[{"language":[{"iso":"eng"}],"date_published":"2018-11-09T00:00:00Z","page":"49","publication":"bioRxiv","oa":1,"citation":{"apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. Cold Spring Harbor Laboratory.","ieee":"R. P. J. Bevers et al., “Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018.","ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv, .","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. 2018.","chicago":"Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring Harbor Laboratory, 2018.","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018).","mla":"Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv, Cold Spring Harbor Laboratory, 2018."},"main_file_link":[{"url":"https://doi.org/10.1101/466771 ","open_access":"1"}],"month":"11","day":"09","article_processing_charge":"No","date_updated":"2021-01-12T08:15:30Z","date_created":"2020-04-30T13:09:37Z","oa_version":"Preprint","author":[{"first_name":"Roel P.J.","last_name":"Bevers","full_name":"Bevers, Roel P.J."},{"full_name":"Litovchenko, Maria","last_name":"Litovchenko","first_name":"Maria"},{"first_name":"Adamandia","last_name":"Kapopoulou","full_name":"Kapopoulou, Adamandia"},{"first_name":"Virginie S.","last_name":"Braman","full_name":"Braman, Virginie S."},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"last_name":"Auwerx","first_name":"Johan","full_name":"Auwerx, Johan"},{"full_name":"Hollis, Brian","first_name":"Brian","last_name":"Hollis"},{"full_name":"Deplancke, Bart","first_name":"Bart","last_name":"Deplancke"}],"publication_status":"published","title":"Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel","status":"public","publisher":"Cold Spring Harbor Laboratory","_id":"7783","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies."}],"type":"preprint"},{"file_date_updated":"2020-07-14T12:48:03Z","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"type":"conference","date_updated":"2023-02-23T13:18:41Z","date_created":"2020-05-10T22:00:51Z","file":[{"relation":"main_file","file_id":"7894","checksum":"a4336c167978e81891970e4e4517a8c3","date_created":"2020-05-26T13:02:00Z","date_updated":"2020-07-14T12:48:03Z","access_level":"open_access","file_name":"2018_ICLR_Polino.pdf","content_type":"application/pdf","file_size":308339,"creator":"dernst"}],"oa_version":"Published Version","author":[{"full_name":"Polino, Antonio","last_name":"Polino","first_name":"Antonio"},{"last_name":"Pascanu","first_name":"Razvan","full_name":"Pascanu, Razvan"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"title":"Model compression via distillation and quantization","status":"public","publication_status":"published","ddc":["000"],"department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7812","year":"2018","month":"05","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2018-05-03","location":"Vancouver, Canada","start_date":"2018-04-30","name":"ICLR: International Conference on Learning Representations"},"date_published":"2018-05-01T00:00:00Z","quality_controlled":"1","publication":"6th International Conference on Learning Representations","oa":1,"external_id":{"arxiv":["1802.05668"]},"citation":{"chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018."}},{"_id":"7983","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 130","ddc":["540"],"title":"Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff","status":"public","file":[{"creator":"dernst","file_size":674789,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_AngChemieDT_Mahne.pdf","checksum":"81506e0f7079e1e3591f3cd9f626bf67","date_updated":"2020-07-14T12:48:06Z","date_created":"2020-06-19T11:58:06Z","file_id":"7988","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"19","abstract":[{"text":"Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien, und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen >3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2 + O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir, dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird. Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.","lang":"ger"}],"citation":{"ama":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 2018;130(19):5627-5631. doi:10.1002/ange.201802277","ieee":"N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie, vol. 130, no. 19. Wiley, pp. 5627–5631, 2018.","apa":"Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277","ista":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 130(19), 5627–5631.","short":"N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie 130 (2018) 5627–5631.","mla":"Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018, pp. 5627–31, doi:10.1002/ange.201802277.","chicago":"Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277."