[{"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","volume":2,"oa_version":"Published Version","quality_controlled":"1","publication_status":"published","file_date_updated":"2018-12-12T10:13:33Z","status":"public","ddc":["580"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"pubrep_id":"757","oa":1,"author":[{"first_name":"Łukasz","full_name":"Łangowski, Łukasz","last_name":"Łangowski"},{"first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5039-9660","last_name":"Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","full_name":"Li, Hongjiang"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"last_name":"Tanaka","full_name":"Tanaka, Hirokazu","first_name":"Hirokazu"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"         2","has_accepted_license":"1","type":"journal_article","year":"2016","month":"07","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"license":"https://creativecommons.org/licenses/by/4.0/","publication":"Cell Discovery","file":[{"file_id":"5017","date_created":"2018-12-12T10:13:33Z","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","date_updated":"2018-12-12T10:13:33Z","file_size":5261671,"relation":"main_file","creator":"system"}],"publisher":"Nature Publishing Group","article_number":"16018","date_published":"2016-07-19T00:00:00Z","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"day":"19","_id":"1081","citation":{"mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>, vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>.","ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","ieee":"Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>, vol. 2. Nature Publishing Group, 2016.","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>"},"article_processing_charge":"No","doi":"10.1038/celldisc.2016.18","external_id":{"isi":["000414797400001"]},"date_created":"2018-12-11T11:50:02Z","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","ec_funded":1,"scopus_import":"1","date_updated":"2025-09-22T14:19:46Z","publist_id":"6299","abstract":[{"lang":"eng","text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells."}]},{"scopus_import":"1","conference":{"end_date":"2016-09-14","name":"CinC: Computing in Cardiology","start_date":"2016-09-11","location":"Vancouver, Canada"},"date_updated":"2026-06-18T08:48:07Z","abstract":[{"text":"The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. ","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"citation":{"apa":"Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., &#38; Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In <i>2016 Computing in Cardiology Conference</i> (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>","ama":"Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: <i>2016 Computing in Cardiology Conference</i>. Vol 43. Computing in Cardiology; 2016:309-312. doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>","ieee":"P. Rubel <i>et al.</i>, “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in <i>2016 Computing in Cardiology Conference</i>, Vancouver, Canada, 2016, vol. 43, pp. 309–312.","short":"P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312.","chicago":"Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In <i>2016 Computing in Cardiology Conference</i>, 43:309–12. Computing in Cardiology, 2016. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>.","ista":"Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312.","mla":"Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>2016 Computing in Cardiology Conference</i>, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>."},"_id":"10810","article_processing_charge":"No","doi":"10.22489/cinc.2016.090-500","date_created":"2022-03-03T10:43:10Z","acknowledgement":"The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments.","publisher":"Computing in Cardiology","publication":"2016 Computing in Cardiology Conference","date_published":"2016-03-01T00:00:00Z","day":"01","type":"conference","publication_identifier":{"issn":["2325-887X"]},"department":[{"_id":"CampIT"}],"month":"03","year":"2016","author":[{"first_name":"Paul","full_name":"Rubel, Paul","last_name":"Rubel"},{"last_name":"Pani","first_name":"Danilo","full_name":"Pani, Danilo"},{"full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"last_name":"Fayn","full_name":"Fayn, Jocelyne","first_name":"Jocelyne"},{"full_name":"Badilini, Fabio","first_name":"Fabio","last_name":"Badilini"},{"first_name":"Peter","full_name":"Macfarlane, Peter","last_name":"Macfarlane"},{"full_name":"Varri, Alpo","first_name":"Alpo","last_name":"Varri"}],"intvolume":"        43","ddc":["000"],"status":"public","oa":1,"quality_controlled":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"page":"309-312","title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","volume":43,"oa_version":"Published Version"},{"publication_status":"published","file_date_updated":"2020-07-14T12:48:01Z","quality_controlled":"1","volume":12,"oa_version":"Published Version","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078","issue":"8","intvolume":"        12","has_accepted_license":"1","author":[{"last_name":"Tang","first_name":"Yong","full_name":"Tang, Yong"},{"last_name":"Zhao","full_name":"Zhao, Chun-Yan","first_name":"Chun-Yan"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","full_name":"Tan, Shutang"},{"first_name":"Hong-Wei","full_name":"Xue, Hong-Wei","last_name":"Xue"}],"oa":1,"ddc":["580"],"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"extern":"1","day":"16","publication":"PLOS Genetics","publisher":"Public Library of Science","file":[{"checksum":"ff0ab9a6bed11cda800a6e59820866a0","access_level":"open_access","file_id":"7612","date_created":"2020-03-23T12:15:31Z","content_type":"application/pdf","date_updated":"2020-07-14T12:48:01Z","file_size":3266119,"creator":"dernst","relation":"main_file","file_name":"2016_PlosGenetics_Tang.PDF"}],"date_published":"2016-08-16T00:00:00Z","article_number":"e1006252","year":"2016","month":"08","publication_identifier":{"issn":["1553-7404"]},"type":"journal_article","abstract":[{"text":"Normal leaf margin development is important for leaf morphogenesis and contributes to diverse leaf shapes in higher plants. We here show the crucial roles of an atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin development. PI4Kγ5 presents a dynamics expression pattern along with leaf development and a T-DNA mutant lacking PI4Kγ5, pi4kγ5–1, presents serrated leaves, which is resulted from the accelerated cell division and increased auxin concentration at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated that membrane-bound transcription factors regulate gene transcription by undergoing proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced in pi4kγ5–1, indicating that PI4Kγ5 is important for the cleavage of ANAC078. This is consistent with the subcellular localization observation showing that fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in pi4kγ5–1 mutant and that expression of ANAC078 deleting of carboxyl terminal, driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5–1. Further analysis showed that ANAC078 suppresses the auxin synthesis by directly binding and regulating the expression of auxin synthesis-related genes. These results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin synthesis and hence influences cell proliferation and leaf development, providing informative clues for the regulation of in situ auxin synthesis and cell division, as well as the cleavage and functional mechanism of membrane-bound transcription factors.","lang":"eng"}],"date_updated":"2021-01-12T08:14:25Z","doi":"10.1371/journal.pgen.1006252","article_type":"original","date_created":"2020-03-21T16:08:33Z","_id":"7599","citation":{"apa":"Tang, Y., Zhao, C.-Y., Tan, S., &#38; Xue, H.-W. (2016). Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078. <i>PLOS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1006252\">https://doi.org/10.1371/journal.pgen.1006252</a>","chicago":"Tang, Yong, Chun-Yan Zhao, Shutang Tan, and Hong-Wei Xue. “Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with Membrane-Bound Transcription Factor ANAC078.” <i>PLOS Genetics</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1006252\">https://doi.org/10.1371/journal.pgen.1006252</a>.","ama":"Tang Y, Zhao C-Y, Tan S, Xue H-W. Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078. <i>PLOS Genetics</i>. 2016;12(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1006252\">10.1371/journal.pgen.1006252</a>","short":"Y. Tang, C.-Y. Zhao, S. Tan, H.-W. Xue, PLOS Genetics 12 (2016).","ieee":"Y. Tang, C.-Y. Zhao, S. Tan, and H.-W. Xue, “Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078,” <i>PLOS Genetics</i>, vol. 12, no. 8. Public Library of Science, 2016.","ista":"Tang Y, Zhao C-Y, Tan S, Xue H-W. 2016. Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078. PLOS Genetics. 12(8), e1006252.","mla":"Tang, Yong, et al. “Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with Membrane-Bound Transcription Factor ANAC078.” <i>PLOS Genetics</i>, vol. 12, no. 8, e1006252, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1006252\">10.1371/journal.pgen.1006252</a>."