[{"title":"Implementation of the inference method in Matlab","department":[{"_id":"GaTk"}],"date_created":"2021-08-09T07:01:24Z","related_material":{"record":[{"id":"406","relation":"used_in_publication","status":"public"}]},"day":"07","article_processing_charge":"No","status":"public","publisher":"Public Library of Science","oa_version":"Published Version","author":[{"full_name":"Bod’Ová, Katarína","first_name":"Katarína","last_name":"Bod’Ová"},{"last_name":"Mitchell","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","full_name":"Mitchell, Gabriel"},{"last_name":"Harpaz","first_name":"Roy","full_name":"Harpaz, Roy"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"year":"2018","month":"03","type":"research_data_reference","_id":"9831","date_published":"2018-03-07T00:00:00Z","citation":{"ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","mla":"Bod’Ová, Katarína, et al. <i>Implementation of the Inference Method in Matlab</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., &#38; Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>"},"doi":"10.1371/journal.pone.0193049.s001","date_updated":"2025-04-15T06:44:30Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.","lang":"eng"}]},{"abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-24T14:50:26Z","doi":"10.5061/dryad.72cg113","citation":{"ieee":"R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, <a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","mla":"Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>"},"date_published":"2018-10-09T00:00:00Z","_id":"9837","type":"research_data_reference","month":"10","year":"2018","oa_version":"Published Version","oa":1,"author":[{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Chaube, Pragya","last_name":"Chaube","first_name":"Pragya"},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"publisher":"Dryad","status":"public","article_processing_charge":"No","day":"09","related_material":{"record":[{"id":"6095","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-09T12:46:39Z","department":[{"_id":"NiBa"}],"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes"},{"type":"research_data_reference","month":"06","date_updated":"2025-04-14T13:02:22Z","doi":"10.5061/dryad.f1s76f2","citation":{"apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","mla":"Kaucka, Marketa, et al. <i>Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>","ieee":"M. Kaucka <i>et al.</i>, “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>."},"abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.f1s76f2"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9838","date_published":"2018-06-14T00:00:00Z","day":"14","related_material":{"record":[{"id":"162","status":"public","relation":"used_in_publication"}]},"status":"public","article_processing_charge":"No","date_created":"2021-08-09T12:54:35Z","department":[{"_id":"AnKi"}],"title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","year":"2018","publisher":"Dryad","oa_version":"Published Version","oa":1,"author":[{"last_name":"Kaucka","first_name":"Marketa","full_name":"Kaucka, Marketa"},{"first_name":"Julian","last_name":"Petersen","full_name":"Petersen, Julian"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"full_name":"Szarowska, Bara","first_name":"Bara","last_name":"Szarowska"},{"full_name":"Kastriti, Maria Eleni","last_name":"Kastriti","first_name":"Maria Eleni"},{"full_name":"Xie, Meng","first_name":"Meng","last_name":"Xie"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"last_name":"Annusver","first_name":"Karl","full_name":"Annusver, Karl"},{"first_name":"Maria","last_name":"Kasper","full_name":"Kasper, Maria"},{"first_name":"Orsolya","last_name":"Symmons","full_name":"Symmons, Orsolya"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"last_name":"Spitz","first_name":"Francois","full_name":"Spitz, Francois"},{"full_name":"Kaiser, Jozef","first_name":"Jozef","last_name":"Kaiser"},{"first_name":"Maria","last_name":"Hovorakova","full_name":"Hovorakova, Maria"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"last_name":"Wang","first_name":"Hui","full_name":"Wang, Hui"},{"full_name":"Marklund, Ulrika","first_name":"Ulrika","last_name":"Marklund"},{"first_name":"Hind","last_name":"Abdo","full_name":"Abdo, Hind"},{"last_name":"Ernfors","first_name":"Patrik","full_name":"Ernfors, Patrik"},{"full_name":"Maire, Pascal","first_name":"Pascal","last_name":"Maire"},{"full_name":"Wurmser, Maud","first_name":"Maud","last_name":"Wurmser"},{"last_name":"Chagin","first_name":"Andrei S","full_name":"Chagin, Andrei S"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"}]},{"type":"research_data_reference","month":"03","doi":"10.5061/dryad.42n44","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, <a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>"},"date_updated":"2025-04-15T08:17:50Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"_id":"9840","date_published":"2018-03-12T00:00:00Z","related_material":{"record":[{"id":"423","relation":"used_in_publication","status":"public"}]},"day":"12","status":"public","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","date_created":"2021-08-09T13:10:02Z","year":"2018","publisher":"Dryad","oa_version":"Published Version","oa":1,"author":[{"full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","first_name":"Pavel","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geyrhofer, Lukas","first_name":"Lukas","last_name":"Geyrhofer"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}]},{"oa":1,"author":[{"full_name":"Harrison, Mark C.","first_name":"Mark C.","last_name":"Harrison"},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"full_name":"Robertson, Hugh M.","first_name":"Hugh M.","last_name":"Robertson"},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"first_name":"Tristan","last_name":"Bitard-Feildel","full_name":"Bitard-Feildel, Tristan"},{"first_name":"Hsu","last_name":"Chao","full_name":"Chao, Hsu"},{"last_name":"Childers","first_name":"Christopher P.","full_name":"Childers, Christopher P."},{"full_name":"Dinh, Huyen","first_name":"Huyen","last_name":"Dinh"},{"full_name":"Doddapaneni, Harshavardhan","last_name":"Doddapaneni","first_name":"Harshavardhan"},{"full_name":"Dugan, Shannon","last_name":"Dugan","first_name":"Shannon"},{"last_name":"Gowin","first_name":"Johannes","full_name":"Gowin, Johannes"},{"last_name":"Greiner","first_name":"Carolin","full_name":"Greiner, Carolin"},{"last_name":"Han","first_name":"Yi","full_name":"Han, Yi"},{"first_name":"Haofu","last_name":"Hu","full_name":"Hu, Haofu"},{"first_name":"Daniel S. T.","last_name":"Hughes","full_name":"Hughes, Daniel S. T."