[{"title":"Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel","article_processing_charge":"No","author":[{"full_name":"Bevers, Roel P. J.","last_name":"Bevers","first_name":"Roel P. J."},{"full_name":"Litovchenko, Maria","last_name":"Litovchenko","first_name":"Maria"},{"full_name":"Kapopoulou, Adamandia","last_name":"Kapopoulou","first_name":"Adamandia"},{"first_name":"Virginie S.","last_name":"Braman","full_name":"Braman, Virginie S."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"first_name":"Johan","full_name":"Auwerx, Johan","last_name":"Auwerx"},{"full_name":"Hollis, Brian","last_name":"Hollis","first_name":"Brian"},{"last_name":"Deplancke","full_name":"Deplancke, Bart","first_name":"Bart"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242.","chicago":"Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3.","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3","apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-019-0147-3","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242.","ieee":"R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019.","mla":"Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3."},"date_updated":"2021-01-12T08:15:01Z","status":"public","article_type":"original","type":"journal_article","_id":"7711","date_created":"2020-04-30T10:40:56Z","issue":"12","volume":1,"doi":"10.1038/s42255-019-0147-3","date_published":"2019-12-09T00:00:00Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-020-0202-0"}]},"page":"1226-1242","language":[{"iso":"eng"}],"publication":"Nature Metabolism","day":"09","publication_status":"published","year":"2019","publication_identifier":{"issn":["2522-5812"]},"intvolume":" 1","month":"12","publisher":"Springer Nature","quality_controlled":"1","oa_version":"None","abstract":[{"text":"The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies.","lang":"eng"}]},{"type":"preprint","status":"public","_id":"7782","article_processing_charge":"No","author":[{"full_name":"Sulc, Jonathan","last_name":"Sulc","first_name":"Jonathan"},{"first_name":"Ninon","full_name":"Mounier, Ninon","last_name":"Mounier"},{"last_name":"Günther","full_name":"Günther, Felix","first_name":"Felix"},{"last_name":"Winkler","full_name":"Winkler, Thomas","first_name":"Thomas"},{"first_name":"Andrew R.","full_name":"Wood, Andrew R.","last_name":"Wood"},{"first_name":"Timothy M.","last_name":"Frayling","full_name":"Frayling, Timothy M."},{"first_name":"Iris M.","full_name":"Heid, Iris M.","last_name":"Heid"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"first_name":"Zoltán","last_name":"Kutalik","full_name":"Kutalik, Zoltán"}],"title":"Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank","date_updated":"2021-01-12T08:15:30Z","citation":{"ista":"Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv, .","chicago":"Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv. Cold Spring Harbor Laboratory, 2019.","apa":"Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. Cold Spring Harbor Laboratory.","ama":"Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. 2019.","ieee":"J. Sulc et al., “Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank,” bioRxiv. Cold Spring Harbor Laboratory, 2019.","short":"J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019).","mla":"Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv, Cold Spring Harbor Laboratory, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/632380 "}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","month":"06","abstract":[{"lang":"eng","text":"As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures."}],"oa_version":"Preprint","page":"20","date_created":"2020-04-30T13:04:26Z","date_published":"2019-06-14T00:00:00Z","year":"2019","publication_status":"published","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"14"},{"file_date_updated":"2020-07-14T12:48:08Z","extern":"1","ddc":["570"],"date_updated":"2021-01-12T08:16:31Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8013","issue":"7","volume":15,"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"file_id":"8079","checksum":"723bdfb6ee5c747cbbb32baf01d17fad","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_PlosCompBio_Currin.pdf","date_created":"2020-07-02T12:22:57Z","file_size":773969,"date_updated":"2020-07-14T12:48:08Z","creator":"cziletti"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","month":"07","intvolume":" 15","oa_version":"Published Version","pmid":1,"title":"Think: Theory for Africa","author":[{"first_name":"Christopher B.","full_name":"Currin, Christopher B.","last_name":"Currin"},{"first_name":"Phumlani N.","last_name":"Khoza","full_name":"Khoza, Phumlani N."},{"last_name":"Antrobus","full_name":"Antrobus, Alexander D.","first_name":"Alexander D."},{"first_name":"Peter E.","last_name":"Latham","full_name":"Latham, Peter E."