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Elegans","publisher":"Institute of Science and Technology Austria","day":"13","article_processing_charge":"No","author":[{"full_name":"Kainmueller, Dagmar","last_name":"Kainmueller","first_name":"Dagmar"},{"first_name":"Florian","last_name":"Jug","full_name":"Jug, Florian"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"},{"first_name":"Gene","full_name":"Meyers, Gene","last_name":"Meyers"}],"doi":"10.15479/AT:ISTA:57","date_created":"2018-12-12T12:31:32Z","type":"research_data","_id":"5561","date_updated":"2024-02-21T13:46:31Z","ddc":["000"],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"abstract":[{"lang":"eng","text":"Graph matching problems as described in \"Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans.\" by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. 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It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. 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Leithner, “Immunological synapse DC-Tcells.” Institute of Science and Technology Austria, 2017."},"status":"public","oa":1,"keyword":["Immunological synapse"],"file":[{"file_id":"5612","date_created":"2018-12-12T13:02:47Z","file_size":236204020,"creator":"system","date_updated":"2020-07-14T12:47:04Z","relation":"main_file","checksum":"3d6942d47d0737d064706b5728c4d8c8","file_name":"IST-2017-71-v1+1_Synapse_1.avi","access_level":"open_access","content_type":"video/x-msvideo"},{"relation":"main_file","checksum":"4850006c047b0147a9e85b3c2f6f0af4","file_name":"IST-2017-71-v1+2_Synapse_2.avi","content_type":"video/x-msvideo","access_level":"open_access","file_id":"5613","date_created":"2018-12-12T13:02:51Z","file_size":226232496,"creator":"system","date_updated":"2020-07-14T12:47:04Z"}],"department":[{"_id":"MiSi"}],"month":"08","year":"2017","file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"lang":"eng","text":"Immunological synapse DC-Tcells"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"ddc":["570"],"has_accepted_license":"1","type":"research_data","date_created":"2018-12-12T12:31:34Z","date_updated":"2024-02-21T13:47:00Z","_id":"5567","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","title":"Immunological synapse DC-Tcells","author":[{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","first_name":"Alexander F"}],"doi":"10.15479/AT:ISTA:71","day":"09","article_processing_charge":"No"},{"file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"lang":"eng","text":"Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)"}],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"ddc":["004"],"has_accepted_license":"1","type":"research_data","date_created":"2018-12-12T12:31:35Z","date_updated":"2024-02-21T13:48:02Z","_id":"5568","title":"Source codes: Brittle fracture simulation with boundary elements for computer graphics","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David","last_name":"Hahn"}],"doi":"10.15479/AT:ISTA:73","day":"16","article_processing_charge":"No","date_published":"2017-08-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"73","citation":{"chicago":"Hahn, David. “Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:73.","ista":"Hahn D. 2017. Source codes: Brittle fracture simulation with boundary elements for computer graphics, Institute of Science and Technology Austria, 10.15479/AT:ISTA:73.","mla":"Hahn, David. Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:73.","apa":"Hahn, D. (2017). Source codes: Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:73","ama":"Hahn D. Source codes: Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:10.15479/AT:ISTA:73","short":"D. Hahn, (2017).","ieee":"D. Hahn, “Source codes: Brittle fracture simulation with boundary elements for computer graphics.” Institute of Science and Technology Austria, 2017."},"ec_funded":1,"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"status":"public","oa":1,"keyword":["Boundary elements","brittle fracture","computer graphics","fracture simulation"],"file":[{"date_created":"2018-12-12T13:02:57Z","file_size":199353471,"date_updated":"2020-07-14T12:47:04Z","creator":"system","file_id":"5615","file_name":"IST-2017-73-v1+1_FractureRB_v1.1_2017_07_20_final_public.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"2323a755842a3399cbc47d76545fc9a0"}],"department":[{"_id":"ChWo"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"839"}]},"month":"08","year":"2017"},{"year":"2017","publist_id":"7254","status":"public","publication":"Investigative Ophthalmology and Visual Science","date_published":"2017-12-14T00:00:00Z","article_processing_charge":"No","doi":"10.1167/iovs.17-22634","publisher":"Association for Research in Vision and Ophthalmology","_id":"557","date_updated":"2023-10-10T14:06:18Z","type":"journal_article","page":"6091 - 6104","ddc":["576"],"quality_controlled":"1","month":"12","department":[{"_id":"SaSi"}],"file":[{"date_updated":"2020-07-14T12:47:04Z","creator":"system","date_created":"2018-12-12T10:17:53Z","file_size":2955559,"file_id":"5311","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-920-v1+1_i1552-5783-58-14-6091.pdf","checksum":"d7a7b6f1fa9211a04e5e65634a0265d9","relation":"main_file"}],"oa":1,"language":[{"iso":"eng"}],"pubrep_id":"920","citation":{"chicago":"Nickells, Robert, Heather Schmitt, Margaret E Maes, and Cassandra Schlamp. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology, 2017. https://doi.org/10.1167/iovs.17-22634.","ista":"Nickells R, Schmitt H, Maes ME, Schlamp C. 2017. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 58(14), 6091–6104.","mla":"Nickells, Robert, et al. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” Investigative Ophthalmology and Visual Science, vol. 58, no. 14, Association for Research in Vision and Ophthalmology, 2017, pp. 6091–104, doi:10.1167/iovs.17-22634.","apa":"Nickells, R., Schmitt, H., Maes, M. E., & Schlamp, C. (2017). AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/iovs.17-22634","ama":"Nickells R, Schmitt H, Maes ME, Schlamp C. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 2017;58(14):6091-6104. doi:10.1167/iovs.17-22634","short":"R. Nickells, H. Schmitt, M.E. Maes, C. Schlamp, Investigative Ophthalmology and Visual Science 58 (2017) 6091–6104.","ieee":"R. Nickells, H. Schmitt, M. E. Maes, and C. Schlamp, “AAV2 mediated transduction of the mouse retina after optic nerve injury,” Investigative Ophthalmology and Visual Science, vol. 58, no. 14. Association for Research in Vision and Ophthalmology, pp. 6091–6104, 2017."},"issue":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"14","scopus_import":"1","author":[{"full_name":"Nickells, Robert","last_name":"Nickells","first_name":"Robert"},{"full_name":"Schmitt, Heather","last_name":"Schmitt","first_name":"Heather"},{"last_name":"Maes","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085"},{"last_name":"Schlamp","full_name":"Schlamp, Cassandra","first_name":"Cassandra"}],"oa_version":"Published Version","title":"AAV2 mediated transduction of the mouse retina after optic nerve injury","volume":58,"date_created":"2018-12-11T11:47:10Z","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":" 58","abstract":[{"text":"PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:04Z","publication_status":"published","publication_identifier":{"issn":["01460404"]}},{"file_date_updated":"2020-07-14T12:47:04Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files."}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"has_accepted_license":"1","date_created":"2018-12-12T12:31:35Z","type":"research_data","_id":"5570","date_updated":"2024-02-21T13:47:14Z","oa_version":"Published Version","title":"Forward migration indexes","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","day":"04","author":[{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert"}],"doi":"10.15479/AT:ISTA:75","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-10-04T00:00:00Z","citation":{"short":"R. Hauschild, (2017).","ieee":"R. Hauschild, “Forward migration indexes.” Institute of Science and Technology Austria, 2017.","ama":"Hauschild R. Forward migration indexes. 2017. doi:10.15479/AT:ISTA:75","mla":"Hauschild, Robert. Forward Migration Indexes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:75.","apa":"Hauschild, R. (2017). Forward migration indexes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:75","chicago":"Hauschild, Robert. “Forward Migration Indexes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:75.","ista":"Hauschild R. 2017. Forward migration indexes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:75."},"datarep_id":"75","status":"public","oa":1,"file":[{"file_size":799,"date_created":"2018-12-12T13:02:29Z","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_id":"5596","file_name":"IST-2017-75-v1+1_FMI.m","access_level":"open_access","content_type":"application/octet-stream","relation":"main_file","checksum":"cb7a2fa622460eca6231d659ce590e32"}],"keyword":["Cell migration","tracking","forward migration index","FMI"],"department":[{"_id":"Bio"}],"month":"10","year":"2017"},{"day":"06","article_processing_charge":"No","contributor":[{"contributor_type":"contact_person","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:78","author":[{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"title":"Data for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","oa_version":"Submitted Version","publisher":"Institute of Science and Technology Austria","_id":"5571","date_updated":"2024-02-21T13:48:16Z","date_created":"2018-12-12T12:31:36Z","type":"research_data","has_accepted_license":"1","ddc":["576"],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"abstract":[{"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","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:04Z","year":"2017","related_material":{"record":[{"relation":"research_paper","status":"public","id":"542"}]},"month":"11","department":[{"_id":"BeVi"}],"file":[{"date_created":"2018-12-12T13:03:00Z","file_size":143697895,"creator":"system","date_updated":"2020-07-14T12:47:04Z","file_id":"5618","file_name":"IST-2017-78-v1+1_Data.zip","access_level":"open_access","content_type":"application/zip","relation":"main_file","checksum":"4520eb2b8379417ee916995719158f16"}],"oa":1,"status":"public","citation":{"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:10.15479/AT:ISTA:78","short":"B. Vicoso, (2017).","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.","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, 10.15479/AT:ISTA:78.","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. https://doi.org/10.15479/AT:ISTA:78.","mla":"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, doi:10.15479/AT:ISTA:78.","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. https://doi.org/10.15479/AT:ISTA:78"},"datarep_id":"78","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-11-06T00:00:00Z"},{"status":"public","oa":1,"date_published":"2017-11-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"79","citation":{"short":"B. Vicoso, (2017).","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.","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:10.15479/AT:ISTA:79 ","mla":"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, doi:10.15479/AT:ISTA:79 .","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. https://doi.org/10.15479/AT:ISTA:79 ","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. https://doi.org/10.15479/AT:ISTA:79 .","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, 10.15479/AT:ISTA:79 ."