},{"first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961"},{"full_name":"Kemena, Carsten","first_name":"Carsten","last_name":"Kemena"},{"full_name":"Kremer, Lukas P. M.","first_name":"Lukas P. M.","last_name":"Kremer"},{"first_name":"Sandra L.","last_name":"Lee","full_name":"Lee, Sandra L."},{"last_name":"Lopez-Ezquerra","first_name":"Alberto","full_name":"Lopez-Ezquerra, Alberto"},{"full_name":"Mallet, Ludovic","first_name":"Ludovic","last_name":"Mallet"},{"first_name":"Jose M.","last_name":"Monroy-Kuhn","full_name":"Monroy-Kuhn, Jose M."},{"last_name":"Moser","first_name":"Annabell","full_name":"Moser, Annabell"},{"last_name":"Murali","first_name":"Shwetha C.","full_name":"Murali, Shwetha C."},{"last_name":"Muzny","first_name":"Donna M.","full_name":"Muzny, Donna M."},{"full_name":"Otani, Saria","last_name":"Otani","first_name":"Saria"},{"last_name":"Piulachs","first_name":"Maria-Dolors","full_name":"Piulachs, Maria-Dolors"},{"full_name":"Poelchau, Monica","first_name":"Monica","last_name":"Poelchau"},{"last_name":"Qu","first_name":"Jiaxin","full_name":"Qu, Jiaxin"},{"last_name":"Schaub","first_name":"Florentine","full_name":"Schaub, Florentine"},{"last_name":"Wada-Katsumata","first_name":"Ayako","full_name":"Wada-Katsumata, Ayako"},{"full_name":"Worley, Kim C.","last_name":"Worley","first_name":"Kim C."},{"full_name":"Xie, Qiaolin","last_name":"Xie","first_name":"Qiaolin"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"full_name":"Poulsen, Michael","last_name":"Poulsen","first_name":"Michael"},{"last_name":"Gibbs","first_name":"Richard A.","full_name":"Gibbs, Richard A."},{"full_name":"Schal, Coby","last_name":"Schal","first_name":"Coby"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"full_name":"Belles, Xavier","first_name":"Xavier","last_name":"Belles"},{"full_name":"Korb, Judith","last_name":"Korb","first_name":"Judith"},{"first_name":"Erich","last_name":"Bornberg-Bauer","full_name":"Bornberg-Bauer, Erich"}],"oa_version":"Published Version","publisher":"Dryad","year":"2018","date_created":"2021-08-09T13:13:48Z","department":[{"_id":"BeVi"}],"title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","article_processing_charge":"No","status":"public","day":"12","related_material":{"record":[{"id":"448","relation":"used_in_publication","status":"public"}]},"date_published":"2018-12-12T00:00:00Z","_id":"9841","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51d4r"}],"date_updated":"2023-09-11T14:10:56Z","citation":{"ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>","ieee":"M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, <a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","mla":"Harrison, Mark C., et al. <i>Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>."},"doi":"10.5061/dryad.51d4r","month":"12","type":"research_data_reference"},{"type":"conference_poster","language":[{"iso":"eng"}],"month":"09","citation":{"ama":"Petritsch B. <i>Open Access at IST Austria 2009-2017</i>. IST Austria; 2018. doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>","ieee":"B. Petritsch, <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","mla":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018, doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>.","apa":"Petritsch, B. (2018). <i>Open Access at IST Austria 2009-2017</i>. Presented at the OAT: Open Access Tage, Graz, Austria: IST Austria. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>","chicago":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>."},"doi":"10.5281/zenodo.1410279","keyword":["Open Access","Publication Analysis"],"date_updated":"2026-03-31T12:35:03Z","conference":{"name":"OAT: Open Access Tage","location":"Graz, Austria","end_date":"2018-09-26","start_date":"2018-09-24"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","_id":"6459","file_date_updated":"2020-07-14T12:47:30Z","date_published":"2018-09-24T00:00:00Z","day":"24","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","title":"Open Access at IST Austria 2009-2017","department":[{"_id":"E-Lib"}],"date_created":"2019-05-16T07:27:14Z","ddc":["020"],"year":"2018","has_accepted_license":"1","publisher":"IST Austria","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"6460","relation":"main_file","date_updated":"2020-07-14T12:47:30Z","file_name":"Poster_Beitrag_125_Petritsch.pdf","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","date_created":"2019-05-16T07:26:25Z","file_size":1967778,"access_level":"open_access"}],"oa_version":"Published Version","oa":1,"author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch","first_name":"Barbara","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614"}]},{"oa":1,"oa_version":"Published Version","isi":1,"file":[{"access_level":"open_access","file_size":3841660,"date_created":"2019-05-28T12:40:05Z","checksum":"86ae5331f9bfced9a6358a790a04bef4","file_name":"2018_rupress_Moalli.pdf","date_updated":"2020-07-14T12:47:32Z","relation":"main_file","file_id":"6498","content_type":"application/pdf","creator":"kschuh"}],"has_accepted_license":"1","ddc":["570"],"year":"2018","title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","volume":2015,"publication":"The Journal of Experimental Medicine","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"page":"1869–1890","publication_status":"published","issue":"7","_id":"6497","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations."}],"doi":"10.1084/jem.20170896","scopus_import":"1","month":"06","author":[{"last_name":"Moalli","first_name":"Federica","full_name":"Moalli, Federica"},{"full_name":"Ficht, Xenia","last_name":"Ficht","first_name":"Xenia"},{"full_name":"Germann, Philipp","last_name":"Germann","first_name":"Philipp"},{"full_name":"Vladymyrov, Mykhailo","first_name":"Mykhailo","last_name":"Vladymyrov"},{"first_name":"Bettina","last_name":"Stolp","full_name":"Stolp, Bettina"},{"full_name":"de Vries, Ingrid","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries"},{"last_name":"Lyck","first_name":"Ruth","full_name":"Lyck, Ruth"},{"full_name":"Balmer, Jasmin","first_name":"Jasmin","last_name":"Balmer"},{"full_name":"Fiocchi, Amleto","first_name":"Amleto","last_name":"Fiocchi"},{"last_name":"Kreutzfeldt","first_name":"Mario","full_name":"Kreutzfeldt, Mario"},{"full_name":"Merkler, Doron","last_name":"Merkler","first_name":"Doron"},{"first_name":"Matteo","last_name":"Iannacone","full_name":"Iannacone, Matteo"},{"first_name":"Akitaka","last_name":"Ariga","full_name":"Ariga, Akitaka"},{"first_name":"Michael H.","last_name":"Stoffel","full_name":"Stoffel, Michael H."