},"publication":"Angewandte Chemie","page":"5627-5631","article_type":"original","date_published":"2018-05-04T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"04","year":"2018","publisher":"Wiley","publication_status":"published","author":[{"last_name":"Mahne","first_name":"Nika","full_name":"Mahne, Nika"},{"last_name":"Renfrew","first_name":"Sara E.","full_name":"Renfrew, Sara E."},{"full_name":"McCloskey, Bryan D.","last_name":"McCloskey","first_name":"Bryan D."},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"}],"volume":130,"date_created":"2020-06-19T08:33:24Z","date_updated":"2021-01-12T08:16:21Z","file_date_updated":"2020-07-14T12:48:06Z","extern":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","doi":"10.1002/ange.201802277","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0044-8249"]},"month":"05"},{"article_processing_charge":"No","day":"04","date_published":"2018-04-04T00:00:00Z","page":"8-9","article_type":"original","citation":{"chicago":"Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028.","mla":"Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.","short":"J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9.","ista":"Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify, transmit. Neuron. 98(1), 8–9.","apa":"Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance, amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028","ieee":"J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify, transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.","ama":"Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit. Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028"},"publication":"Neuron","issue":"1","abstract":[{"lang":"eng","text":"The neural code of cortical processing remains uncracked; however, it must necessarily rely on faithful signal propagation between cortical areas. In this issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation balanced by local inhibition can enable reliable signal propagation in data-constrained network models of macaque cortex. "}],"type":"journal_article","oa_version":"Published Version","intvolume":" 98","status":"public","title":"Cortical signal propagation: Balance, amplify, transmit","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8015","publication_identifier":{"issn":["0896-6273"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2018.03.028","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2018.03.028","open_access":"1"}],"external_id":{"pmid":["29621492"]},"extern":"1","volume":98,"date_created":"2020-06-25T12:53:39Z","date_updated":"2021-01-12T08:16:31Z","author":[{"last_name":"Stroud","first_name":"Jake P.","full_name":"Stroud, Jake P."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2018"},{"extern":"1","publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2018","volume":21,"date_updated":"2021-01-12T08:16:46Z","date_created":"2020-06-30T13:18:02Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41593-018-0307-x","relation":"erratum"}]},"author":[{"full_name":"Stroud, Jake P.","first_name":"Jake P.","last_name":"Stroud"},{"first_name":"Mason A.","last_name":"Porter","full_name":"Porter, Mason A."},{"last_name":"Hennequin","first_name":"Guillaume","full_name":"Hennequin, Guillaume"},{"full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"}],"publication_identifier":{"issn":["1097-6256","1546-1726"]},"month":"12","quality_controlled":"1","oa":1,"external_id":{"pmid":["30482949"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41593-018-0276-0","type":"journal_article","issue":"12","abstract":[{"text":"Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support the generation of complex movements. Although recent neuronal-network models capture many qualitative aspects of M1 dynamics, they can generate only a few distinct movements. Additionally, it is unclear how M1 efficiently controls movements over a wide range of shapes and speeds. We demonstrate that modulation of neuronal input–output gains in recurrent neuronal-network models with a fixed architecture can dramatically reorganize neuronal activity and thus downstream muscle outputs. Consistent with the observation of diffuse neuromodulatory projections to M1, a relatively small number of modulatory control units provide sufficient flexibility to adjust high-dimensional network activity using a simple reward-based learning rule. Furthermore, it is possible to assemble novel movements from previously learned primitives, and one can separately change movement speed while preserving movement shape. Our results provide a new perspective on the role of modulatory systems in controlling recurrent cortical activity.","lang":"eng"}],"intvolume":" 21","status":"public","title":"Motor primitives in space and time via targeted gain modulation in cortical networks","_id":"8073","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"Submitted