},"month":"11","related_material":{"record":[{"id":"542","relation":"research_paper","status":"public"}]},"year":"2017","file":[{"relation":"main_file","checksum":"3e70a7bcd6ff0c38b79e4c8a7d137034","file_name":"IST-2017-79-v1+1_Code.zip","content_type":"application/zip","access_level":"open_access","file_id":"5643","date_created":"2018-12-12T13:05:15Z","file_size":49823,"creator":"system","date_updated":"2020-07-14T12:47:05Z"}],"department":[{"_id":"BeVi"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"abstract":[{"lang":"eng","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.)"}],"ddc":["576"],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:05Z","title":"Code 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_version":"Submitted Version","doi":"10.15479/AT:ISTA:79 ","author":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"day":"06","article_processing_charge":"No","type":"research_data","date_created":"2018-12-12T12:31:36Z","date_updated":"2024-02-21T13:48:28Z","_id":"5572"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Futo M, Sell M, Kutzer M, Kurtz J. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0632","short":"M. Futo, M. Sell, M. Kutzer, J. Kurtz, Biology Letters 13 (2017).","ieee":"M. Futo, M. Sell, M. Kutzer, and J. Kurtz, “Specificity of oral immune priming in the red flour beetle Tribolium castaneum,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","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.","chicago":"Futo, Momir, Marie Sell, Megan Kutzer, and Joachim Kurtz. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0632.","mla":"Futo, Momir, et al. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” Biology Letters, vol. 13, no. 12, 0632, The Royal Society, 2017, doi:10.1098/rsbl.2017.0632.","apa":"Futo, M., Sell, M., Kutzer, M., & Kurtz, J. (2017). Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0632"},"issue":"12","language":[{"iso":"eng"}],"article_number":"0632","department":[{"_id":"SyCr"}],"month":"12","publication_status":"published","publication_identifier":{"issn":["1744-9561"]},"intvolume":" 13","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."}],"date_created":"2018-12-11T11:47:10Z","article_type":"original","volume":13,"oa_version":"None","title":"Specificity of oral immune priming in the red flour beetle Tribolium castaneum","day":"01","scopus_import":"1","author":[{"full_name":"Futo, Momir","last_name":"Futo","first_name":"Momir"},{"first_name":"Marie","full_name":"Sell, Marie","last_name":"Sell"},{"first_name":"Megan","orcid":"0000-0002-8696-6978","full_name":"Kutzer, Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer"},{"first_name":"Joachim","full_name":"Kurtz, Joachim","last_name":"Kurtz"}],"date_published":"2017-12-01T00:00:00Z","pmid":1,"publication":"Biology Letters","status":"public","publist_id":"7255","external_id":{"pmid":["29237813"]},"year":"2017","quality_controlled":"1","type":"journal_article","_id":"558","date_updated":"2023-10-18T06:42:25Z","publisher":"The Royal Society","article_processing_charge":"No","doi":"10.1098/rsbl.2017.0632"},{"abstract":[{"lang":"eng","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)."}],"intvolume":" 10625","publication_status":"published","publication_identifier":{"isbn":["978-331970696-2"]},"title":"Beyond Hellman’s time-memory trade-offs with applications to proofs of space","oa_version":"Submitted Version","author":[{"last_name":"Abusalah","full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"},{"first_name":"Joel F","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen"},{"first_name":"Bram","last_name":"Cohen","full_name":"Cohen, Bram"},{"last_name":"Khilko","full_name":"Khilko, Danylo","first_name":"Danylo"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"},{"first_name":"Leonid","full_name":"Reyzin, Leonid","last_name":"Reyzin"}],"scopus_import":1,"day":"18","date_created":"2018-12-11T11:47:10Z","volume":10625,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379.","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.","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:10.1007/978-3-319-70697-9_13","mla":"Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13.","apa":"Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., & 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. https://doi.org/10.1007/978-3-319-70697-9_13","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. https://doi.org/10.1007/978-3-319-70697-9_13."