},{"last_name":"Sharpe","first_name":"James","full_name":"Sharpe, James"},{"full_name":"Bähler, Martin","first_name":"Martin","last_name":"Bähler"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Diz-Muñoz","first_name":"Alba","full_name":"Diz-Muñoz, Alba"},{"first_name":"Jens V.","last_name":"Stein","full_name":"Stein, Jens V."}],"publisher":"Rockefeller University Press","external_id":{"isi":["000440822900011"]},"department":[{"_id":"MiSi"}],"date_created":"2019-05-28T12:36:47Z","article_processing_charge":"No","publication_identifier":{"issn":["0022-1007"],"eissn":["1540-9538"]},"status":"public","day":"06","date_published":"2018-06-06T00:00:00Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:32Z","citation":{"apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>.","short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>.","ieee":"F. Moalli <i>et al.</i>, “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.","ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. 2018;2015(7):1869–1890. doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>"},"date_updated":"2023-09-19T14:52:08Z","intvolume":"      2015","language":[{"iso":"eng"}],"type":"journal_article"},{"doi":"10.15252/embr.201845836","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"publication_status":"published","_id":"6499","issue":"9","month":"09","ddc":["580"],"year":"2018","has_accepted_license":"1","isi":1,"file":[{"date_updated":"2020-07-14T12:47:32Z","relation":"main_file","file_id":"6500","creator":"kschuh","content_type":"application/pdf","access_level":"open_access","file_size":2005572,"date_created":"2019-05-28T13:17:19Z","file_name":"2018_embo_Truckenbrodt.pdf","checksum":"6ec90abc637f09cca3a7b6424d7e7a26"}],"oa_version":"Published Version","oa":1,"publication":"EMBO reports","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","volume":19,"citation":{"mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>, vol. 19, no. 9, e45836, Embo Press, 2018, doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &#38; Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO Reports</i>. Embo Press. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>","chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>. Embo Press, 2018. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>.","ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” <i>EMBO reports</i>, vol. 19, no. 9. Embo Press, 2018.","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO reports</i>. 2018;19(9). doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>"},"date_updated":"2024-12-11T11:48:40Z","file_date_updated":"2020-07-14T12:47:32Z","quality_controlled":"1","date_published":"2018-09-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"intvolume":"        19","publisher":"Embo Press","external_id":{"isi":["000443682200009"]},"author":[{"last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","full_name":"Truckenbrodt, Sven M"},{"full_name":"Maidorn, Manuel","first_name":"Manuel","last_name":"Maidorn"},{"last_name":"Crzan","first_name":"Dagmar","full_name":"Crzan, Dagmar"},{"full_name":"Wildhagen, Hanna","last_name":"Wildhagen","first_name":"Hanna"},{"full_name":"Kabatas, Selda","last_name":"Kabatas","first_name":"Selda"},{"full_name":"Rizzoli, Silvio O","last_name":"Rizzoli","first_name":"Silvio O"}],"article_number":"e45836","day":"01","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"status":"public","article_processing_charge":"No","department":[{"_id":"JoDa"}],"date_created":"2019-05-28T13:16:08Z"},{"publisher":"Oxford University Press","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamás","full_name":"Hausel, Tamás","orcid":"0000-0002-9582-2634"},{"first_name":"Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87","last_name":"Mellit","full_name":"Mellit, Anton"},{"full_name":"Pei, Du","last_name":"Pei","first_name":"Du"}],"oa_version":"None","year":"2018","date_created":"2019-06-06T12:42:01Z","title":"Mirror symmetry with branes by equivariant verlinde formulas","department":[{"_id":"TaHa"}],"day":"01","article_processing_charge":"No","status":"public","publication_identifier":{"isbn":["9780198802013"],"eisbn":["9780191840500"]},"publication":"Geometry and Physics: Volume I","quality_controlled":"1","_id":"6525","publication_status":"published","page":"189-218","date_published":"2018-01-01T00:00:00Z","date_updated":"2026-04-16T10:30:22Z","scopus_import":"1","citation":{"short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218, doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>.","chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In <i>Geometry and Physics: Volume I</i>, 189–218. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>.","apa":"Hausel, T., Mellit, A., &#38; Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In <i>Geometry and Physics: Volume I</i> (pp. 189–218). Oxford University Press. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>","ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: <i>Geometry and Physics: Volume I</i>. Oxford University Press; 2018:189-218. doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218."},"doi":"10.1093/oso/9780198802013.003.0009","abstract":[{"lang":"eng","text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","type":"book_chapter","language":[{"iso":"eng"}]},{"year":"2018","ddc":["000"],"oa_version":"Published Version","oa":1,"isi":1,"publication":"Advances in Neural Information Processing Systems","title":"Byzantine stochastic gradient descent","volume":2018,"arxiv":1,"abstract":[{"lang":"eng","text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08917"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","_id":"6558","publication_status":"published","page":"4613-4623","month":"12","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Allen-Zhu, Zeyuan","last_name":"Allen-Zhu","first_name":"Zeyuan"},{"full_name":"Li, Jerry","last_name":"Li","first_name":"Jerry"}],"external_id":{"isi":["000461823304061"],"arxiv":["1803.08917"]},"publisher":"Neural Information Processing Systems Foundation","status":"public","article_processing_charge":"No","day":"01","date_created":"2019-06-13T08:22:37Z","department":[{"_id":"DaAl"}],"conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","location":"Montreal, Canada","end_date":"2018-12-08","start_date":"2018-12-02"},"date_updated":"2026-06-18T19:08:25Z","citation":{"short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623.","mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” <i>Advances in Neural Information Processing Systems</i>, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In <i>Advances in Neural Information Processing Systems</i>, 2018:4613–23. Neural Information Processing Systems Foundation, 2018.","apa":"Alistarh, D.