Version","article_processing_charge":"No","day":"01","page":"1774-1783","article_type":"original","citation":{"mla":"Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12, Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0.","short":"J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience 21 (2018) 1774–1783.","chicago":"Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0.","ama":"Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0","ista":"Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 21(12), 1774–1783.","ieee":"J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives in space and time via targeted gain modulation in cortical networks,” Nature Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018.","apa":"Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0"},"publication":"Nature Neuroscience","date_published":"2018-12-01T00:00:00Z"},{"publisher":"Elsevier","intvolume":" 142","publication_status":"published","status":"public","title":"AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor","_id":"8231","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":142,"oa_version":"Published Version","date_updated":"2021-01-12T08:17:37Z","date_created":"2020-08-10T11:51:36Z","author":[{"full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","first_name":"Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"full_name":"Ilieva, Kristina M.","last_name":"Ilieva","first_name":"Kristina M."},{"last_name":"Matz","first_name":"Miroslawa","full_name":"Matz, Miroslawa"},{"last_name":"Herrmann","first_name":"Ina","full_name":"Herrmann, Ina"},{"last_name":"Spillner","first_name":"Edzard","full_name":"Spillner, Edzard"},{"first_name":"Sophia N.","last_name":"Karagiannis","full_name":"Karagiannis, Sophia N."},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"type":"journal_article","extern":"1","issue":"3","page":"973-976.e11","article_type":"letter_note","quality_controlled":"1","citation":{"ista":"Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 142(3), 973–976.e11.","ieee":"J. Singer et al., “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” Journal of Allergy and Clinical Immunology, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.","apa":"Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E., … Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2018.04.021","ama":"Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 2018;142(3):973-976.e11. doi:10.1016/j.jaci.2018.04.021","chicago":"Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann, Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology. Elsevier, 2018. https://doi.org/10.1016/j.jaci.2018.04.021.","mla":"Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:10.1016/j.jaci.2018.04.021.","short":"J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N. Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142 (2018) 973–976.e11."},"main_file_link":[{"url":"https://doi.org/10.1016/j.jaci.2018.04.021","open_access":"1"}],"oa":1,"publication":"Journal of Allergy and Clinical Immunology","language":[{"iso":"eng"}],"doi":"10.1016/j.jaci.2018.04.021","date_published":"2018-09-01T00:00:00Z","article_processing_charge":"No","publication_identifier":{"issn":["0091-6749"]},"day":"01","month":"09"},{"type":"journal_article","article_number":"1269830","extern":"1","abstract":[{"text":"Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY.","lang":"eng"}],"intvolume":" 2018","publisher":"Hindawi","publication_status":"published","status":"public","title":"Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8234","year":"2018","oa_version":"Published Version","volume":2018,"date_updated":"2021-01-12T08:17:38Z","date_created":"2020-08-10T11:53:07Z","author":[{"first_name":"T.","last_name":"Balber","full_name":"Balber, T."},{"last_name":"Singer","first_name":"Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Singer, Judit"},{"last_name":"Berroterán-Infante","first_name":"N.","full_name":"Berroterán-Infante, N."},{"full_name":"Dumanic, M.","last_name":"Dumanic","first_name":"M."},{"full_name":"Fetty, L.","first_name":"L.","last_name":"Fetty"},{"full_name":"Fazekas-Singer, J.","last_name":"Fazekas-Singer","first_name":"J.","orcid":"0000-0002-8777-3502"},{"full_name":"Vraka, C.","first_name":"C.","last_name":"Vraka"},{"first_name":"L.","last_name":"Nics","full_name":"Nics, L."},{"full_name":"Bergmann, M.","first_name":"M.","last_name":"Bergmann"},{"first_name":"K.","last_name":"Pallitsch","full_name":"Pallitsch, K."},{"first_name":"H.","last_name":"Spreitzer","full_name":"Spreitzer, H."},{"last_name":"Wadsak","first_name":"W.","orcid":"0000-0003-4479-8053","full_name":"Wadsak, W."},{"first_name":"M.","last_name":"Hacker","full_name":"Hacker, M."},{"full_name":"Jensen-Jarolim, E.","first_name":"E.","last_name":"Jensen-Jarolim"},{"last_name":"Viernstein","first_name":"H.","full_name":"Viernstein, H."