},"month":"11","department":[{"_id":"KrPi"}],"page":"357 - 379","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/893.pdf"}],"publisher":"Springer","doi":"10.1007/978-3-319-70697-9_13","alternative_title":["LNCS"],"type":"conference","date_updated":"2023-09-07T12:30:22Z","_id":"559","project":[{"call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"status":"public","date_published":"2017-11-18T00:00:00Z","conference":{"location":"Hong Kong, China","name":"ASIACRYPT: Theory and Applications of Cryptology and Information Security","start_date":"2017-12-03","end_date":"2017-12-07"},"ec_funded":1,"related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"year":"2017","publist_id":"7257"},{"year":"2017","publist_id":"7256","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_published":"2017-11-01T00:00:00Z","ec_funded":1,"publisher":"Royal Society of London","doi":"10.1098/rspa.2017.0104","type":"journal_article","_id":"560","date_updated":"2021-01-12T08:03:04Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.03229"}],"month":"11","article_number":"0104","department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “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, vol. 473, no. 2207. Royal Society of London, 2017.","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. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104","apa":"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. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104","mla":"Gerencser, Mate, et al. “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, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.","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.","chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “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. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104."},"issue":"2207","title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","oa_version":"Submitted Version","day":"01","scopus_import":1,"author":[{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","first_name":"Mate"},{"first_name":"Arnulf","full_name":"Jentzen, Arnulf","last_name":"Jentzen"},{"last_name":"Salimova","full_name":"Salimova, Diyora","first_name":"Diyora"}],"date_created":"2018-12-11T11:47:11Z","volume":473,"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"}],"intvolume":" 473","publication_status":"published","publication_identifier":{"issn":["13645021"]}},{"year":"2017","external_id":{"pmid":["29237814"]},"related_material":{"record":[{"id":"9847","status":"public","relation":"research_data"},{"id":"202","status":"public","relation":"dissertation_contains"}]},"publist_id":"7253","project":[{"grant_number":"RGY0079/2011","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"status":"public","publication":"Biology Letters","pmid":1,"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.","date_published":"2017-12-01T00:00:00Z","doi":"10.1098/rsbl.2017.0646","article_processing_charge":"No","publisher":"The Royal Society","date_updated":"2023-09-07T11:59:32Z","_id":"561","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"quality_controlled":"1","month":"12","department":[{"_id":"CaGu"}],"article_number":"20170646","oa":1,"language":[{"iso":"eng"}],"issue":"12","citation":{"ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","apa":"Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","first_name":"Maros","orcid":"0000-0001-7460-7479"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C"}],"day":"01","scopus_import":"1","oa_version":"Published Version","title":"Effects of mutations in phage restriction sites during escape from restriction–modification","volume":13,"article_type":"original","date_created":"2018-12-11T11:47:11Z","intvolume":" 13","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"issn":["1744-9561"]},"publication_status":"published"},{"publist_id":"7247","year":"2017","ec_funded":1,"date_published":"2017-01-01T00:00:00Z","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"status":"public","date_updated":"2022-05-24T06:57:28Z","_id":"567","type":"book","series_title":"Courant Lecture Notes","doi":"10.1090/cln/028","article_processing_charge":"No","alternative_title":["Courant Lecture Notes"],"publisher":"American Mathematical Society","quality_controlled":"1","page":"226","department":[{"_id":"LaEr"}],"month":"01","citation":{"chicago":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. https://doi.org/10.1090/cln/028.","ista":"Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p.","mla":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.","apa":"Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory (Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028","ama":"Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28. American Mathematical Society; 2017. doi:10.1090/cln/028","short":"L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017.","ieee":"L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory, vol. 28. American Mathematical Society, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":28,"date_created":"2018-12-11T11:47:13Z","author":[{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Yau, Horng","last_name":"Yau","first_name":"Horng"}],"day":"01","oa_version":"None","title":"A Dynamical Approach to Random Matrix Theory","publication_identifier":{"eisbn":["978-1-4704-4194-4"],"isbn":["9-781-4704-3648-3"]},"publication_status":"published","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"}],"intvolume":" 28"},{"citation":{"ama":"Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16","short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.","chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16.","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342.","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.","apa":"Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16"},"issue":"2","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"month":"01","publication_status":"published","publication_identifier":{"issn":["15320073"]},"intvolume":" 19","abstract":[{"lang":"eng","text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < 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< 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 > 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)."