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"last_name":"Raimondo","full_name":"Raimondo, Joseph V.","first_name":"Joseph V."}],"external_id":{"pmid":["31295253"]},"article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.","apa":"Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P., & Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049","ama":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think: Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049","ieee":"C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","short":"C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo, PLOS Computational Biology 15 (2019).","chicago":"Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.","ista":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019. Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049."},"article_number":"e1007049","date_published":"2019-07-11T00:00:00Z","doi":"10.1371/journal.pcbi.1007049","date_created":"2020-06-25T12:50:39Z","day":"11","publication":"PLOS Computational Biology","has_accepted_license":"1","year":"2019","quality_controlled":"1","publisher":"Public Library of Science","oa":1},{"ddc":["570"],"extern":"1","date_updated":"2021-01-12T08:16:31Z","file_date_updated":"2020-07-14T12:48:08Z","_id":"8014","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2020-07-02T13:17:52Z","file_name":"2019_NeurosBiobehavRev_Manohar.pdf","creator":"cziletti","date_updated":"2020-07-14T12:48:08Z","file_size":1754418,"file_id":"8080","checksum":"7b972e3d6f7bb3122c8c5648f44e60ca","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0149-7634"]},"volume":101,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Working memory, the ability to keep recently accessed information available for immediate manipulation, has been proposed to rely on two mechanisms that appear difficult to reconcile: self-sustained neural firing, or the opposite—activity-silent synaptic traces. Here we review and contrast models of these two mechanisms, and then show that both phenomena can co-exist within a unified system in which neurons hold information in both activity and synapses. Rapid plasticity in flexibly-coding neurons allows features to be bound together into objects, with an important emergent property being the focus of attention. One memory item is held by persistent activity in an attended or “focused” state, and is thus remembered better than other items. Other, previously attended items can remain in memory but in the background, encoded in activity-silent synaptic traces. This dual functional architecture provides a unified common mechanism accounting for a diversity of perplexing attention and memory effects that have been hitherto difficult to explain in a single theoretical framework."}],"intvolume":" 101","month":"06","main_file_link":[{"url":"https://doi.org/10.1101/233007 ","open_access":"1"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Manohar, Sanjay G., et al. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews, vol. 101, Elsevier , 2019, pp. 1–12, doi:10.1016/j.neubiorev.2019.03.017.","ieee":"S. G. Manohar, N. Zokaei, S. J. Fallon, T. P. Vogels, and M. Husain, “Neural mechanisms of attending to items in working memory,” Neuroscience and Biobehavioral Reviews, vol. 101. Elsevier , pp. 1–12, 2019.","short":"S.G. Manohar, N. Zokaei, S.J. Fallon, T.P. Vogels, M. Husain, Neuroscience and Biobehavioral Reviews 101 (2019) 1–12.","ama":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 2019;101:1-12. doi:10.1016/j.neubiorev.2019.03.017","apa":"Manohar, S. G., Zokaei, N., Fallon, S. J., Vogels, T. P., & Husain, M. (2019). Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. Elsevier . https://doi.org/10.1016/j.neubiorev.2019.03.017","chicago":"Manohar, Sanjay G., Nahid Zokaei, Sean J. Fallon, Tim P Vogels, and Masud Husain. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews. Elsevier , 2019. https://doi.org/10.1016/j.neubiorev.2019.03.017.","ista":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. 2019. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 101, 1–12."},"title":"Neural mechanisms of attending to items in working memory","external_id":{"pmid":["30922977"]},"article_processing_charge":"No","author":[{"full_name":"Manohar, Sanjay G.","last_name":"Manohar","first_name":"Sanjay G."