},{"orcid":"0000-0003-3173-5272","first_name":"M.","last_name":"Mitterhauser","full_name":"Mitterhauser, M."}],"article_processing_charge":"No","publication_identifier":{"issn":["1555-4309","1555-4317"]},"month":"02","day":"13","article_type":"original","quality_controlled":"1","citation":{"short":"T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker, E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular Imaging 2018 (2018).","mla":"Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018, doi:10.1155/2018/1269830.","chicago":"Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018. https://doi.org/10.1155/2018/1269830.","ama":"Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018. doi:10.1155/2018/1269830","ieee":"T. Balber et al., “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.","apa":"Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer, J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830","ista":"Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M, Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830."},"main_file_link":[{"url":"https://doi.org/10.1155/2018/1269830","open_access":"1"}],"oa":1,"publication":"Contrast Media & Molecular Imaging","language":[{"iso":"eng"}],"date_published":"2018-02-13T00:00:00Z","doi":"10.1155/2018/1269830"},{"article_processing_charge":"No","publication_identifier":{"eissn":["1949-2553"]},"day":"10","month":"04","page":"19026-19038","article_type":"original","quality_controlled":"1","citation":{"ama":"Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876","ista":"Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 9, 19026–19038.","apa":"Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis, S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.24876","ieee":"T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget, vol. 9. Impact Journals, pp. 19026–19038, 2018.","mla":"Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876.","short":"T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis, J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget 9 (2018) 19026–19038.","chicago":"Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.18632/oncotarget.24876"}],"publication":"Oncotarget","language":[{"iso":"eng"}],"doi":"10.18632/oncotarget.24876","date_published":"2018-04-10T00:00:00Z","type":"journal_article","extern":"1","abstract":[{"text":"Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans.","lang":"eng"}],"publisher":"Impact Journals","intvolume":" 9","publication_status":"published","title":"Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody","status":"public","_id":"8232","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","volume":9,"oa_version":"Published Version","date_updated":"2021-01-12T08:17:37Z","date_created":"2020-08-10T11:52:54Z","author":[{"first_name":"Tadanobu","last_name":"Nagaya","full_name":"Nagaya, Tadanobu"},{"last_name":"Okuyama","first_name":"Shuhei","full_name":"Okuyama, Shuhei"},{"full_name":"Ogata, Fusa","first_name":"Fusa","last_name":"Ogata"},{"full_name":"Maruoka, Yasuhiro","last_name":"Maruoka","first_name":"Yasuhiro"},{"full_name":"Knapp, Deborah W.","last_name":"Knapp","first_name":"Deborah W."},{"full_name":"Karagiannis, Sophia N.","first_name":"Sophia N.","last_name":"Karagiannis"},{"full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","first_name":"Judit","last_name":"Fazekas-Singer"},{"last_name":"Choyke","first_name":"Peter L.","full_name":"Choyke, Peter L."},{"last_name":"LeBlanc","first_name":"Amy K.","full_name":"LeBlanc, Amy K."},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"},{"full_name":"Kobayashi, Hisataka","last_name":"Kobayashi","first_name":"Hisataka"}]},{"page":"118-127","article_type":"original","citation":{"short":"I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127.","mla":"Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005.","chicago":"Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005.","ama":"Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005","ieee":"I. Herrmann et al., “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” Developmental & Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.","apa":"Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005","ista":"Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim E. 2018. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 82(5), 118–127."