-A., Allen-Zhu, Z., &#38; Li, J. (2018). Byzantine stochastic gradient descent. In <i>Advances in Neural Information Processing Systems</i> (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: <i>Advances in Neural Information Processing Systems</i>. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623."},"date_published":"2018-12-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","intvolume":"      2018"},{"oa_version":"Published Version","oa":1,"file":[{"access_level":"open_access","file_size":1056278,"file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8","date_created":"2019-08-08T06:55:21Z","relation":"main_file","date_updated":"2020-07-14T12:47:40Z","creator":"dernst","content_type":"application/pdf","file_id":"6775"}],"has_accepted_license":"1","ddc":["514"],"year":"2018","title":"Computing simplicial representatives of homotopy group elements","volume":2,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Journal of Applied and Computational Topology","issue":"3-4","_id":"6774","page":"177-231","publication_status":"published","abstract":[{"lang":"eng","text":"A central problem of algebraic topology is to understand the homotopy groups  𝜋𝑑(𝑋)  of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group  𝜋1(𝑋)  of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with   𝜋1(𝑋)  trivial), compute the higher homotopy group   𝜋𝑑(𝑋)  for any given   𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of   𝜋𝑑(𝑋) ,   𝑑≥2  as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of   𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere   𝑆𝑑  to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes   𝜋𝑑(𝑋)  and represents its elements as simplicial maps from a suitable triangulation of the d-sphere   𝑆𝑑  to X. For fixed d, the algorithm runs in time exponential in   size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed   𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of   𝜋𝑑(𝑋) , the size of the triangulation of   𝑆𝑑  on which the map is defined, is exponential in size(𝑋) ."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1007/s41468-018-0021-5","month":"12","author":[{"id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","last_name":"Filakovský","first_name":"Marek","full_name":"Filakovský, Marek"},{"last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0001-8878-8397","full_name":"Franek, Peter"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"},{"id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev","first_name":"Stephan Y","full_name":"Zhechev, Stephan Y"}],"publisher":"Springer","article_type":"original","corr_author":"1","date_created":"2019-08-08T06:47:40Z","department":[{"_id":"UlWa"}],"publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"status":"public","day":"01","related_material":{"record":[{"id":"6681","relation":"dissertation_contains","status":"public"}]},"date_published":"2018-12-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:40Z","quality_controlled":"1","date_updated":"2026-04-08T13:56:01Z","citation":{"short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","mla":"Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” <i>Journal of Applied and Computational Topology</i>, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:<a href=\"https://doi.org/10.1007/s41468-018-0021-5\">10.1007/s41468-018-0021-5</a>.","apa":"Filakovský, M., Franek, P., Wagner, U., &#38; Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. <i>Journal of Applied and Computational Topology</i>. Springer. <a href=\"https://doi.org/10.1007/s41468-018-0021-5\">https://doi.org/10.1007/s41468-018-0021-5</a>","chicago":"Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” <i>Journal of Applied and Computational Topology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s41468-018-0021-5\">https://doi.org/10.1007/s41468-018-0021-5</a>.","ista":"Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231.","ama":"Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. <i>Journal of Applied and Computational Topology</i>. 2018;2(3-4):177-231. doi:<a href=\"https://doi.org/10.1007/s41468-018-0021-5\">10.1007/s41468-018-0021-5</a>","ieee":"M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” <i>Journal of Applied and Computational Topology</i>, vol. 2, no. 3–4. Springer, pp. 177–231, 2018."},"intvolume":"         2","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","grant_number":"M01980","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","name":"Robust Invariants of Nonlinear Systems"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"type":"journal_article"},{"file_date_updated":"2020-07-14T12:47:44Z","publist_id":"7985","date_published":"2018-09-01T00:00:00Z","citation":{"apa":"Vukušić, L. (2018). <i>Charge sensing and spin relaxation times of holes in Ge hut wires</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">https://doi.org/10.15479/AT:ISTA:TH_1047</a>","chicago":"Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">https://doi.org/10.15479/AT:ISTA:TH_1047</a>.","mla":"Vukušić, Lada. <i>Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">10.15479/AT:ISTA:TH_1047</a>.","short":"L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires, Institute of Science and Technology Austria, 2018.","ieee":"L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,” Institute of Science and Technology Austria, 2018.","ista":"Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria.","ama":"Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">10.15479/AT:ISTA:TH_1047</a>"},"date_updated":"2026-04-08T14:09:47Z","degree_awarded":"PhD","pubrep_id":"1047","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada","first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić"}],"department":[{"_id":"GeKa"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:44:28Z","corr_author":"1","related_material":{"record":[{"id":"23","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"840"}]},"day":"01","article_processing_charge":"No","status":"public","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","page":"103","_id":"69","doi":"10.15479/AT:ISTA:TH_1047","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"text":"A