},{"last_name":"Zokaei","full_name":"Zokaei, Nahid","first_name":"Nahid"},{"first_name":"Sean J.","full_name":"Fallon, Sean J.","last_name":"Fallon"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Husain, Masud","last_name":"Husain","first_name":"Masud"}],"publication":"Neuroscience and Biobehavioral Reviews","day":"01","year":"2019","has_accepted_license":"1","date_created":"2020-06-25T12:52:13Z","date_published":"2019-06-01T00:00:00Z","doi":"10.1016/j.neubiorev.2019.03.017","page":"1-12","oa":1,"publisher":"Elsevier ","quality_controlled":"1"},{"acknowledgement":"D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n","oa":1,"quality_controlled":"1","publisher":"Formal Power Series and Algebraic Combinatorics","publication":"Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics","day":"01","year":"2019","date_created":"2020-07-26T22:01:04Z","date_published":"2019-07-01T00:00:00Z","article_number":"34","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.","chicago":"Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019.","ama":"Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019.","mla":"Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019."},"title":"New edge asymptotics of skew Young diagrams via free boundaries","article_processing_charge":"No","external_id":{"arxiv":["1902.08750"]},"author":[{"first_name":"Dan","last_name":"Betea","full_name":"Betea, Dan"},{"last_name":"Bouttier","full_name":"Bouttier, Jérémie","first_name":"Jérémie"},{"full_name":"Nejjar, Peter","last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mirjana","last_name":"Vuletíc","full_name":"Vuletíc, Mirjana"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices."}],"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.08750"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"_id":"8175","status":"public","conference":{"end_date":"2019-07-05","location":"Ljubljana, Slovenia","start_date":"2019-07-01","name":"FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics"},"type":"conference","date_updated":"2021-01-12T08:17:18Z","department":[{"_id":"LaEr"}]},{"extern":"1","date_updated":"2021-01-12T08:17:36Z","_id":"8228","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1939-4551"]},"publication_status":"published","volume":12,"issue":"7","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE.\r\nMethods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy.\r\nConclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge."}],"month":"07","intvolume":" 12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.waojou.2019.100044"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G, Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 12(7), 100044.","chicago":"Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.","ama":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044","apa":"Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044","ieee":"J. Singer et al., “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” World Allergy Organization Journal, vol. 12, no. 7. Elsevier, 2019.","short":"J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz, S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019).","mla":"Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal, vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044."},"title":"AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice","author":[{"last_name":"Singer","orcid":"0000-0002-8701-2412","full_name":"Singer, Josef","first_name":"Josef"},{"first_name":"Gertrude","full_name":"Achatz-Straussberger, Gertrude","last_name":"Achatz-Straussberger"},{"full_name":"Bentley-Lukschal, Anna","last_name":"Bentley-Lukschal","first_name":"Anna"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"first_name":"Gernot","full_name":"Achatz, Gernot","last_name":"Achatz"},{"full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis","first_name":"Sophia N."},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"}],"article_processing_charge":"No","article_number":"100044","day":"29","publication":"World Allergy Organization Journal","year":"2019","doi":"10.1016/j.waojou.2019.100044","date_published":"2019-07-29T00:00:00Z","date_created":"2020-08-10T11:50:54Z","publisher":"Elsevier","quality_controlled":"1","oa":1},{"extern":"1","date_updated":"2021-01-12T08:17:36Z","_id":"8229","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2072-6643"]},"issue":"10","volume":11,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Food proteins may get nitrated by various exogenous or endogenous mechanisms. As individuals might get recurrently exposed to nitrated proteins via daily diet, we aimed to investigate the effect of repeatedly ingested nitrated food proteins on the subsequent immune response in non-allergic and allergic mice using the milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model. Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine (3-NT) in extracts of different foods and in stomach content extracts of non-allergic mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited enhanced susceptibility to degradation in simulated gastric fluid experiments compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased interferon-γ and interleukin-10 release of stimulated spleen cells and led to the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic mice receiving BLGu. Regardless of the preceding immune status, non-allergic or allergic, repeatedly ingested nitrated food proteins seem to considerably influence the subsequent immune response."