},"article_processing_charge":"No"},{"title":"Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","page":"1189-1195","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2168-622X"]},"oa_version":"None","month":"11","volume":73,"year":"2016","date_published":"2016-11-01T00:00:00Z","quality_controlled":"1","publisher":"American Medical Association","publication":"JAMA Psychiatry","day":"01","extern":"1","publication_status":"published","article_processing_charge":"No","citation":{"ieee":"W. J. Peyrot, M. R. Robinson, B. W. J. H. Penninx, and N. R. Wray, “Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits,” <i>JAMA Psychiatry</i>, vol. 73, no. 11. American Medical Association, pp. 1189–1195, 2016.","short":"W.J. Peyrot, M.R. Robinson, B.W.J.H. Penninx, N.R. Wray, JAMA Psychiatry 73 (2016) 1189–1195.","chicago":"Peyrot, Wouter J., Matthew Richard Robinson, Brenda W. J. H. Penninx, and Naomi R. Wray. “Exploring Boundaries for the Genetic Consequences of Assortative Mating for Psychiatric Traits.” <i>JAMA Psychiatry</i>. American Medical Association, 2016. <a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">https://doi.org/10.1001/jamapsychiatry.2016.2566</a>.","ama":"Peyrot WJ, Robinson MR, Penninx BWJH, Wray NR. Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits. <i>JAMA Psychiatry</i>. 2016;73(11):1189-1195. doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">10.1001/jamapsychiatry.2016.2566</a>","mla":"Peyrot, Wouter J., et al. “Exploring Boundaries for the Genetic Consequences of Assortative Mating for Psychiatric Traits.” <i>JAMA Psychiatry</i>, vol. 73, no. 11, American Medical Association, 2016, pp. 1189–95, doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">10.1001/jamapsychiatry.2016.2566</a>.","ista":"Peyrot WJ, Robinson MR, Penninx BWJH, Wray NR. 2016. Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits. JAMA Psychiatry. 73(11), 1189–1195.","apa":"Peyrot, W. J., Robinson, M. R., Penninx, B. W. J. H., &#38; Wray, N. R. (2016). Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits. <i>JAMA Psychiatry</i>. American Medical Association. <a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">https://doi.org/10.1001/jamapsychiatry.2016.2566</a>"},"_id":"7734","status":"public","date_created":"2020-04-30T10:48:41Z","article_type":"original","doi":"10.1001/jamapsychiatry.2016.2566","author":[{"last_name":"Peyrot","full_name":"Peyrot, Wouter J.","first_name":"Wouter J."},{"first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Penninx, Brenda W. J. H.","first_name":"Brenda W. J. H.","last_name":"Penninx"},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."}],"date_updated":"2021-01-12T08:15:11Z","abstract":[{"text":"Importance: Considerable partner resemblances have been found for a wide range of psychiatric disorders, meaning that partners of affected individuals have an increased risk of being affected compared with partners of unaffected individuals. If this resemblance is reflected in genetic similarity between partners, genetic risk is anticipated to accumulate in offspring, but these potential consequences have not been quantified and have been left implicit.\r\n\r\nObservations: The anticipated consequences of partner resemblance on prevalence and heritability of psychiatric traits in the offspring generation were modeled for disorders with varying heritabilities, population prevalence (lifetime risk), and magnitudes of partner resemblance. These models facilitate interpretation for a wide range of psychiatric disorders, such as autism, schizophrenia, and depression. The genetic consequences of partner resemblance are most pronounced when attributable to phenotypic assortment (driven by the psychiatric trait). Phenotypic assortment results in increased genetic variance in the offspring generation, which may result in increased heritability and population prevalence. These consequences add generation after generation to a limit, but assortative mating is unlikely to balance the impact of reduced fecundity of patients with psychiatric disorders in the long term. This modeling suggests that the heritabilities of psychiatric disorders are unlikely to increase by more than 5% from 1 generation of assortative mating (maximally 13% across multiple generations). The population prevalence will increase most for less common disorders with high heritability; for example, the prevalence of autism might increase by 1.5-fold after 1 generation of assortative mating (≥2.4-fold in the long term) depending on several assumptions.\r\n\r\nConclusions and Relevance: The considerable partner resemblances found for psychiatric disorders deserve more detailed interpretation than has been provided thus far. Although the limitations of modeling are emphasized, the anticipated consequences are at most modest for the heritability but may be considerable for the population prevalence of rare disorders with a high heritability.","lang":"eng"}],"issue":"11","intvolume":"        73"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"51-61","publication_identifier":{"issn":["0018-067X","1365-2540"]},"language":[{"iso":"eng"}],"title":"EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations","month":"05","year":"2016","volume":117,"oa_version":"None","publisher":"Springer Nature","publication":"Heredity","quality_controlled":"1","date_published":"2016-05-04T00:00:00Z","extern":"1","publication_status":"published","day":"04","citation":{"ista":"Chen G-B, Lee SH, Zhu Z-X, Benyamin B, Robinson MR. 2016. EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations. Heredity. 117, 51–61.","mla":"Chen, G. B., et al. “EigenGWAS: Finding Loci under Selection through Genome-Wide Association Studies of Eigenvectors in Structured Populations.” <i>Heredity</i>, vol. 117, Springer Nature, 2016, pp. 51–61, doi:<a href=\"https://doi.org/10.1038/hdy.2016.25\">10.1038/hdy.2016.25</a>.","ama":"Chen G-B, Lee SH, Zhu Z-X, Benyamin B, Robinson MR. EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations. <i>Heredity</i>. 2016;117:51-61. doi:<a href=\"https://doi.org/10.1038/hdy.2016.25\">10.1038/hdy.2016.25</a>","ieee":"G.-B. Chen, S. H. Lee, Z.-X. Zhu, B. Benyamin, and M. R. Robinson, “EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations,” <i>Heredity</i>, vol. 117. Springer Nature, pp. 51–61, 2016.","chicago":"Chen, G-B, S H Lee, Z-X Zhu, B Benyamin, and Matthew Richard Robinson. “EigenGWAS: Finding Loci under Selection through Genome-Wide Association Studies of Eigenvectors in Structured Populations.” <i>Heredity</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/hdy.2016.25\">https://doi.org/10.1038/hdy.2016.25</a>.","short":"G.-B. Chen, S.H. Lee, Z.-X. Zhu, B. Benyamin, M.R. Robinson, Heredity 117 (2016) 51–61.","apa":"Chen, G.-B., Lee, S. H., Zhu, Z.-X., Benyamin, B., &#38; Robinson, M. R. (2016). EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations. <i>Heredity</i>. Springer Nature. <a href=\"https://doi.org/10.1038/hdy.2016.25\">https://doi.org/10.1038/hdy.2016.25</a>"},"status":"public","_id":"7736","article_processing_charge":"No","doi":"10.1038/hdy.2016.25","date_created":"2020-04-30T10:50:03Z","article_type":"original","author":[{"full_name":"Chen, G-B","first_name":"G-B","last_name":"Chen"},{"full_name":"Lee, S H","first_name":"S H","last_name":"Lee"},{"full_name":"Zhu, Z-X","first_name":"Z-X","last_name":"Zhu"},{"last_name":"Benyamin","full_name":"Benyamin, B","first_name":"B"},{"first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"date_updated":"2021-01-12T08:15:11Z","intvolume":"       117","abstract":[{"text":"We develop a novel approach to identify regions of the genome underlying population genetic differentiation in any genetic data where the underlying population structure is unknown, or where the interest is assessing divergence along a gradient. By combining the statistical framework for genome-wide association studies (GWASs) with eigenvector decomposition (EigenGWAS), which is commonly used in population genetics to characterize the structure of genetic data, loci under selection can be identified without a requirement for discrete populations. We show through theory and simulation that our approach can identify regions under selection along gradients of ancestry, and in real data we confirm this by demonstrating LCT to be under selection between HapMap CEU–TSI cohorts, and we then validate this selection signal across European countries in the POPRES samples. HERC2 was also found to be differentiated between both the CEU–TSI cohort and within the POPRES sample, reflecting the likely anthropological differences in skin and hair colour between northern and southern European populations. Controlling for population stratification is of great importance in any quantitative genetic study and our approach also provides a simple, fast and accurate way of predicting principal components in independent samples. With ever increasing sample sizes across many fields, this approach is likely to be greatly utilized to gain individual-level eigenvectors avoiding the computational challenges associated with conducting singular value decomposition in large data sets. We have developed freely available software, Genetic Analysis Repository (GEAR), to facilitate the application of the methods.","lang":"eng"}]},{"status":"public","oa":1,"author":[{"last_name":"Zhu","first_name":"Zhihong","full_name":"Zhu, Zhihong"},{"last_name":"Zhang","full_name":"Zhang, Futao","first_name":"Futao"},{"first_name":"Han","full_name":"Hu, Han","last_name":"Hu"},{"full_name":"Bakshi, Andrew","first_name":"Andrew","last_name":"Bakshi"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"last_name":"Powell","first_name":"Joseph E","full_name":"Powell, Joseph E"},{"last_name":"Montgomery","first_name":"Grant W","full_name":"Montgomery, Grant W"},{"last_name":"Goddard","full_name":"Goddard, Michael E","first_name":"Michael E"},{"first_name":"Naomi R","full_name":"Wray, Naomi R","last_name":"Wray"},{"last_name":"Visscher","first_name":"Peter M","full_name":"Visscher, Peter M"},{"last_name":"Yang","full_name":"Yang, Jian","first_name":"Jian"}],"intvolume":"        48","issue":"5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"481-487","language":[{"iso":"eng"}],"title":"Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets","volume":48,"oa_version":"Published Version","quality_controlled":"1","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1038/ng.3538","open_access":"1"}],"citation":{"ista":"Zhu Z, Zhang F, Hu H, Bakshi A, Robinson MR, Powell JE, Montgomery GW, Goddard ME, Wray NR, Visscher PM, Yang J. 2016. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nature Genetics. 48(5), 481–487.","mla":"Zhu, Zhihong, et al. “Integration of Summary Data from GWAS and EQTL Studies Predicts Complex Trait Gene Targets.” <i>Nature Genetics</i>, vol. 48, no. 5, Springer Nature, 2016, pp. 481–87, doi:<a href=\"https://doi.org/10.1038/ng.3538\">10.1038/ng.3538</a>.","ama":"Zhu Z, Zhang F, Hu H, et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. <i>Nature Genetics</i>. 2016;48(5):481-487. doi:<a href=\"https://doi.org/10.1038/ng.3538\">10.1038/ng.3538</a>","chicago":"Zhu, Zhihong, Futao Zhang, Han Hu, Andrew Bakshi, Matthew Richard Robinson, Joseph E Powell, Grant W Montgomery, et al. “Integration of Summary Data from GWAS and EQTL Studies Predicts Complex Trait Gene Targets.” <i>Nature Genetics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/ng.3538\">https://doi.org/10.1038/ng.3538</a>.","ieee":"Z. Zhu <i>et al.</i>, “Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets,” <i>Nature Genetics</i>, vol. 48, no. 5. Springer Nature, pp. 481–487, 2016.","short":"Z. Zhu, F. Zhang, H. Hu, A. Bakshi, M.R. Robinson, J.E. Powell, G.W. Montgomery, M.E. Goddard, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 48 (2016) 481–487.","apa":"Zhu, Z., Zhang, F., Hu, H., Bakshi, A., Robinson, M. R., Powell, J. E., … Yang, J. (2016). Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ng.3538\">https://doi.org/10.1038/ng.3538</a>"},"_id":"7737","article_processing_charge":"No","doi":"10.1038/ng.3538","date_created":"2020-04-30T10:50:26Z","article_type":"original","date_updated":"2021-01-12T08:15:11Z","abstract":[{"text":"Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human complex traits. However, the genes or functional DNA elements through which these variants exert their effects on the traits are often unknown. We propose a method (called SMR) that integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. We apply the method to five human complex traits using GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates; 77 genes are not the nearest annotated gene to the top associated GWAS SNP. These genes provide important leads to design future functional studies to understand the mechanism whereby DNA variation leads to complex trait variation.","lang":"eng"}],"type":"journal_article","publication_identifier":{"issn":["1061-4036","1546-1718"]},"month":"03","year":"2016","publisher":"Springer Nature","publication":"Nature Genetics","date_published":"2016-03-28T00:00:00Z","extern":"1","day":"28"},{"date_updated":"2021-01-12T08:15:21Z","author":[{"first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"last_name":"Sethna","first_name":"James P.","full_name":"Sethna, James P."}],"abstract":[{"text":"We propose a Widom-like scaling ansatz for the critical jamming transition. Our ansatz for the elastic energy shows that the scaling of the energy, compressive strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear modulus are all related to each other via scaling relations, with only three independent scaling exponents. We extract the values of these exponents from already known numerical or theoretical results, and we numerically verify the resulting predictions of the scaling theory for the energy and residual shear stress. We also derive a scaling relation between pressure and residual shear stress that yields insight into why the shear and bulk moduli scale differently. Our theory shows that the jamming transition exhibits an emergent scale invariance, setting the stage for the potential development of a renormalization group theory for jamming.","lang":"eng"}],"issue":"35","intvolume":"       113","article_processing_charge":"No","_id":"7760","status":"public","citation":{"apa":"Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>","ama":"Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(35):9745-9750. doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>.","ieee":"C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming transition,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016.","short":"C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy of Sciences 113 (2016) 9745–9750.","ista":"Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. 113(35), 9745–9750.","mla":"Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35, Proceedings of the National Academy of Sciences, 2016, pp. 9745–50, doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>."},"article_type":"original","date_created":"2020-04-30T11:39:53Z","doi":"10.1073/pnas.1601858113","date_published":"2016-08-30T00:00:00Z","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","publisher":"Proceedings of the National Academy of Sciences","day":"30","publication_status":"published","extern":"1","title":"Scaling ansatz for the jamming transition","page":"9745-9750","publication_identifier":{"issn":["0027-8424","1091-6490"]},"language":[{"iso":"eng"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":113,"year":"2016","month":"08"},{"author":[{"last_name":"Graves","first_name":"Amy L.","full_name":"Graves, Amy L."},{"first_name":"Samer","full_name":"Nashed, Samer","last_name":"Nashed"},{"last_name":"Padgett","full_name":"Padgett, Elliot","first_name":"Elliot"},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"full_name":"Sethna, James P.","first_name":"James P.","last_name":"Sethna"}],"date_updated":"2021-01-12T08:15:21Z","intvolume":"       116","issue":"23","abstract":[{"text":"We study the effect of dilute pinning on the jamming transition. Pinning reduces the average contact number needed to jam unpinned particles and shifts the jamming threshold to lower densities, leading to a pinning susceptibility, χp. Our main results are that this susceptibility obeys scaling form and diverges in the thermodynamic limit as χp∝|ϕ−ϕ∞c|−γp where ϕ∞c is the jamming threshold in the absence of pins. Finite-size scaling arguments yield these values with associated statistical (systematic) errors γp=1.018±0.026(0.291) in d=2 and γp=1.534±0.120(0.822) in d=3. Logarithmic corrections raise the exponent in d=2 to close to the d=3 value, although the systematic errors are very large.","lang":"eng"}],"citation":{"chicago":"Graves, Amy L., Samer Nashed, Elliot Padgett, Carl Peter Goodrich, Andrea J. Liu, and James P. Sethna. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/physrevlett.116.235501\">https://doi.org/10.1103/physrevlett.116.235501</a>.","short":"A.L. Graves, S. Nashed, E. Padgett, C.P. Goodrich, A.J. Liu, J.P. Sethna, Physical Review Letters 116 (2016).","ieee":"A. L. Graves, S. Nashed, E. Padgett, C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Pinning susceptibility: The effect of dilute, quenched disorder on jamming,” <i>Physical Review Letters</i>, vol. 116, no. 23. American Physical Society, 2016.","ama":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. <i>Physical Review Letters</i>. 2016;116(23). doi:<a href=\"https://doi.org/10.1103/physrevlett.116.235501\">10.1103/physrevlett.116.235501</a>","mla":"Graves, Amy L., et al. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” <i>Physical Review Letters</i>, vol. 116, no. 23, 235501, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/physrevlett.116.235501\">10.1103/physrevlett.116.235501</a>.","ista":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. 2016. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. Physical Review Letters. 116(23), 235501.","apa":"Graves, A. L., Nashed, S., Padgett, E., Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Pinning susceptibility: The effect of dilute, quenched disorder on jamming. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.116.235501\">https://doi.org/10.1103/physrevlett.116.235501</a>"},"_id":"7761","status":"public","article_processing_charge":"No","doi":"10.1103/physrevlett.116.235501","date_created":"2020-04-30T11:40:10Z","article_type":"original","publisher":"American Physical Society","publication":"Physical Review Letters","article_number":"235501","quality_controlled":"1","date_published":"2016-06-10T00:00:00Z","extern":"1","publication_status":"published","day":"10","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007","1079-7114"]},"title":"Pinning susceptibility: The effect of dilute, quenched disorder on jamming","month":"06","year":"2016","volume":116,"oa_version":"None"},{"oa_version":"None","volume":116,"year":"2016","month":"02","title":"Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007","1079-7114"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"23","publication_status":"published","extern":"1","quality_controlled":"1","date_published":"2016-02-23T00:00:00Z","article_number":"088001 ","publication":"Physical Review Letters","publisher":"American Physical Society","article_type":"original","date_created":"2020-04-30T11:40:25Z","doi":"10.1103/physrevlett.116.088001","article_processing_charge":"No","status":"public","_id":"7762","citation":{"apa":"Rieser, J. M., Goodrich, C. P., Liu, A. J., &#38; Durian, D. J. (2016). Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.116.088001\">https://doi.org/10.1103/physrevlett.116.088001</a>","ama":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. <i>Physical Review Letters</i>. 2016;116(8). doi:<a href=\"https://doi.org/10.1103/physrevlett.116.088001\">10.1103/physrevlett.116.088001</a>","ieee":"J. M. Rieser, C. P. Goodrich, A. J. Liu, and D. J. Durian, “Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials,” <i>Physical Review Letters</i>, vol. 116, no. 8. American Physical Society, 2016.","chicago":"Rieser, Jennifer M., Carl Peter Goodrich, Andrea J. Liu, and Douglas J. Durian. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/physrevlett.116.088001\">https://doi.org/10.1103/physrevlett.116.088001</a>.","short":"J.M. Rieser, C.P. Goodrich, A.J. Liu, D.J. Durian, Physical Review Letters 116 (2016).","mla":"Rieser, Jennifer M., et al. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” <i>Physical Review Letters</i>, vol. 116, no. 8, 088001, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/physrevlett.116.088001\">10.1103/physrevlett.116.088001</a>.","ista":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. 2016. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. Physical Review Letters. 116(8), 088001."},"abstract":[{"lang":"eng","text":"Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to the centroid of the Voronoi cell in which the particle resides. These vectors tend to point in toward regions of high free volume and away from regions of low free volume, reminiscent of sinks and sources in a vector field. We compute the local divergence of these vectors, where positive values correspond to overpacked regions and negative values identify underpacked regions within the material. Distributions of this divergence are nearly Gaussian with zero mean, allowing for structural characterization using only the moments of the distribution. We explore how the standard deviation and skewness vary with the packing fraction for simulations of bidisperse systems and find a kink in these moments that coincides with the jamming transition."}],"issue":"8","intvolume":"       116","date_updated":"2021-01-12T08:15:22Z","author":[{"last_name":"Rieser","full_name":"Rieser, Jennifer M.","first_name":"Jennifer M."},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"first_name":"Douglas J.","full_name":"Durian, Douglas J.","last_name":"Durian"}]},{"abstract":[{"text":"An orthogonal wavelet basis is characterized by its approximation order, which relates to the ability of the basis to represent general smooth functions on a given scale. It is known, though perhaps not widely known, that there are ways of exceeding the approximation order, i.e., achieving higher-order error in the discretized wavelet transform and its inverse. The focus here is on the development of a practical formulation to accomplish this first for 1D smooth functions, then for 1D functions with discontinuities and then for multidimensional (here 2D) functions with discontinuities. It is shown how to transcend both the wavelet approximation order and the 2D Gibbs phenomenon in representing electromagnetic fields at discontinuous dielectric interfaces that do not simply follow the wavelet-basis grid.","lang":"eng"}],"intvolume":"       305","date_updated":"2021-01-12T08:15:22Z","author":[{"full_name":"Lombardini, Richard","first_name":"Richard","last_name":"Lombardini"},{"full_name":"Acevedo, Ramiro","first_name":"Ramiro","last_name":"Acevedo"},{"last_name":"Kuczala","first_name":"Alexander","full_name":"Kuczala, Alexander"},{"first_name":"Kerry P.","full_name":"Keys, Kerry P.","last_name":"Keys"},{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"last_name":"Johnson","full_name":"Johnson, Bruce R.","first_name":"Bruce R."}],"article_type":"original","date_created":"2020-04-30T11:40:41Z","doi":"10.1016/j.jcp.2015.10.035","article_processing_charge":"No","status":"public","_id":"7763","citation":{"chicago":"Lombardini, Richard, Ramiro Acevedo, Alexander Kuczala, Kerry P. Keys, Carl Peter Goodrich, and Bruce R. Johnson. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” <i>Journal of Computational Physics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">https://doi.org/10.1016/j.jcp.2015.10.035</a>.","ama":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. <i>Journal of Computational Physics</i>. 2016;305:244-262. doi:<a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">10.1016/j.jcp.2015.10.035</a>","ieee":"R. Lombardini, R. Acevedo, A. Kuczala, K. P. Keys, C. P. Goodrich, and B. R. Johnson, “Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena,” <i>Journal of Computational Physics</i>, vol. 305. Elsevier, pp. 244–262, 2016.","short":"R. Lombardini, R. Acevedo, A. Kuczala, K.P. Keys, C.P. Goodrich, B.R. Johnson, Journal of Computational Physics 305 (2016) 244–262.","ista":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. 2016. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal of Computational Physics. 305, 244–262.","mla":"Lombardini, Richard, et al. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” <i>Journal of Computational Physics</i>, vol. 305, Elsevier, 2016, pp. 244–62, doi:<a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">10.1016/j.jcp.2015.10.035</a>.","apa":"Lombardini, R., Acevedo, R., Kuczala, A., Keys, K. P., Goodrich, C. P., &#38; Johnson, B. R. (2016). Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">https://doi.org/10.1016/j.jcp.2015.10.035</a>"},"day":"15","publication_status":"published","extern":"1","date_published":"2016-01-15T00:00:00Z","quality_controlled":"1","publication":"Journal of Computational Physics","publisher":"Elsevier","oa_version":"None","year":"2016","volume":305,"month":"01","title":"Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena","page":"244-262","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9991"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3982-3990","publication_identifier":{"issn":["1744-683X","1744-6848"]},"language":[{"iso":"eng"}],"title":"Spatial structure of states of self stress in jammed systems","month":"03","year":"2016","volume":12,"oa_version":"None","publisher":"Royal Society of Chemistry","publication":"Soft Matter","quality_controlled":"1","date_published":"2016-03-14T00:00:00Z","extern":"1","publication_status":"published","day":"14","citation":{"apa":"Sussman, D. M., Goodrich, C. P., &#38; Liu, A. J. (2016). Spatial structure of states of self stress in jammed systems. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6sm00094k\">https://doi.org/10.1039/c6sm00094k</a>","chicago":"Sussman, Daniel M., Carl Peter Goodrich, and Andrea J. Liu. “Spatial Structure of States of Self Stress in Jammed Systems.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6sm00094k\">https://doi.org/10.1039/c6sm00094k</a>.","ieee":"D. M. Sussman, C. P. Goodrich, and A. J. Liu, “Spatial structure of states of self stress in jammed systems,” <i>Soft Matter</i>, vol. 12, no. 17. Royal Society of Chemistry, pp. 3982–3990, 2016.","ama":"Sussman DM, Goodrich CP, Liu AJ. Spatial structure of states of self stress in jammed systems. <i>Soft Matter</i>. 2016;12(17):3982-3990. doi:<a href=\"https://doi.org/10.1039/c6sm00094k\">10.1039/c6sm00094k</a>","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, Soft Matter 12 (2016) 3982–3990.","mla":"Sussman, Daniel M., et al. “Spatial Structure of States of Self Stress in Jammed Systems.” <i>Soft Matter</i>, vol. 12, no. 17, Royal Society of Chemistry, 2016, pp. 3982–90, doi:<a href=\"https://doi.org/10.1039/c6sm00094k\">10.1039/c6sm00094k</a>.","ista":"Sussman DM, Goodrich CP, Liu AJ. 2016. Spatial structure of states of self stress in jammed systems. Soft Matter. 12(17), 3982–3990."},"_id":"7764","status":"public","article_processing_charge":"No","doi":"10.1039/c6sm00094k","date_created":"2020-04-30T11:40:56Z","article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1039/c6sm02496c","relation":"other"}]},"author":[{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."