qubit, a unit of quantum information, is essentially any quantum mechanical two-level system which can be coherently controlled. Still, to be used for computation, it has to fulfill criteria. Qubits, regardless of the system in which they are realized, suffer from decoherence. This leads to loss of the information stored in the qubit. The upper bound of the time scale on which decoherence happens is set by the spin relaxation time. In this thesis I studied a two-level system consisting of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire. Such Ge hut wires have emerged as a promising material system for the realization of spin qubits, due to the combination of two significant properties: long spin coherence time as expected for group IV semiconductors due to the low hyperfine interaction and a strong valence band spin-orbit coupling. Here, I present how to fabricate quantum dot devices suitable for electrical transport measurements. Coupled quantum dot devices allowed the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot. By integrating the charge sensor into a radio-frequency reflectometry setup, I performed for the first time single-shot readout measurements of hole spins and extracted the hole spin relaxation times in Ge hut wires.","lang":"eng"}],"OA_place":"publisher","month":"09","supervisor":[{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"alternative_title":["ISTA Thesis"],"file":[{"file_size":28452385,"access_level":"open_access","checksum":"c570b656e30749cd65b1c7e13a9ce0a8","file_name":"2018_Thesis_Vukusic.pdf","date_created":"2019-04-09T07:00:40Z","relation":"main_file","date_updated":"2020-07-14T12:47:44Z","content_type":"application/pdf","creator":"dernst","file_id":"6247"},{"content_type":"application/zip","creator":"dernst","file_id":"6248","relation":"source_file","date_updated":"2020-07-14T12:47:44Z","file_name":"2018_Thesis_Vukusic_source.zip","checksum":"7856771d9cd401fe0b311191076db6e1","date_created":"2019-04-09T07:00:40Z","access_level":"closed","file_size":53058704}],"oa":1,"oa_version":"Published Version","year":"2018","ddc":["530","600"],"has_accepted_license":"1","title":"Charge sensing and spin relaxation times of holes in Ge hut wires","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"day":"14","article_number":"543-616","status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:47:56Z","department":[{"_id":"LaEr"}],"external_id":{"arxiv":["1605.08767"],"isi":["000432129600012"]},"publisher":"Springer","author":[{"first_name":"Jii","last_name":"Lee","full_name":"Lee, Jii"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231"}],"type":"journal_article","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"language":[{"iso":"eng"}],"intvolume":"       171","date_updated":"2025-09-10T14:00:58Z","citation":{"ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616.","ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” <i>Probability Theory and Related Fields</i>, vol. 171, no. 1–2. Springer, 2018.","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. <i>Probability Theory and Related Fields</i>. 2018;171(1-2). doi:<a href=\"https://doi.org/10.1007/s00440-017-0787-8\">10.1007/s00440-017-0787-8</a>","apa":"Lee, J., &#38; Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-017-0787-8\">https://doi.org/10.1007/s00440-017-0787-8</a>","chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00440-017-0787-8\">https://doi.org/10.1007/s00440-017-0787-8</a>.","mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” <i>Probability Theory and Related Fields</i>, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s00440-017-0787-8\">10.1007/s00440-017-0787-8</a>.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018)."},"quality_controlled":"1","publist_id":"7017","date_published":"2018-06-14T00:00:00Z","publication":"Probability Theory and Related Fields","volume":171,"title":"Local law and Tracy–Widom limit for sparse random matrices","ec_funded":1,"year":"2018","isi":1,"oa":1,"oa_version":"Preprint","month":"06","scopus_import":"1","doi":"10.1007/s00440-017-0787-8","abstract":[{"lang":"eng","text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1."}],"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.08767"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1-2","_id":"690","publication_status":"published"},{"volume":55,"title":"A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features","publication":"Journal of Medical Genetics","isi":1,"oa":1,"oa_version":"Submitted Version","year":"2018","month":"01","issue":"1","_id":"691","page":"48 - 54","pmid":1,"publication_status":"published","scopus_import":"1","doi":"10.1136/jmedgenet-2017-104627","abstract":[{"text":"Background: Transport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective: We aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods: Linkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function.","lang":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:57Z","department":[{"_id":"GaNo"}],"day":"01","publication_identifier":{"issn":["0022-2593"]},"article_processing_charge":"No","status":"public","external_id":{"isi":["000418199800007"],"pmid":["28626029"]},"publisher":"BMJ Publishing Group","article_type":"original","author":[{"full_name":"Marin Valencia, Isaac","first_name":"Isaac","last_name":"Marin Valencia"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johansen","first_name":"Anide","full_name":"Johansen, Anide"},{"full_name":"Rosti, Başak","first_name":"Başak","last_name":"Rosti"},{"last_name":"Issa","first_name":"Mahmoud","full_name":"Issa, Mahmoud"},{"last_name":"Musaev","first_name":"Damir","full_name":"Musaev, Damir"},{"first_name":"Gifty","last_name":"Bhat","full_name":"Bhat, Gifty"},{"full_name":"Scott, Eric","last_name":"Scott","first_name":"Eric"},{"full_name":"Silhavy, Jennifer","last_name":"Silhavy","first_name":"Jennifer"},{"first_name":"Valentina","last_name":"Stanley","full_name":"Stanley, Valentina"},{"last_name":"Rosti","first_name":"Rasim","full_name":"Rosti, Rasim"},{"first_name":"Jeremy","last_name":"Gleeson","full_name":"Gleeson, Jeremy"},{"last_name":"Imam","first_name":"Farhad","full_name":"Imam, Farhad"},{"first_name":"Maha","last_name":"Zaki","full_name":"Zaki, Maha"},{"full_name":"Gleeson, Joseph","first_name":"Joseph","last_name":"Gleeson"}],"intvolume":"        55","project":[{"name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","language":[{"iso":"eng"}],"publist_id":"7016","quality_controlled":"1","date_published":"2018-01-01T00:00:00Z","date_updated":"2025-04-15T07:50:28Z","citation":{"ista":"Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 55(1), 48–54.","ama":"Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. <i>Journal of Medical Genetics</i>. 