}],"intvolume":" 11","month":"10","main_file_link":[{"url":"https://doi.org/10.3390/nu11102463","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 11(10), 2463.","chicago":"Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst, Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463.","apa":"Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr, C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463","ama":"Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 2019;11(10). doi:10.3390/nu11102463","ieee":"A. S. Ondracek et al., “Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol. 11, no. 10. MDPI, 2019.","short":"A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr, J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019).","mla":"Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463, MDPI, 2019, doi:10.3390/nu11102463."},"title":"Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model","article_processing_charge":"No","author":[{"first_name":"Anna S.","orcid":"0000-0001-7625-3651","full_name":"Ondracek, Anna S.","last_name":"Ondracek"},{"first_name":"Denise","last_name":"Heiden","full_name":"Heiden, Denise"},{"last_name":"Oostingh","full_name":"Oostingh, Gertie J.","first_name":"Gertie J."},{"full_name":"Fuerst, Elisabeth","last_name":"Fuerst","first_name":"Elisabeth"},{"full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer","first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Cornelia","full_name":"Bergmayr, Cornelia","last_name":"Bergmayr"},{"first_name":"Johanna","orcid":"0000-0002-2783-2099","full_name":"Rohrhofer, Johanna","last_name":"Rohrhofer"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","orcid":"0000-0003-4019-5765","first_name":"Erika"},{"first_name":"Albert","orcid":"0000-0002-7034-9860","full_name":"Duschl, Albert","last_name":"Duschl"},{"first_name":"Eva","last_name":"Untersmayr","full_name":"Untersmayr, Eva","orcid":"0000-0002-1963-499X"}],"article_number":"2463","publication":"Nutrients","day":"15","year":"2019","date_created":"2020-08-10T11:51:04Z","doi":"10.3390/nu11102463","date_published":"2019-10-15T00:00:00Z","oa":1,"publisher":"MDPI","quality_controlled":"1"},{"citation":{"ista":"Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989.","chicago":"Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy. Wiley, 2019. https://doi.org/10.1111/all.13818.","apa":"Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L., Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley. https://doi.org/10.1111/all.13818","ama":"Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989. doi:10.1111/all.13818","short":"K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele, H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim, A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989.","ieee":"K. M. Ilieva et al., “AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74, no. 10. Wiley, pp. 1985–1989, 2019.","mla":"Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74, no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818."},"date_updated":"2021-01-12T08:17:35Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ilieva","full_name":"Ilieva, Kristina M.","first_name":"Kristina M."},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer"},{"full_name":"Bax, Heather J.","last_name":"Bax","first_name":"Heather J."},{"full_name":"Crescioli, Silvia","last_name":"Crescioli","first_name":"Silvia"},{"first_name":"Laura","last_name":"Montero‐Morales","full_name":"Montero‐Morales, Laura"},{"last_name":"Mele","full_name":"Mele, Silvia","first_name":"Silvia"},{"first_name":"Heng Sheng","full_name":"Sow, Heng Sheng","last_name":"Sow"},{"full_name":"Stavraka, Chara","last_name":"Stavraka","first_name":"Chara"},{"first_name":"Debra H.","last_name":"Josephs","full_name":"Josephs, Debra H."},{"last_name":"Spicer","full_name":"Spicer, James F.","first_name":"James F."},{"first_name":"Herta","orcid":"0000-0003-4823-1505","full_name":"Steinkellner, Herta","last_name":"Steinkellner"},{"first_name":"Erika","full_name":"Jensen‐Jarolim, Erika","orcid":"0000-0003-4019-5765","last_name":"Jensen‐Jarolim"},{"full_name":"Tutt, Andrew N. J.","orcid":"0000-0001-8715-2901","last_name":"Tutt","first_name":"Andrew N. J."},{"orcid":"0000-0002-4100-7810","full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis","first_name":"Sophia N."