}],"date_updated":"2021-01-12T08:15:22Z","intvolume":"        12","issue":"17","abstract":[{"lang":"eng","text":"States of self stress, organizations of internal forces in many-body systems that are in equilibrium with an absence of external forces, can be thought of as the constitutive building blocks of the elastic response of a material. In overconstrained disordered packings they have a natural mathematical correspondence with the zero-energy vibrational modes in underconstrained systems. While substantial attention in the literature has been paid to diverging length scales associated with zero- and finite-energy vibrational modes in jammed systems, less is known about the spatial structure of the states of self stress. In this work we define a natural way in which a unique state of self stress can be associated with each bond in a disordered spring network derived from a jammed packing, and then investigate the spatial structure of these bond-localized states of self stress. This allows for an understanding of how the elastic properties of a system would change upon changing the strength or even existence of any bond in the system."}]},{"publisher":"ACM","quality_controlled":"1","date_published":"2016-02-27T00:00:00Z","publication_status":"published","extern":"1","day":"27","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","title":"Lease/Release: Architectural support for scaling contended data structures","year":"2016","volume":"12-16-March-2016","month":"02","oa_version":"None","scopus_import":"1","date_updated":"2022-03-18T12:56:29Z","conference":{"name":"PPoPP: Principles and Practice of Parallel Pogramming"},"author":[{"last_name":"Haider","first_name":"Syed","full_name":"Haider, Syed"},{"first_name":"William","full_name":"Hasenplaugh, William","last_name":"Hasenplaugh"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"}],"abstract":[{"text":"High memory contention is generally agreed to be a worst-case scenario for concurrent data structures. There has been a significant amount of research effort spent investigating designs which minimize contention, and several programming techniques have been proposed to mitigate its effects. However, there are currently few architectural mechanisms to allow scaling contended data structures at high thread counts. In this paper, we investigate hardware support for scalable contended data structures. We propose Lease/Release, a simple addition to standard directory-based MSI cache coherence protocols, allowing participants to lease memory, at the granularity of cache lines, by delaying coherence messages for a short, bounded period of time. Our analysis shows that Lease/Release can significantly reduce the overheads of contention for both non-blocking (lock-free) and lock-based data structure implementations, while ensuring that no deadlocks are introduced. We validate Lease/Release empirically on the Graphite multiprocessor simulator, on a range of data structures, including queue, stack, and priority queue implementations, as well as on transactional applications. Results show that Lease/Release consistently improves both throughput and energy usage, by up to 5x, both for lock-free and lock-based data structure designs.","lang":"eng"}],"publist_id":"6871","_id":"785","status":"public","citation":{"mla":"Haider, Syed, et al. <i>Lease/Release: Architectural Support for Scaling Contended Data Structures</i>. Vol. 12-16-March-2016, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2851141.2851155\">10.1145/2851141.2851155</a>.","ista":"Haider S, Hasenplaugh W, Alistarh D-A. 2016. Lease/Release: Architectural support for scaling contended data structures. PPoPP: Principles and Practice of Parallel Pogramming vol. 12-16-March-2016.","chicago":"Haider, Syed, William Hasenplaugh, and Dan-Adrian Alistarh. “Lease/Release: Architectural Support for Scaling Contended Data Structures,” Vol. 12-16-March-2016. ACM, 2016. <a href=\"https://doi.org/10.1145/2851141.2851155\">https://doi.org/10.1145/2851141.2851155</a>.","ama":"Haider S, Hasenplaugh W, Alistarh D-A. Lease/Release: Architectural support for scaling contended data structures. In: Vol 12-16-March-2016. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2851141.2851155\">10.1145/2851141.2851155</a>","short":"S. Haider, W. Hasenplaugh, D.-A. Alistarh, in:, ACM, 2016.","ieee":"S. Haider, W. Hasenplaugh, and D.-A. Alistarh, “Lease/Release: Architectural support for scaling contended data structures,” presented at the PPoPP: Principles and Practice of Parallel Pogramming, 2016, vol. 12-16-March-2016.","apa":"Haider, S., Hasenplaugh, W., &#38; Alistarh, D.-A. (2016). Lease/Release: Architectural support for scaling contended data structures (Vol. 12-16-March-2016). Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. <a href=\"https://doi.org/10.1145/2851141.2851155\">https://doi.org/10.1145/2851141.2851155</a>"},"article_processing_charge":"No","doi":"10.1145/2851141.2851155","date_created":"2018-12-11T11:48:29Z","acknowledgement":"We would like to thank Richard Black, Miguel Castro, Dave Dice, Aleksandar Dragojevic, Maurice Herlihy, Ant Rowstron, Nir Shavit, and Vasileios Trigonakis, as well as the anonymous reviewers, for helpful suggestions during the development of this paper."},{"intvolume":"        63","issue":"4","author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Censor Hillel","first_name":"Keren","full_name":"Censor Hillel, Keren"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"oa":1,"status":"public","publication_status":"published","quality_controlled":"1","oa_version":"Preprint","volume":63,"arxiv":1,"title":"Are lock free concurrent algorithms practically wait free ","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6870","abstract":[{"text":"Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. Although obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most nonblocking commercial code is only lock-free. This article suggests a simple solution to this problem.We show that for a large class of lock-free algorithms, under scheduling conditions that approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can continue to design simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes to the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1 but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst-case adversary, in a stochastic model capturing their expected asymptotic behavior.","lang":"eng"}],"date_updated":"2023-02-23T13:19:04Z","acknowledgement":"Part of this work was performed while the first author was a postdoctoral associate at MIT CSAIL, where he was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations. The second author was supported in part by ISF grant 1696/14. The third author was supported in part by NSF grants CCF-1217921, CCF-1301926, IIS-1447786, and CCF-1561807, and the U.S. Department of Energy under grant DE-SC0008923, and by equipment grants from Intel Corporation.","date_created":"2018-12-11T11:48:29Z","external_id":{"arxiv":["1311.3200"]},"doi":"10.1145/2903136","article_processing_charge":"No","_id":"786","citation":{"apa":"Alistarh, D.-A., Censor Hillel, K., &#38; Shavit, N. (2016). Are lock free concurrent algorithms practically wait free . <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2903136\">https://doi.org/10.1145/2903136</a>","mla":"Alistarh, Dan-Adrian, et al. “Are Lock Free Concurrent Algorithms Practically Wait Free .” <i>Journal of the ACM</i>, vol. 63, no. 4, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2903136\">10.1145/2903136</a>.","ista":"Alistarh D-A, Censor Hillel K, Shavit N. 2016. Are lock free concurrent algorithms practically wait free . Journal of the ACM. 63(4).","short":"D.-A. Alistarh, K. Censor Hillel, N. Shavit, Journal of the ACM 63 (2016).","chicago":"Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock Free Concurrent Algorithms Practically Wait Free .” <i>Journal of the ACM</i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2903136\">https://doi.org/10.1145/2903136</a>.","ama":"Alistarh D-A, Censor Hillel K, Shavit N. Are lock free concurrent algorithms practically wait free . <i>Journal of the ACM</i>. 2016;63(4). doi:<a href=\"https://doi.org/10.1145/2903136\">10.1145/2903136</a>","ieee":"D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock free concurrent algorithms practically wait free ,” <i>Journal of the ACM</i>, vol. 63, no. 4. ACM, 2016."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3200"}],"day":"01","extern":"1","date_published":"2016-09-01T00:00:00Z","publication":"Journal of the ACM","publisher":"ACM","year":"2016","month":"09","type":"journal_article"},{"has_accepted_license":"1","issue":"1","intvolume":"        90","author":[{"last_name":"Barron","full_name":"Barron, H.C.","first_name":"H.C."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P"},{"last_name":"Emir","first_name":"U.E.","full_name":"Emir, U.E."},{"full_name":"Makin, T.R.","first_name":"T.R.","last_name":"Makin"},{"first_name":"J.","full_name":"O’Shea, J.","last_name":"O’Shea"},{"last_name":"Clare","full_name":"Clare, S.","first_name":"S."},{"last_name":"Jbabdi","full_name":"Jbabdi, S.","first_name":"S."