2018;55(1):48-54. doi:<a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">10.1136/jmedgenet-2017-104627</a>","ieee":"I. Marin Valencia <i>et al.</i>, “A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features,” <i>Journal of Medical Genetics</i>, vol. 55, no. 1. BMJ Publishing Group, pp. 48–54, 2018.","short":"I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev, G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki, J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.","mla":"Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” <i>Journal of Medical Genetics</i>, vol. 55, no. 1, BMJ Publishing Group, 2018, pp. 48–54, doi:<a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">10.1136/jmedgenet-2017-104627</a>.","chicago":"Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” <i>Journal of Medical Genetics</i>. BMJ Publishing Group, 2018. <a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">https://doi.org/10.1136/jmedgenet-2017-104627</a>.","apa":"Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev, D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. <i>Journal of Medical Genetics</i>. BMJ Publishing Group. <a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">https://doi.org/10.1136/jmedgenet-2017-104627</a>"}},{"oa":1,"oa_version":"Published Version","isi":1,"file":[{"date_updated":"2020-07-14T12:47:44Z","relation":"main_file","file_id":"7222","creator":"kschuh","content_type":"application/pdf","access_level":"open_access","file_size":1140860,"date_created":"2020-01-03T11:35:08Z","checksum":"1febcfc1266486053a069e3425ea3713","file_name":"2018_Springer_Akopyan.pdf"}],"has_accepted_license":"1","year":"2018","ddc":["510"],"ec_funded":1,"title":"3-Webs generated by confocal conics and circles","volume":194,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Geometriae Dedicata","page":"55 - 64","publication_status":"published","_id":"692","issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them.","lang":"eng"}],"doi":"10.1007/s10711-017-0265-6","scopus_import":"1","month":"06","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"}],"article_type":"original","publisher":"Springer","external_id":{"isi":["000431418800004"]},"corr_author":"1","department":[{"_id":"HeEd"}],"date_created":"2018-12-11T11:47:57Z","status":"public","article_processing_charge":"Yes (via OA deal)","day":"01","date_published":"2018-06-01T00:00:00Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:44Z","publist_id":"7014","citation":{"ista":"Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64.","ama":"Akopyan A. 3-Webs generated by confocal conics and circles. <i>Geometriae Dedicata</i>. 2018;194(1):55-64. doi:<a href=\"https://doi.org/10.1007/s10711-017-0265-6\">10.1007/s10711-017-0265-6</a>","ieee":"A. Akopyan, “3-Webs generated by confocal conics and circles,” <i>Geometriae Dedicata</i>, vol. 194, no. 1. Springer, pp. 55–64, 2018.","short":"A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.","mla":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” <i>Geometriae Dedicata</i>, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:<a href=\"https://doi.org/10.1007/s10711-017-0265-6\">10.1007/s10711-017-0265-6</a>.","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. <i>Geometriae Dedicata</i>. Springer. <a href=\"https://doi.org/10.1007/s10711-017-0265-6\">https://doi.org/10.1007/s10711-017-0265-6</a>","chicago":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” <i>Geometriae Dedicata</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10711-017-0265-6\">https://doi.org/10.1007/s10711-017-0265-6</a>."},"date_updated":"2025-04-15T06:50:29Z","intvolume":"       194","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"type":"journal_article"},{"page":"480-499","publication_status":"published","_id":"6941","doi":"10.1007/978-3-662-58387-6_26","scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/528"}],"abstract":[{"lang":"eng","text":"Bitcoin has become the most successful cryptocurrency ever deployed, and its most distinctive feature is that it is decentralized. Its underlying protocol (Nakamoto consensus) achieves this by using proof of work, which has the drawback that it causes the consumption of vast amounts of energy to maintain the ledger. Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather than computation. We argue that SpaceMint’s design solves or alleviates several of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also rewards smaller miners fairly according to their contribution to the network, thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof of space to enable its use in cryptocurrency, studies the attacks that can arise against a Bitcoin-like blockchain that uses proof of space, and proposes a new blockchain format and transaction types to address these attacks. Our prototype shows that initializing 1 TB for mining takes about a day (a one-off setup cost), and miners spend on average just a fraction of a second per block mined. Finally, we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the canonical game-theoretic notion for games that take place over time) and show that this stylized game satisfies a strong equilibrium notion, thereby arguing for SpaceMint ’s stability and consensus."}],"month":"12","alternative_title":["LNCS"],"isi":1,"oa_version":"Submitted Version","oa":1,"year":"2018","title":"SpaceMint: A cryptocurrency based on proofs of space","volume":10957,"ec_funded":1,"publication":"22nd International Conference on Financial Cryptography and Data Security","quality_controlled":"1","date_published":"2018-12-07T00:00:00Z","citation":{"chicago":"Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen, and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” In <i>22nd International Conference on Financial Cryptography and Data Security</i>, 10957:480–99. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">https://doi.org/10.1007/978-3-662-58387-6_26</a>.","apa":"Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., &#38; Pietrzak, K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In <i>22nd International Conference on Financial Cryptography and Data Security</i> (Vol. 10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">https://doi.org/10.1007/978-3-662-58387-6_26</a>","mla":"Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” <i>22nd International Conference on Financial Cryptography and Data Security</i>, vol. 10957, Springer Nature, 2018, pp. 480–99, doi:<a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">10.1007/978-3-662-58387-6_26</a>.","short":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:, 22nd International Conference on Financial Cryptography and Data Security, Springer Nature, 2018, pp. 480–499.","ista":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint: A cryptocurrency based on proofs of space. 22nd International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 10957, 480–499.","ama":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A cryptocurrency based on proofs of space. In: <i>22nd International Conference on Financial Cryptography and Data Security</i>. Vol 10957. Springer Nature; 2018:480-499. doi:<a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">10.1007/978-3-662-58387-6_26</a>","ieee":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak, “SpaceMint: A cryptocurrency based on proofs of space,” in <i>22nd International Conference on Financial Cryptography and Data Security</i>, Nieuwpoort, Curacao, 2018, vol. 10957, pp. 480–499."},"date_updated":"2026-04-16T10:30:49Z","conference":{"location":"Nieuwpoort, Curacao","name":"FC: Financial Cryptography and Data Security","start_date":"2018-02-26","end_date":"2018-03-02"},"intvolume":"     10957","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"type":"conference","language":[{"iso":"eng"}],"publisher":"Springer Nature","external_id":{"isi":["000540656400026"]},"author":[{"full_name":"Park, Sunoo","first_name":"Sunoo","last_name":"Park"},{"full_name":"Kwon, Albert","first_name":"Albert","last_name":"Kwon"},{"first_name":"Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"full_name":"Gazi, Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","full_name":"Alwen, Joel F"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"department":[{"_id":"KrPi"}],"date_created":"2019-10-14T06:35:38Z","day":"07","status":"public","article_processing_charge":"No","publication_identifier":{"isbn":["9783662583869"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783662583876"]}},{"author":[{"first_name":"Nathalie","last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Alessandro","last_name":"Crespi","full_name":"Crespi, Alessandro"},{"full_name":"Mersch, Danielle","first_name":"Danielle","last_name":"Mersch"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Keller","first_name":"Laurent","full_name":"Keller, Laurent"}],"external_id":{"isi":["000451124500041"]},"publisher":"AAAS","article_type":"original","date_created":"2018-12-11T11:44:07Z","department":[{"_id":"SyCr"}],"article_processing_charge":"No","status":"public","publication_identifier":{"issn":["1095-9203"]},"day":"23","related_material":{"link":[{"url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"13055","relation":"research_data","status":"public"}]},"date_published":"2018-11-23T00:00:00Z","quality_controlled":"1","publist_id":"8049","date_updated":"2026-06-18T19:15:22Z","citation":{"apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aat4793\">https://doi.org/10.1126/science.aat4793</a>","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” <i>Science</i>. AAAS, 2018. <a href=\"https://doi.org/10.1126/science.aat4793\">https://doi.org/10.1126/science.aat4793</a>.","mla":"Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” <i>Science</i>, vol. 362, no. 6417, AAAS, 2018, pp. 941–45, doi:<a href=\"https://doi.org/10.1126/science.aat4793\">10.1126/science.aat4793</a>.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science 362 (2018) 941–945.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect. Science. 362(6417), 941–945.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect,” <i>Science</i>, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. <i>Science</i>. 2018;362(6417):941-945. doi:<a href=\"https://doi.org/10.1126/science.aat4793\">10.1126/science.aat4793</a>"},"intvolume":"       362","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","oa":1,"oa_version":"Published Version","isi":1,"year":"2018","ddc":["570"],"ec_funded":1,"title":"Social network plasticity decreases disease transmission in a eusocial insect","volume":362,"publication":"Science","issue":"6417","_id":"7","publication_status":"published","page":"941 - 945","abstract":[{"lang":"eng","text":"Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups."}],"main_file_link":[{"url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1126/science.aat4793","month":"11","acknowledgement":"This project was funded by two European Research Council Advanced Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research Council Starting Grant (SocialVaccines, 243071) to S.C."},{"article_processing_charge":"No","publication_identifier":{"issn":["1980-0436"]},"status":"public","day":"01","date_created":"2018-12-11T11:44:28Z","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"author":[{"full_name":"Nejjar, Peter","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","last_name":"Nejjar"}],"external_id":{"isi":["000460475800022"],"arxiv":["1705.08836"]},"article_type":"original","publisher":"Instituto Nacional de Matematica Pura e Aplicada","language":[{"iso":"eng"}],"type":"journal_article","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"intvolume":"        15","date_updated":"2025-04-14T07:27:49Z","citation":{"ista":"Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. 15(2), 1311–1334.","ieee":"P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,” <i>Latin American Journal of Probability and Mathematical Statistics</i>, vol. 15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018.","ama":"Nejjar P. Transition to shocks in TASEP and decoupling of last passage times. <i>Latin American Journal of Probability and Mathematical Statistics</i>. 