}],"volume":19,"date_created":"2018-12-11T11:47:14Z","day":"01","scopus_import":1,"author":[{"first_name":"Peter","last_name":"Franek","full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marek","full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál"}],"oa_version":"Submitted Version","title":"Persistence of zero sets","ec_funded":1,"date_published":"2017-01-01T00:00:00Z","status":"public","publication":"Homology, Homotopy and Applications","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2590DB08-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"701309","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"publist_id":"7246","year":"2017","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.04310"}],"quality_controlled":"1","page":"313 - 342","_id":"568","date_updated":"2021-01-12T08:03:12Z","type":"journal_article","doi":"10.4310/HHA.2017.v19.n2.a16","publisher":"International Press"},{"date_published":"2017-11-06T00:00:00Z","status":"public","publication":"eLife","publist_id":"7245","year":"2017","quality_controlled":"1","ddc":["570"],"date_updated":"2023-02-23T12:30:29Z","_id":"569","type":"journal_article","doi":"10.7554/eLife.30867","publisher":"eLife Sciences Publications","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. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867","mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.","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.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867.","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 et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).","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. eLife. 2017;6. doi:10.7554/eLife.30867"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"pubrep_id":"919","department":[{"_id":"MiSi"}],"article_number":"e30867","file":[{"checksum":"ba09c1451153d39e4f4b7cee013e314c","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","file_id":"4829","date_updated":"2020-07-14T12:47:10Z","creator":"system","date_created":"2018-12-12T10:10:40Z","file_size":9666973},{"file_size":5951246,"date_created":"2018-12-12T10:10:41Z","date_updated":"2020-07-14T12:47:10Z","creator":"system","file_id":"4830","file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"01eb51f1d6ad679947415a51c988e137"}],"month":"11","publication_status":"published","publication_identifier":{"issn":["2050084X"]},"file_date_updated":"2020-07-14T12:47:10Z","has_accepted_license":"1","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"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 6","volume":6,"date_created":"2018-12-11T11:47:14Z","author":[{"full_name":"Spira, Felix","last_name":"Spira","first_name":"Felix"},{"full_name":"Cuylen Haering, Sara","last_name":"Cuylen Haering","first_name":"Sara"},{"first_name":"Shalin","last_name":"Mehta","full_name":"Mehta, Shalin"},{"first_name":"Matthias","last_name":"Samwer","full_name":"Samwer, Matthias"},{"first_name":"Anne","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat"},{"last_name":"Verma","full_name":"Verma, Amitabh","first_name":"Amitabh"},{"first_name":"Rudolf","full_name":"Oldenbourg, Rudolf","last_name":"Oldenbourg"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Gerlich","full_name":"Gerlich, Daniel","first_name":"Daniel"}],"day":"06","scopus_import":1,"title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"pubrep_id":"918","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","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,” eLife, vol. 6. eLife Sciences Publications, 2017.","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. eLife. 2017;6. doi:10.7554/eLife.28921"},"month":"11","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","checksum":"273ab17f33305e4eaafd911ff88e7c5b","relation":"main_file","date_updated":"2020-07-14T12:47:10Z","creator":"system","date_created":"2018-12-12T10:14:42Z","file_size":8453470,"file_id":"5096"},{"relation":"main_file","checksum":"b433f90576c7be597cd43367946f8e7f","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"5097","date_created":"2018-12-12T10:14:43Z","file_size":1953221,"creator":"system","date_updated":"2020-07-14T12:47:10Z"}],"article_number":"e28921","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"intvolume":" 6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:10Z","publication_identifier":{"issn":["2050084X"]},"publication_status":"published","oa_version":"Published Version","title":"Regulatory network structure determines patterns of intermolecular epistasis","day":"13","scopus_import":1,"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan","last_name":"Sarikas","first_name":"Srdjan"},{"orcid":"0000-0003-1986-9753","first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","full_name":"Acar, Hande","last_name":"Acar"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet"}],"date_created":"2018-12-11T11:47:14Z","volume":6,"status":"public","publication":"eLife","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","call_identifier":"H2020"}],"date_published":"2017-11-13T00:00:00Z","ec_funded":1,"year":"2017","publist_id":"7244","ddc":["576"],"quality_controlled":"1","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.28921","type":"journal_article","_id":"570","date_updated":"2021-01-12T08:03:15Z"}]