},"publication":"Developmental & Comparative Immunology","date_published":"2018-05-01T00:00:00Z","article_processing_charge":"No","day":"01","intvolume":" 82","status":"public","title":"Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy","_id":"8233","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"text":"The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages.","lang":"eng"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.dci.2018.01.005","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.dci.2018.01.005","publication_identifier":{"issn":["0145-305X"]},"month":"05","publisher":"Elsevier","publication_status":"published","year":"2018","volume":82,"date_updated":"2021-01-12T08:17:38Z","date_created":"2020-08-10T11:53:01Z","author":[{"last_name":"Herrmann","first_name":"Ina","full_name":"Herrmann, Ina"},{"first_name":"Jelena","last_name":"Gotovina","full_name":"Gotovina, Jelena"},{"full_name":"Fazekas-Singer, Judit","first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"last_name":"Fischer","first_name":"Michael B.","full_name":"Fischer, Michael B."},{"full_name":"Hufnagl, Karin","first_name":"Karin","last_name":"Hufnagl"},{"first_name":"Rodolfo","last_name":"Bianchini","full_name":"Bianchini, Rodolfo"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"extern":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8262","year":"2018","publisher":"Springer Nature","intvolume":" 19","title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.","publication_status":"published","status":"public","author":[{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Elena V.","last_name":"Moroz","full_name":"Moroz, Elena V."},{"full_name":"Davydov, Iakov I.","first_name":"Iakov I.","last_name":"Davydov"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"oa_version":"Published Version","volume":19,"date_created":"2020-08-15T11:02:08Z","date_updated":"2023-02-23T13:28:52Z","type":"journal_article","article_number":"965","abstract":[{"lang":"eng","text":"Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei."}],"extern":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1186/s12864-018-5245-1","open_access":"1"}],"citation":{"ama":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1","ieee":"O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics, vol. 19. Springer Nature, 2018.","apa":"Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1","ista":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965.","short":"O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature, 2018, doi:10.1186/s12864-018-5245-1.","chicago":"Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1."},"publication":"BMC Genomics","quality_controlled":"1","article_type":"original","date_published":"2018-12-27T00:00:00Z","doi":"10.1186/s12864-018-5245-1","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["1471-2164"]},"month":"12","day":"27"},{"abstract":[{"lang":"eng","text":"Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8265","title":"Genome rearrangements and phylogeny reconstruction in Yersinia pestis","status":"public","intvolume":" 6","day":"27","article_processing_charge":"No","date_published":"2018-03-27T00:00:00Z","publication":"PeerJ","citation":{"chicago":"Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky, Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S. Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545.","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545.","short":"O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky, V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).","ista":"Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 6, e4545.","apa":"Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky, Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545","ieee":"O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018.","ama":"Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545"},"article_type":"original","extern":"1","article_number":"e4545","author":[{"last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"full_name":"Dranenko, Natalia O.","last_name":"Dranenko","first_name":"Natalia O."},{"last_name":"Ocheredko","first_name":"Elena S.","full_name":"Ocheredko, Elena S."},{"full_name":"Kanevsky, German M.","first_name":"German M.","last_name":"Kanevsky"},{"full_name":"Lozinsky, Yaroslav N.","last_name":"Lozinsky","first_name":"Yaroslav N."},{"full_name":"Khalaycheva, Vera A.","first_name":"Vera A.","last_name":"Khalaycheva"},{"last_name":"Artamonova","first_name":"Irena I.","full_name":"Artamonova, Irena I."},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"date_created":"2020-08-15T11:08:23Z","date_updated":"2023-02-23T13:28:57Z","volume":6,"year":"2018","pmid":1,"publication_status":"published","publisher":"PeerJ","month":"03","publication_identifier":{"issn":["2167-8359"]},"doi":"10.7717/peerj.4545","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["29607260"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7717/peerj.4545"}],"quality_controlled":"1"},{"publication_identifier":{"issn":["2375-1207"],"isbn":["9781538643532"]},"article_processing_charge":"No","day":"26","month":"07","language":[{"iso":"eng"}],"doi":"10.1109/sp.2018.000-5","date_published":"2018-07-26T00:00:00Z","conference":{"name":"SP: Symposium