name":"Gupta, Aniket","last_name":"Gupta","first_name":"Aniket"},{"first_name":"Siddhant","last_name":"Roy","full_name":"Roy, Siddhant"},{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","orcid":"0000-0002-5372-7890","first_name":"Ranita","full_name":"Biswas, Ranita"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"type":"conference","day":"22","conference":{"location":"Vienna, Austria","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2017-09-21","start_date":"2017-09-19"},"article_processing_charge":"No","year":"2017","oa_version":"None","volume":10502,"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2019-01-08T20:42:22Z","extern":"1"},{"volume":10502,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","date_created":"2019-01-08T20:42:39Z","oa_version":"None","extern":"1","article_processing_charge":"No","year":"2017","author":[{"first_name":"Eric","last_name":"Andres","full_name":"Andres, Eric"},{"full_name":"Biswas, Ranita","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"type":"conference","day":"22","conference":{"start_date":"2017-09-19","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2017-09-21","location":"Vienna, Austria"},"title":"Digital primitives defined by weighted focal set","place":"Cham","quality_controlled":"1","page":"388-398","publisher":"Springer Nature","language":[{"iso":"eng"}],"citation":{"ieee":"E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted focal set,” in <i>20th IAPR International Conference</i>, Vienna, Austria, 2017, vol. 10502, pp. 388–398.","ista":"Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted focal set. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.","chicago":"Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives Defined by Weighted Focal Set.” In <i>20th IAPR International Conference</i>, 10502:388–98. Cham: Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">https://doi.org/10.1007/978-3-319-66272-5_31</a>.","ama":"Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal set. In: <i>20th IAPR International Conference</i>. Vol 10502. Cham: Springer Nature; 2017:388-398. doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">10.1007/978-3-319-66272-5_31</a>","short":"E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 388–398.","apa":"Andres, E., Biswas, R., &#38; Bhowmick, P. (2017). Digital primitives defined by weighted focal set. In <i>20th IAPR International Conference</i> (Vol. 10502, pp. 388–398). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">https://doi.org/10.1007/978-3-319-66272-5_31</a>","mla":"Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” <i>20th IAPR International Conference</i>, vol. 10502, Springer Nature, 2017, pp. 388–98, doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">10.1007/978-3-319-66272-5_31</a>."},"abstract":[{"lang":"eng","text":"This papers introduces a definition of digital primitives based on focal points and weighted distances (with positive weights). The proposed definition is applicable to general dimensions and covers in its gamut various regular curves and surfaces like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids, Cartesian k-ovals, etc. Several interesting properties are presented for this class of digital primitives such as space partitioning, topological separation, and connectivity properties. To demonstrate further the potential of this new way of defining digital primitives, we propose, as extension, another class of digital conics defined by focus-directrix combination."}],"alternative_title":["LNCS"],"doi":"10.1007/978-3-319-66272-5_31","intvolume":"     10502","month":"08","date_updated":"2022-01-27T15:38:35Z","publication_identifier":{"eissn":["1611-3349"],"eisbn":["978-3-319-66272-5"],"issn":["0302-9743"],"isbn":["978-3-319-66271-8"]},"status":"public","date_published":"2017-08-22T00:00:00Z","publication":"20th IAPR International Conference","_id":"5802"},{"place":"Cham","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept."}],"citation":{"ieee":"R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in <i>Combinatorial image analysis</i>, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.","ista":"Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.","short":"R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104.","ama":"Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: <i>Combinatorial Image Analysis</i>. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:<a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">10.1007/978-3-319-59108-7_8</a>","chicago":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In <i>Combinatorial Image Analysis</i>, 10256:93–104. Cham: Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">https://doi.org/10.1007/978-3-319-59108-7_8</a>.","mla":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” <i>Combinatorial Image Analysis</i>, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:<a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">10.1007/978-3-319-59108-7_8</a>.","apa":"Biswas, R., &#38; Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In <i>Combinatorial image analysis</i> (Vol. 10256, pp. 93–104). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">https://doi.org/10.1007/978-3-319-59108-7_8</a>"},"month":"05","date_updated":"2022-01-28T07:48:24Z","date_published":"2017-05-17T00:00:00Z","_id":"5803","date_created":"2019-01-08T20:42:56Z","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2017","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"title":"Construction of persistent Voronoi diagram on 3D digital plane","quality_controlled":"1","page":"93-104","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"doi":"10.1007/978-3-319-59108-7_8","intvolume":"     10256","status":"public","publication_identifier":{"isbn":["978-3-319-59107-0","978-3-319-59108-7"],"issn":["0302-9743","1611-3349"]},"publication":"Combinatorial image analysis","volume":10256,"oa_version":"None","extern":"1","department":[{"_id":"HeEd"}],"article_processing_charge":"No","type":"book_chapter","conference":{"name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2017-06-21","location":"Plovdiv, Bulgaria","start_date":"2017-06-19"},"day":"17"},{"title":"Bell correlations in spin-squeezed states of 500 000 atoms","publisher":"American Physical Society","abstract":[{"text":"Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements.","lang":"eng"}],"citation":{"ama":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed states of 500 000 atoms. <i>Physical Review Letters</i>. 2017;118(14). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">10.1103/PhysRevLett.118.140401</a>","short":"N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters 118 (2017).","chicago":"Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">https://doi.org/10.1103/PhysRevLett.118.140401</a>.","mla":"Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” <i>Physical Review Letters</i>, vol. 118, no. 14, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">10.1103/PhysRevLett.118.140401</a>.","apa":"Engelsen, N., Krishnakumar, R., Hosten, O., &#38; Kasevich, M. (2017). Bell correlations in spin-squeezed states of 500 000 atoms. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">https://doi.org/10.1103/PhysRevLett.118.140401</a>","ieee":"N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations in spin-squeezed states of 500 000 atoms,” <i>Physical Review Letters</i>, vol. 118, no. 14. American Physical Society, 2017.","ista":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14)."},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.118.140401","intvolume":"       118","month":"04","date_updated":"2021-01-12T08:05:16Z","status":"public","date_published":"2017-04-03T00:00:00Z","publication":"Physical Review Letters","publist_id":"7212","_id":"593","volume":118,"publication_status":"published","date_created":"2018-12-11T11:47:23Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","extern":"1","issue":"14","year":"2017","author":[{"last_name":"Engelsen","first_name":"Nils","full_name":"Engelsen, Nils"},{"full_name":"Krishnakumar, Rajiv","first_name":"Rajiv","last_name":"Krishnakumar"},{"full_name":"Hosten, Onur","last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","last_name":"Kasevich","full_name":"Kasevich, Mark"}],"day":"03","type":"journal_article"},{"status":"public","publication_identifier":{"issn":["00928674"]},"month":"03","date_updated":"2021-01-12T08:05:36Z","_id":"600","publication":"Cell","date_published":"2017-03-23T00:00:00Z","publist_id":"7204","page":"120 - 131.e22","publisher":"Cell Press","title":"Structural basis of RNA polymerase I transcription initiation","quality_controlled":"1","intvolume":"       169","language":[{"iso":"eng"}],"citation":{"mla":"Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription Initiation.” <i>Cell</i>, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">10.1016/j.cell.2017.03.003</a>.","apa":"Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C., … Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">https://doi.org/10.1016/j.cell.2017.03.003</a>","ama":"Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription initiation. <i>Cell</i>. 2017;169(1):120-131.e22. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">10.1016/j.cell.2017.03.003</a>","short":"C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C. Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.","chicago":"Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis of RNA Polymerase I Transcription Initiation.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">https://doi.org/10.1016/j.cell.2017.03.003</a>.","ista":"Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation. Cell. 169(1), 120–131.e22.","ieee":"C. Engel <i>et al.</i>, “Structural basis of RNA polymerase I transcription initiation,” <i>Cell</i>, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017."},"abstract":[{"text":"Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.","lang":"eng"}],"doi":"10.1016/j.cell.2017.03.003","author":[{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"},{"last_name":"Gubbey","first_name":"Tobias","full_name":"Gubbey, Tobias"},{"full_name":"Neyer, Simon","last_name":"Neyer","first_name":"Simon"},{"full_name":"Sainsbury, Sarah","first_name":"Sarah","last_name":"Sainsbury"},{"first_name":"Christiane","last_name":"Oberthuer","full_name":"Oberthuer, Christiane"},{"last_name":"Baejen","first_name":"Carlo","full_name":"Baejen, Carlo"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","last_name":"Bernecky","first_name":"Carrie A","full_name":"Bernecky, Carrie A"},{"full_name":"Cramer, Patrick","first_name":"Patrick","last_name":"Cramer"}],"day":"23","type":"journal_article","issue":"1","article_processing_charge":"No","year":"2017","oa_version":"None","volume":169,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:25Z","extern":"1"},{"year":"2017","has_accepted_license":"1","author":[{"full_name":"Xu, Youwei","last_name":"Xu","first_name":"Youwei"},{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky"},{"last_name":"Lee","first_name":"Chung","full_name":"Lee, Chung"},{"full_name":"Maier, Kerstin","last_name":"Maier","first_name":"Kerstin"},{"first_name":"Björn","last_name":"Schwalb","full_name":"Schwalb, Björn"},{"last_name":"Tegunov","first_name":"Dimitri","full_name":"Tegunov, Dimitri"},{"first_name":"Jürgen","last_name":"Plitzko","full_name":"Plitzko, Jürgen"},{"last_name":"Urlaub","first_name":"Henning","full_name":"Urlaub, Henning"},{"first_name":"Patrick","last_name":"Cramer","full_name":"Cramer, Patrick"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:47:25Z","publist_id":"7203","date_published":"2017-06-06T00:00:00Z","_id":"601","month":"06","date_updated":"2021-01-12T08:05:40Z","abstract":[{"text":"The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:16Z","citation":{"ista":"Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741.","ieee":"Y. Xu <i>et al.</i>, “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","apa":"Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer, P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>","mla":"Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>, vol. 8, 15741, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>.","chicago":"Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>.","short":"Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko, H. Urlaub, P. Cramer, Nature Communications 8 (2017).","ama":"Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>"},"publisher":"Nature Publishing Group","article_processing_charge":"No","type":"journal_article","day":"06","extern":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":8,"oa_version":"Published Version","article_number":"15741","ddc":["570"],"publication":"Nature Communications","publication_identifier":{"issn":["20411723"]},"status":"public","language":[{"iso":"eng"}],"doi":"10.1038/ncomms15741","intvolume":"         8","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:16Z","file_name":"2017_NatureComm_Xu.pdf","checksum":"940742282a9a285dc4aeae0c2b5ebe96","access_level":"open_access","relation":"main_file","date_created":"2019-01-21T14:48:10Z","file_id":"5865","content_type":"application/pdf","file_size":3018075}],"title":"Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex","quality_controlled":"1","oa":1}]