}],"article_processing_charge":"No","title":"AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody","_id":"8227","article_type":"letter_note","type":"journal_article","status":"public","publication_identifier":{"issn":["0105-4538","1398-9995"]},"year":"2019","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Allergy","page":"1985-1989","issue":"10","doi":"10.1111/all.13818","volume":74,"date_published":"2019-10-01T00:00:00Z","date_created":"2020-08-10T11:50:42Z","oa_version":"Published Version","quality_controlled":"1","publisher":"Wiley","oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/all.13818","open_access":"1"}],"month":"10","intvolume":" 74"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.1186/s12862-019-1403-6","open_access":"1"}],"quality_controlled":"1","publisher":"Springer Nature","intvolume":" 19","month":"03","abstract":[{"text":"Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.","lang":"eng"}],"oa_version":"Published Version","date_created":"2020-08-15T11:04:07Z","date_published":"2019-03-27T00:00:00Z","volume":19,"doi":"10.1186/s12862-019-1403-6","publication_status":"published","year":"2019","publication_identifier":{"issn":["1471-2148"]},"language":[{"iso":"eng"}],"publication":"BMC Evolutionary Biology","day":"27","article_type":"original","type":"journal_article","status":"public","_id":"8263","article_number":"83","article_processing_charge":"No","author":[{"full_name":"Shelyakin, Pavel V.","orcid":"0000-0003-0120-9319","last_name":"Shelyakin","first_name":"Pavel V."},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva"},{"first_name":"Anna A.","last_name":"Karan","full_name":"Karan, Anna A."},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","date_updated":"2023-02-23T13:28:54Z","citation":{"ieee":"P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.","short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019).","apa":"Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6","ama":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6","mla":"Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.","ista":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83.","chicago":"Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:17:56Z","citation":{"short":"E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112.","ieee":"E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating Systems, Bertinoro, Italy, 2019, pp. 105–112.","apa":"Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking general-purpose decentralized computing. In Proceedings of the Workshop on Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448","ama":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448","mla":"Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.” Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–12, doi:10.1145/3317550.3321448.","ista":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose decentralized computing. Proceedings of the Workshop on Hot Topics in Operating Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.","chicago":"Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448."},"title":"Rethinking general-purpose decentralized computing","author":[{"full_name":"Alp, Enis Ceyhun","last_name":"Alp","first_name":"Enis Ceyhun"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Fragkouli, Georgia","last_name":"Fragkouli","first_name":"Georgia"},{"first_name":"Bryan","full_name":"Ford, Bryan","last_name":"Ford"}],"article_processing_charge":"No","_id":"8296","status":"public","type":"conference","conference":{"name":"HotOS: Workshop on Hot Topics in Operating Systems","end_date":"2019-05-15","location":"Bertinoro, Italy","start_date":"2019-05-13"},"day":"01","publication":"Proceedings of the Workshop on Hot Topics in Operating Systems","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450367271"]},"publication_status":"published","year":"2019","doi":"10.1145/3317550.3321448","date_published":"2019-05-01T00:00:00Z","date_created":"2020-08-26T11:45:45Z","page":"105-112","oa_version":"None","abstract":[{"lang":"eng","text":"While showing great promise, smart contracts are difficult to program correctly, as they need a deep understanding of cryptography and distributed algorithms, and offer limited functionality, as they have to be deterministic and cannot operate on secret data. In this paper we present Protean, a general-purpose decentralized computing platform that addresses these limitations by moving from a monolithic execution model, where all participating nodes store all the state and execute every computation, to a modular execution-model. Protean employs secure specialized modules, called functional units, for building decentralized applications that are currently insecure or impossible to implement with smart contracts. Each functional unit is a distributed system that provides a special-purpose functionality by exposing atomic transactions to the smart-contract developer. Combining these transactions into arbitrarily-defined workflows, developers can build a larger class of decentralized applications, such as provably-secure and fair lotteries or e-voting."}],"month":"05","quality_controlled":"1","scopus_import":"1","publisher":"ACM"}]