2018;15(2):1311-1334. doi:<a href=\"https://doi.org/10.30757/ALEA.v15-49\">10.30757/ALEA.v15-49</a>","short":"P. Nejjar, Latin American Journal of Probability and Mathematical Statistics 15 (2018) 1311–1334.","mla":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” <i>Latin American Journal of Probability and Mathematical Statistics</i>, vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34, doi:<a href=\"https://doi.org/10.30757/ALEA.v15-49\">10.30757/ALEA.v15-49</a>.","apa":"Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage times. <i>Latin American Journal of Probability and Mathematical Statistics</i>. Instituto Nacional de Matematica Pura e Aplicada. <a href=\"https://doi.org/10.30757/ALEA.v15-49\">https://doi.org/10.30757/ALEA.v15-49</a>","chicago":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” <i>Latin American Journal of Probability and Mathematical Statistics</i>. Instituto Nacional de Matematica Pura e Aplicada, 2018. <a href=\"https://doi.org/10.30757/ALEA.v15-49\">https://doi.org/10.30757/ALEA.v15-49</a>."},"date_published":"2018-10-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:46Z","quality_controlled":"1","publication":"Latin American Journal of Probability and Mathematical Statistics","ec_funded":1,"title":"Transition to shocks in TASEP and decoupling of last passage times","volume":15,"has_accepted_license":"1","year":"2018","ddc":["510"],"oa_version":"Published Version","oa":1,"file":[{"file_id":"5981","creator":"kschuh","content_type":"application/pdf","date_updated":"2020-07-14T12:47:46Z","relation":"main_file","date_created":"2019-02-14T09:44:10Z","file_name":"2018_ALEA_Nejjar.pdf","checksum":"2ded46aa284a836a8cbb34133a64f1cb","access_level":"open_access","file_size":394851}],"isi":1,"month":"10","abstract":[{"lang":"eng","text":"We consider the totally asymmetric simple exclusion process in a critical scaling parametrized by a≥0, which creates a shock in the particle density of order aT−1/3, T the observation time. When starting from step initial data, we provide bounds on the limiting law which in particular imply that in the double limit lima→∞limT→∞ one recovers the product limit law and the degeneration of the correlation length observed at shocks of order 1. This result is shown to apply to a general last-passage percolation model. We also obtain bounds on the two-point functions of several airy processes."}],"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.30757/ALEA.v15-49","_id":"70","issue":"2","publication_status":"published","page":"1311-1334"},{"intvolume":"        40","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publist_id":"6992","date_published":"2018-07-01T00:00:00Z","date_updated":"2026-04-16T09:54:52Z","citation":{"ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682.","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2018;40(7):1668-1682. doi:<a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">10.1109/TPAMI.2017.2730884</a>","short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:<a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">10.1109/TPAMI.2017.2730884</a>.","chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">https://doi.org/10.1109/TPAMI.2017.2730884</a>.","apa":"Shekhovtsov, A., Swoboda, P., &#38; Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">https://doi.org/10.1109/TPAMI.2017.2730884</a>"},"date_created":"2018-12-11T11:48:01Z","department":[{"_id":"VlKo"}],"corr_author":"1","day":"01","article_processing_charge":"No","status":"public","publication_identifier":{"issn":["0162-8828"]},"external_id":{"isi":["000434294800010"],"arxiv":["1508.07902"]},"publisher":"IEEE","author":[{"last_name":"Shekhovtsov","first_name":"Alexander","full_name":"Shekhovtsov, Alexander"},{"last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","full_name":"Swoboda, Paul"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"month":"07","_id":"703","issue":"7","publication_status":"published","page":"1668-1682","scopus_import":"1","doi":"10.1109/TPAMI.2017.2730884","abstract":[{"text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision.","lang":"eng"}],"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.07902"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Maximum persistency via iterative relaxed inference with graphical models","volume":40,"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","isi":1,"oa":1,"oa_version":"Preprint","year":"2018"},{"day":"01","article_processing_charge":"No","status":"public","department":[{"_id":"RySh"}],"date_created":"2018-12-11T11:48:02Z","publisher":"Springer","external_id":{"isi":["000431991500025"]},"author":[{"full_name":"Miklosi, Andras","first_name":"Andras","last_name":"Miklosi"},{"first_name":"Giorgia","last_name":"Del Favero","full_name":"Del Favero, Giorgia"},{"last_name":"Bulat","first_name":"Tanja","full_name":"Bulat, Tanja"},{"first_name":"Harald","last_name":"Höger","full_name":"Höger, Harald"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"first_name":"Doris","last_name":"Marko","full_name":"Marko, Doris"},{"last_name":"Lubec","first_name":"Gert","full_name":"Lubec, Gert"}],"type":"journal_article","language":[{"iso":"eng"}],"intvolume":"        55","citation":{"ama":"Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. <i>Molecular Neurobiology</i>. 2018;55(6):4857 – 4869. doi:<a href=\"https://doi.org/10.1007/s12035-017-0688-y\">10.1007/s12035-017-0688-y</a>","ieee":"A. Miklosi <i>et al.</i>, “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” <i>Molecular Neurobiology</i>, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.","ista":"Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.","short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.","mla":"Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” <i>Molecular Neurobiology</i>, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:<a href=\"https://doi.org/10.1007/s12035-017-0688-y\">10.1007/s12035-017-0688-y</a>.","apa":"Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., &#38; Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. <i>Molecular Neurobiology</i>. Springer. <a href=\"https://doi.org/10.1007/s12035-017-0688-y\">https://doi.org/10.1007/s12035-017-0688-y</a>","chicago":"Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” <i>Molecular Neurobiology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s12035-017-0688-y\">https://doi.org/10.1007/s12035-017-0688-y</a>."},"date_updated":"2023-09-19T09:58:11Z","quality_controlled":"1","publist_id":"6991","date_published":"2018-06-01T00:00:00Z","publication":"Molecular Neurobiology","volume":55,"title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes","year":"2018","isi":1,"oa_version":"None","month":"06","doi":"10.1007/s12035-017-0688-y","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins."}],"page":"4857 – 4869","publication_status":"published","issue":"6","_id":"705"}]