},{"full_name":"Dolan, R.J.","first_name":"R.J.","last_name":"Dolan"},{"first_name":"T.E.J.","full_name":"Behrens, T.E.J.","last_name":"Behrens"}],"oa":1,"pmid":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"status":"public","file_date_updated":"2020-07-14T12:48:08Z","publication_status":"published","quality_controlled":"1","oa_version":"Published Version","volume":90,"title":"Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","language":[{"iso":"eng"}],"page":"191-203","abstract":[{"lang":"eng","text":"Balance of cortical excitation and inhibition (EI) is thought to be disrupted in several neuropsychiatric conditions, yet it is not clear how it is maintained in the healthy human brain. When EI balance is disturbed during learning and memory in animal models, it can be restabilized via formation of inhibitory replicas of newly formed excitatory connections. Here we assess evidence for such selective inhibitory rebalancing in humans. Using fMRI repetition suppression we measure newly formed cortical associations in the human brain. We show that expression of these associations reduces over time despite persistence in behavior, consistent with inhibitory rebalancing. To test this, we modulated excitation/inhibition balance with transcranial direct current stimulation (tDCS). Using ultra-high-field (7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations to be re-expressed. This suggests that in humans associative memories are stored in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory connections are unmasked."}],"date_updated":"2021-01-12T08:16:34Z","date_created":"2020-06-25T13:05:33Z","external_id":{"pmid":["26996082"]},"article_type":"original","doi":"10.1016/j.neuron.2016.02.031","article_processing_charge":"No","citation":{"mla":"Barron, H. C., et al. “Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories.” <i>Neuron</i>, vol. 90, no. 1, Elsevier, 2016, pp. 191–203, doi:<a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">10.1016/j.neuron.2016.02.031</a>.","ista":"Barron HC, Vogels TP, Emir UE, Makin TR, O’Shea J, Clare S, Jbabdi S, Dolan RJ, Behrens TEJ. 2016. Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. Neuron. 90(1), 191–203.","short":"H.C. Barron, T.P. Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S. Jbabdi, R.J. Dolan, T.E.J. Behrens, Neuron 90 (2016) 191–203.","ama":"Barron HC, Vogels TP, Emir UE, et al. Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. <i>Neuron</i>. 2016;90(1):191-203. doi:<a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">10.1016/j.neuron.2016.02.031</a>","ieee":"H. C. Barron <i>et al.</i>, “Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories,” <i>Neuron</i>, vol. 90, no. 1. Elsevier, pp. 191–203, 2016.","chicago":"Barron, H.C., Tim P Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S. Jbabdi, R.J. Dolan, and T.E.J. Behrens. “Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories.” <i>Neuron</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">https://doi.org/10.1016/j.neuron.2016.02.031</a>.","apa":"Barron, H. C., Vogels, T. P., Emir, U. E., Makin, T. R., O’Shea, J., Clare, S., … Behrens, T. E. J. (2016). Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2016.02.031\">https://doi.org/10.1016/j.neuron.2016.02.031</a>"},"_id":"8020","day":"06","extern":"1","date_published":"2016-04-06T00:00:00Z","file":[{"relation":"main_file","creator":"cziletti","date_updated":"2020-07-14T12:48:08Z","file_size":5334136,"file_name":"2016_Neuron_Barron.pdf","access_level":"open_access","checksum":"9ce7a1c64986dce0435c070285a7ef9b","content_type":"application/pdf","date_created":"2020-07-09T09:57:04Z","file_id":"8104"}],"publisher":"Elsevier","publication":"Neuron","month":"04","year":"2016","type":"journal_article","publication_identifier":{"issn":["0896-6273"]}},{"intvolume":"        28","has_accepted_license":"1","author":[{"last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S"},{"last_name":"Hostettler","first_name":"Rafael","full_name":"Hostettler, Rafael"},{"full_name":"Knoll, Alois","first_name":"Alois","last_name":"Knoll"},{"full_name":"Der, Ralf","first_name":"Ralf","last_name":"Der"}],"oa":1,"ddc":["610"],"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:48:09Z","publication_status":"published","quality_controlled":"1","volume":28,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"142-143","language":[{"iso":"eng"}],"corr_author":"1","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"scopus_import":"1","conference":{"end_date":"2016-07-08","name":"ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems","start_date":"2016-07-04","location":"Cancun, Mexico"},"date_updated":"2025-07-10T11:55:05Z","doi":"10.7551/978-0-262-33936-0-ch029","date_created":"2020-07-05T22:00:47Z","ec_funded":1,"citation":{"apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. 15th International Conference on the Synthesis and Simulation of Living Systems. ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, 15th International Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2016, pp. 142–143.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>."},"_id":"8094","article_processing_charge":"No","day":"01","publisher":"MIT Press","file":[{"file_size":678670,"date_updated":"2020-07-14T12:48:09Z","relation":"main_file","creator":"cziletti","file_name":"2016_ProcALIFE_Martius.pdf","access_level":"open_access","checksum":"cff63e7a4b8ac466ba51a9c84153a940","date_created":"2020-07-06T12:59:09Z","file_id":"8096","content_type":"application/pdf"}],"publication":"15th International Conference on the Synthesis and Simulation of Living Systems","date_published":"2016-09-01T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"month":"09","year":"2016","type":"conference","publication_identifier":{"isbn":["9780262339360"]}},{"date_published":"2016-07-29T00:00:00Z","publisher":"Cold Spring Harbor Laboratory","publication":"bioRxiv","day":"29","extern":"1","publication_status":"published","title":"Receptive field formation by interacting excitatory and inhibitory synaptic plasticity","type":"preprint","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","language":[{"iso":"eng"}],"page":"43","oa_version":"Preprint","month":"07","year":"2016","author":[{"first_name":"Claudia","full_name":"Clopath, Claudia","last_name":"Clopath"},{"full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","last_name":"Vogels"},{"full_name":"Froemke, Robert C.","first_name":"Robert C.","last_name":"Froemke"},{"first_name":"Henning","full_name":"Sprekeler, Henning","last_name":"Sprekeler"}],"date_updated":"2021-01-12T08:17:02Z","abstract":[{"lang":"eng","text":"The stimulus selectivity of synaptic currents in cortical neurons often shows a co-tuning of excitation and inhibition, but the mechanisms that underlie the emergence and plasticity of this co-tuning are not fully understood. Using a computational model, we show that an interaction of excitatory and inhibitory synaptic plasticity reproduces both the developmental and – when combined with a disinhibitory gate – the adult plasticity of excitatory and inhibitory receptive fields in auditory cortex. The co-tuning arises from inhibitory plasticity that balances excitation and inhibition, while excitatory stimulus selectivity can result from two different mechanisms. Inhibitory inputs with a broad stimulus tuning introduce a sliding threshold as in Bienenstock-Cooper-Munro rules, introducing an excitatory stimulus selectivity at the cost of a broader inhibitory receptive field. Alternatively, input asymmetries can be amplified by synaptic competition. The latter leaves any receptive field plasticity transient, a prediction we verify in recordings in auditory cortex."}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/066589 "}],"citation":{"ama":"Clopath C, Vogels TP, Froemke RC, Sprekeler H. Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. <i>bioRxiv</i>. 2016.","ieee":"C. Clopath, T. P. Vogels, R. C. Froemke, and H. Sprekeler, “Receptive field formation by interacting excitatory and inhibitory synaptic plasticity,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2016.","chicago":"Clopath, Claudia, Tim P Vogels, Robert C. Froemke, and Henning Sprekeler. “Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2016.","short":"C. Clopath, T.P. Vogels, R.C. Froemke, H. Sprekeler, BioRxiv (2016).","ista":"Clopath C, Vogels TP, Froemke RC, Sprekeler H. 2016. Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. bioRxiv, .","mla":"Clopath, Claudia, et al. “Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2016.","apa":"Clopath, C., Vogels, T. P., Froemke, R. C., &#38; Sprekeler, H. (2016). Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"status":"public","_id":"8128","date_created":"2020-07-16T12:26:55Z","oa":1},{"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","DOAJ_listed":"1","volume":90,"title":"Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"4593 - 4603","language":[{"iso":"eng"}],"intvolume":"        90","issue":"9","author":[{"full_name":"Füzik, Tibor","first_name":"Tibor","last_name":"Füzik"},{"last_name":"Píchalová","first_name":"Růžena","full_name":"Píchalová, Růžena"},{"full_name":"Schur, Florian","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078"},{"last_name":"Strohalmová","first_name":"Karolína","full_name":"Strohalmová, Karolína"},{"last_name":"Křížová","first_name":"Ivana","full_name":"Křížová, Ivana"},{"last_name":"Hadravová","full_name":"Hadravová, Romana","first_name":"Romana"},{"last_name":"Rumlová","full_name":"Rumlová, Michaela","first_name":"Michaela"},{"first_name":"John","full_name":"Briggs, John","last_name":"Briggs"},{"last_name":"Ulbrich","full_name":"Ulbrich, Pavel","first_name":"Pavel"},{"last_name":"Ruml","first_name":"Tomáš","full_name":"Ruml, Tomáš"}],"oa":1,"pmid":1,"OA_place":"publisher","status":"public","day":"01","extern":"1","date_published":"2016-05-01T00:00:00Z","publisher":"American Society for Microbiology","publication":"Journal of Virology","month":"05","year":"2016","OA_type":"gold","type":"journal_article","publication_identifier":{"eissn":["1098-5514"],"issn":["0022-538X"]},"publist_id":"6835","abstract":[{"lang":"eng","text":"The Gag polyprotein of retroviruses drives immature virus assembly by forming hexameric protein lattices. The assembly is primarily mediated by protein-protein interactions between capsid (CA) domains and by interactions between nucleocapsid (NC) domains and RNA. Specific interactions between NC and the viral RNA are required for genome packaging. Previously reported cryoelectron microscopy analysis of immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region (residues RKK) in CA may serve as an additional binding site for nucleic acids. Here, we have introduced mutations into the RKK region in both bacterial and proviral M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA binding, budding/release, nuclear trafficking, and infectivity using in vitro and in vivo systems. Our data indicate that the RKK region binds and structures nucleic acid that serves to promote virus particle assembly in the cytoplasm. Moreover, the RKK region appears to be important for recruitment of viral genomic RNA into Gag particles, and this function could be linked to changes in nuclear trafficking. Together these observations suggest that in M-PMV, direct interactions between CA and nucleic acid play important functions in the late stages of the viral life cycle."}],"date_updated":"2026-05-20T07:34:00Z","scopus_import":"1","acknowledgement":"Work in the laboratory of John A. G. Briggs was funded by Deutsche\r\nForschungsgemeinschaft (DFG) (BR 3635/2-1). This work, including the\r\nefforts of Tomas Ruml, was funded by the Grant Agency of the Czech\r\nRepublic (14-15326S) and the Czech Ministry of Education (NPU I sus-\r\ntainability projects LO1302 and LO1304).","date_created":"2018-12-11T11:48:38Z","external_id":{"pmid":["26912613"]},"article_type":"original","doi":"10.1128/JVI.03197-15","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1128/jvi.03197-15"}],"citation":{"ieee":"T. Füzik <i>et al.</i>, “Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging,” <i>Journal of Virology</i>, vol. 90, no. 9. American Society for Microbiology, pp. 4593–4603, 2016.","short":"T. Füzik, R. Píchalová, F.K. Schur, K. Strohalmová, I. Křížová, R. Hadravová, M. Rumlová, J. Briggs, P. Ulbrich, T. Ruml, Journal of Virology 90 (2016) 4593–4603.","ama":"Füzik T, Píchalová R, Schur FK, et al. Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. <i>Journal of Virology</i>. 2016;90(9):4593-4603. doi:<a href=\"https://doi.org/10.1128/JVI.03197-15\">10.1128/JVI.03197-15</a>","chicago":"Füzik, Tibor, Růžena Píchalová, Florian KM Schur, Karolína Strohalmová, Ivana Křížová, Romana Hadravová, Michaela Rumlová, John Briggs, Pavel Ulbrich, and Tomáš Ruml. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.” <i>Journal of Virology</i>. American Society for Microbiology, 2016. <a href=\"https://doi.org/10.1128/JVI.03197-15\">https://doi.org/10.1128/JVI.03197-15</a>.","mla":"Füzik, Tibor, et al. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.” <i>Journal of Virology</i>, vol. 90, no. 9, American Society for Microbiology, 2016, pp. 4593–603, doi:<a href=\"https://doi.org/10.1128/JVI.03197-15\">10.1128/JVI.03197-15</a>.","ista":"Füzik T, Píchalová R, Schur FK, Strohalmová K, Křížová I, Hadravová R, Rumlová M, Briggs J, Ulbrich P, Ruml T. 2016. Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. Journal of Virology. 90(9), 4593–4603.","apa":"Füzik, T., Píchalová, R., Schur, F. K., Strohalmová, K., Křížová, I., Hadravová, R., … Ruml, T. (2016). Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. <i>Journal of Virology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/JVI.03197-15\">https://doi.org/10.1128/JVI.03197-15</a>"},"_id":"813"},{"acknowledgement":"The authors thank B. Glass for preparation of the immature HIV-1 (D25A) sample; J. Plitzko and D. Tegunov for providing the K2Align software; and S. Mattei, N. Hoffman, F. Thommen, A. Sonnen, and S. Dodonova for technical assistance and/or discussion. This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.). The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory (EMBL) and from the Chica und Heinz Schaller Stiftung. W.W. was supported by a European Molecular Biology Organization Long-Term Fellowship (ALTF 748-2014). A.J.J. acknowledges support by the EMBL Interdisciplinary Postdoc Program under the Marie Curie Action COFUND (PCOFUND-GA-2008-229597) and by the Joachim Herz Stiftung. This study was technically supported by the EMBL information technology services unit and the EMBL Proteomics Core Facility. F.K.M.S., M.O., H.-G.K., and J.A.G.B. designed the experiments, with J.M.K. assisting in the design of those involving mass spectrometry. F.K.M.S. and M.O. prepared samples. W.J.H.H. implemented tomography acquisition schemes. F.K.M.S. and W.J.H.H. acquired the data. F.K.M.S. and W.W. processed images. F.K.M.S., A.J.J., and C.S. refined the model. F.K.M.S., M.O., and J.A.G.B. analyzed the data. F.K.M.S. and J.A.G.B. wrote the manuscript with support from all authors. Representative tomograms and the final electron microscopy structures have been deposited in the Electron Microscopy Data Bank with accession numbers EMD-4015, EMD-4016, EMD-4017, EMD-4018, EMD-4019, and EMD-4020. The refined HIV-1 CA-SP1 model has been deposited in the Protein Data Bank with accession number 5L93.","date_created":"2018-12-11T11:48:39Z","external_id":{"pmid":["27417497"]},"doi":"10.1126/science.aaf9620","pmid":1,"article_processing_charge":"No","status":"public","_id":"816","citation":{"mla":"Schur, Florian KM, et al. <i>An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation</i>. Vol. 353, American Association for the Advancement of Science, 2016, pp. 506–08, doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>.","ista":"Schur FK, Obr M, Hagen W, Wan W, Jakobi A, Kirkpatrick J, Sachse C, Kraüsslich H, Briggs J. 2016. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation, American Association for the Advancement of Science,p.","short":"F.K. Schur, M. Obr, W. Hagen, W. Wan, A. Jakobi, J. Kirkpatrick, C. Sachse, H. Kraüsslich, J. Briggs, An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation, American Association for the Advancement of Science, 2016.","ama":"Schur FK, Obr M, Hagen W, et al. <i>An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation</i>. Vol 353. American Association for the Advancement of Science; 2016:506-508. doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>","ieee":"F. K. Schur <i>et al.</i>, <i>An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation</i>, vol. 353. American Association for the Advancement of Science, 2016, pp. 506–508.","chicago":"Schur, Florian KM, Martin Obr, Wim Hagen, William Wan, Arjen Jakobi, Joanna Kirkpatrick, Carsten Sachse, Hans Kraüsslich, and John Briggs. <i>An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation</i>. Vol. 353. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>.","apa":"Schur, F. K., Obr, M., Hagen, W., Wan, W., Jakobi, A., Kirkpatrick, J., … Briggs, J. (2016). <i>An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation</i> (Vol. 353, pp. 506–508). American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>"},"abstract":[{"lang":"eng","text":"Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs.We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- And intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease.We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1."}],"publist_id":"6834","intvolume":"       353","date_updated":"2026-05-20T07:41:16Z","author":[{"last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Schur, Florian"},{"last_name":"Obr","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Obr, Martin"},{"full_name":"Hagen, Wim","first_name":"Wim","last_name":"Hagen"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"first_name":"Arjen","full_name":"Jakobi, Arjen","last_name":"Jakobi"},{"last_name":"Kirkpatrick","first_name":"Joanna","full_name":"Kirkpatrick, Joanna"},{"first_name":"Carsten","full_name":"Sachse, Carsten","last_name":"Sachse"},{"full_name":"Kraüsslich, Hans","first_name":"Hans","last_name":"Kraüsslich"},{"last_name":"Briggs","full_name":"Briggs, John","first_name":"John"}],"scopus_import":"1","oa_version":"None","volume":353,"year":"2016","month":"07","title":"An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation","page":"506 - 508","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"type":"report","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"29","publication_status":"published","extern":"1","date_published":"2016-07-29T00:00:00Z","publisher":"American Association for the Advancement of Science"},{"date_published":"2016-06-30T00:00:00Z","article_number":"e1171446","publication":"OncoImmunology","publisher":"Taylor & Francis","day":"30","extern":"1","publication_identifier":{"issn":["2162-402X"]},"type":"journal_article","year":"2016","month":"06","date_updated":"2021-01-12T08:17:41Z","abstract":[{"lang":"eng","text":"Background: Anticancer vaccines could represent a valuable complementary strategy to established therapies, especially in settings of early stage and minimal residual disease. HER-2 is an important target for immunotherapy and addressed by the monoclonal antibody trastuzumab. We have previously generated HER-2 mimotope peptides from phage display libraries. The synthesized peptides were coupled to carriers and applied for epitope-specific induction of trastuzumab-like IgG. For simplification and to avoid methodological limitations of synthesis and coupling chemistry, we herewith present a novel and optimized approach by using adeno-associated viruses (AAV) as effective and high-density mimotope-display system, which can be directly used for vaccination. Methods: An AAV capsid display library was constructed by genetically incorporating random peptides in a plasmid encoding the wild-type AAV2 capsid protein. AAV clones, expressing peptides specifically reactive to trastuzumab, were employed to immunize BALB/c mice. Antibody titers against human HER-2 were determined, and the isotype composition and functional properties of these were tested. Finally, prophylactically immunized mice were challenged with human HER-2 transfected mouse D2F2/E2 cells. Results: HER-2 mimotope AAV-vaccines induced antibodies specific to human HER-2. Two clones were selected for immunization of mice, which were subsequently grafted D2F2/E2 cells. Both mimotope AAV clones delayed the growth of tumors significantly, as compared to controls. Conclusion: In this study, a novel mimotope AAV-based platform was created allowing the isolation of mimotopes, which can be directly used as anticancer vaccines. The example of trastuzumab AAV-mimotopes demonstrates that this vaccine strategy could help to establish active immunotherapy for breast-cancer patients."}],"article_processing_charge":"No","_id":"8241","citation":{"short":"J. Singer, K. Manzano-Szalai, J. Singer, K. Thell, A. Bentley-Lukschal, C. Stremnitzer, F. Roth-Walter, M. Weghofer, M. Ritter, K. Pino Tossi, M. Hörer, U. Michaelis, E. Jensen-Jarolim, OncoImmunology 5 (2016).","chicago":"Singer, Josef, Krisztina Manzano-Szalai, Judit Singer, Kathrin Thell, Anna Bentley-Lukschal, Caroline Stremnitzer, Franziska Roth-Walter, et al. “Proof of Concept Study with an HER-2 Mimotope Anticancer Vaccine Deduced from a Novel AAV-Mimotope Library Platform.” <i>OncoImmunology</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">https://doi.org/10.1080/2162402x.2016.1171446</a>.","ieee":"J. Singer <i>et al.</i>, “Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform,” <i>OncoImmunology</i>, vol. 5, no. 7. Taylor &#38; Francis, 2016.","ama":"Singer J, Manzano-Szalai K, Singer J, et al. Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform. <i>OncoImmunology</i>. 2016;5(7). doi:<a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">10.1080/2162402x.2016.1171446</a>","mla":"Singer, Josef, et al. “Proof of Concept Study with an HER-2 Mimotope Anticancer Vaccine Deduced from a Novel AAV-Mimotope Library Platform.” <i>OncoImmunology</i>, vol. 5, no. 7, e1171446, Taylor &#38; Francis, 2016, doi:<a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">10.1080/2162402x.2016.1171446</a>.","ista":"Singer J, Manzano-Szalai K, Singer J, Thell K, Bentley-Lukschal A, Stremnitzer C, Roth-Walter F, Weghofer M, Ritter M, Pino Tossi K, Hörer M, Michaelis U, Jensen-Jarolim E. 2016. Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform. OncoImmunology. 5(7), e1171446.","apa":"Singer, J., Manzano-Szalai, K., Singer, J., Thell, K., Bentley-Lukschal, A., Stremnitzer, C., … Jensen-Jarolim, E. (2016). Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform. <i>OncoImmunology</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">https://doi.org/10.1080/2162402x.2016.1171446</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/2162402X.2016.1171446"}],"article_type":"original","date_created":"2020-08-10T11:54:03Z","doi":"10.1080/2162402x.2016.1171446","quality_controlled":"1","publication_status":"published","title":"Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","volume":5,"author":[{"last_name":"Singer","first_name":"Josef","full_name":"Singer, Josef"},{"first_name":"Krisztina","full_name":"Manzano-Szalai, Krisztina","last_name":"Manzano-Szalai"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","last_name":"Fazekas","full_name":"Fazekas, Judit","first_name":"Judit"},{"last_name":"Thell","full_name":"Thell, Kathrin","first_name":"Kathrin"},{"last_name":"Bentley-Lukschal","first_name":"Anna","full_name":"Bentley-Lukschal, Anna"},{"last_name":"Stremnitzer","first_name":"Caroline","full_name":"Stremnitzer, Caroline"},{"first_name":"Franziska","full_name":"Roth-Walter, Franziska","last_name":"Roth-Walter"},{"full_name":"Weghofer, Margit","first_name":"Margit","last_name":"Weghofer"},{"full_name":"Ritter, Mirko","first_name":"Mirko","last_name":"Ritter"},{"last_name":"Pino Tossi","full_name":"Pino Tossi, Kerstin","first_name":"Kerstin"},{"last_name":"Hörer","full_name":"Hörer, Markus","first_name":"Markus"},{"last_name":"Michaelis","first_name":"Uwe","full_name":"Michaelis, Uwe"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"}],"intvolume":"         5","issue":"7","status":"public","oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781509013142"]},"title":"TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet of Things","month":"09","year":"2016","oa_version":"None","publisher":"IEEE","publication":"2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation","quality_controlled":"1","date_published":"2016-09-09T00:00:00Z","article_number":"7733612","extern":"1","publication_status":"published","day":"09","citation":{"ieee":"E. Kokoris Kogias, O. Voutyras, and T. Varvarigou, “TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things,” in <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>, Berlin, Germany, 2016.","ama":"Kokoris Kogias E, Voutyras O, Varvarigou T. TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things. In: <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/etfa.2016.7733612\">10.1109/etfa.2016.7733612</a>","chicago":"Kokoris Kogias, Eleftherios, Orfefs Voutyras, and Theodora Varvarigou. “TRM-SIoT: A Scalable Hybrid Trust &#38; Reputation Model for the Social Internet of Things.” In <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>. IEEE, 2016. <a href=\"https://doi.org/10.1109/etfa.2016.7733612\">https://doi.org/10.1109/etfa.2016.7733612</a>.","short":"E. Kokoris Kogias, O. Voutyras, T. Varvarigou, in:, 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation, IEEE, 2016.","mla":"Kokoris Kogias, Eleftherios, et al. “TRM-SIoT: A Scalable Hybrid Trust &#38; Reputation Model for the Social Internet of Things.” <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>, 7733612, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/etfa.2016.7733612\">10.1109/etfa.2016.7733612</a>.","ista":"Kokoris Kogias E, Voutyras O, Varvarigou T. 2016. TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things. 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation. ETFA: Conference on Emerging Technologies and Factory Automation, 7733612.","apa":"Kokoris Kogias, E., Voutyras, O., &#38; Varvarigou, T. (2016). TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things. In <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>. Berlin, Germany: IEEE. <a href=\"https://doi.org/10.1109/etfa.2016.7733612\">https://doi.org/10.1109/etfa.2016.7733612</a>"},"_id":"8300","status":"public","article_processing_charge":"No","doi":"10.1109/etfa.2016.7733612","date_created":"2020-08-26T11:48:54Z","author":[{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios"},{"full_name":"Voutyras, Orfefs","first_name":"Orfefs","last_name":"Voutyras"},{"full_name":"Varvarigou, Theodora","first_name":"Theodora","last_name":"Varvarigou"}],"conference":{"end_date":"2016-09-09","name":"ETFA: Conference on Emerging Technologies and Factory Automation","start_date":"2016-09-06","location":"Berlin, Germany"},"date_updated":"2021-01-12T08:17:59Z","abstract":[{"lang":"eng","text":"The integration of social networking concepts into Internet of Things systems is a burgeoning topic of research that promises to support novel and more powerful applications. In this paper we focus on the design and implementation of a highly scalable Trust and Reputation Model for the Internet of Things based on the social approach that the COSMOS project introduces, as part of its final results. We create our model by combining popular solutions proposed for Peer-to-Peer and mobile ad-hoc networks and adapting them on the Internet of Things concept. Each Thing can compute the Trust index of another Thing based on its own experiences, while it has the capability of determining its Reputation Index either by consulting its other “friends” (Followees) or referring to the Platform, a management system used in COSMOS. The model is tested through simulations of the proposed social system, demonstrating the ability of TRM-SIoT to achieve the Social Exclusion of malicious nodes and collectives from the network, with low computational overhead and high scalability. Furthermore, due to the adaptive nature of the system, Social Reintegration of these nodes is also possible."}]}]