on Security and Privacy","end_date":"2018-05-24","start_date":"2018-05-20","location":"San Francisco, CA, United States"},"page":"583-598","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/406"}],"citation":{"chicago":"Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98. IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.","short":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford, in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598.","mla":"Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–98, doi:10.1109/sp.2018.000-5.","ieee":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford, “OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018 IEEE Symposium on Security and Privacy, San Francisco, CA, United States, 2018, pp. 583–598.","apa":"Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., & Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco, CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5","ista":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018. OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598.","ama":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5"},"publication":"2018 IEEE Symposium on Security and Privacy","extern":"1","abstract":[{"lang":"eng","text":"Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment\r\nprocessors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput\r\nscales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds."}],"type":"conference","oa_version":"Preprint","date_created":"2020-08-26T11:46:35Z","date_updated":"2021-01-12T08:17:56Z","author":[{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Jovanovic, Philipp","last_name":"Jovanovic","first_name":"Philipp"},{"last_name":"Gasser","first_name":"Linus","full_name":"Gasser, Linus"},{"last_name":"Gailly","first_name":"Nicolas","full_name":"Gailly, Nicolas"},{"full_name":"Syta, Ewa","first_name":"Ewa","last_name":"Syta"},{"full_name":"Ford, Bryan","first_name":"Bryan","last_name":"Ford"}],"publisher":"IEEE","publication_status":"published","title":"OmniLedger: A secure, scale-out, decentralized ledger via sharding","status":"public","_id":"8297","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ec_funded":1,"abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"type":"preprint","oa_version":"Preprint","date_created":"2020-09-21T12:01:50Z","date_updated":"2021-01-12T08:20:00Z","author":[{"full_name":"Llorca, Alfredo","last_name":"Llorca","first_name":"Alfredo"},{"last_name":"Ciceri","first_name":"Gabriele","full_name":"Ciceri, Gabriele"},{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J"},{"first_name":"Fong K.","last_name":"Wong","full_name":"Wong, Fong K."},{"last_name":"Diana","first_name":"Giovanni","full_name":"Diana, Giovanni"},{"last_name":"Serafeimidou","first_name":"Eleni","full_name":"Serafeimidou, Eleni"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"first_name":"Sebastian J.","last_name":"Arnold","full_name":"Arnold, Sebastian J."},{"first_name":"Martin","last_name":"Meyer","full_name":"Meyer, Martin"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"department":[{"_id":"SiHi"}],"publisher":"Cold Spring Harbor Laboratory","status":"public","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","publication_status":"submitted","_id":"8547","year":"2018","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"13","month":"12","language":[{"iso":"eng"}],"date_published":"2018-12-13T00:00:00Z","doi":"10.1101/494088","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF","grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"oa":1,"publication":"bioRxiv"},{"type":"book_chapter","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"86","ddc":["000"],"status":"public","title":"Computing average response time","intvolume":" 10760","file":[{"access_level":"open_access","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","creator":"dernst","content_type":"application/pdf","file_size":516307,"file_id":"7053","relation":"main_file","checksum":"9995c6ce6957333baf616fc4f20be597","date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z"}],"oa_version":"Submitted Version","scopus_import":1,"day":"20","has_accepted_license":"1","publication":"Principles of Modeling","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9."},"page":"143 - 161","date_published":"2018-07-20T00:00:00Z","file_date_updated":"2020-07-14T12:48:14Z","publist_id":"7968","ec_funded":1,"year":"2018","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","editor":[{"first_name":"Marten","last_name":"Lohstroh","full_name":"Lohstroh, Marten"},{"full_name":"Derler, Patricia","last_name":"Derler","first_name":"Patricia"},{"full_name":"Sirjani, Marjan","first_name":"Marjan","last_name":"Sirjani"}],"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"date_updated":"2021-01-12T08:20:14Z","date_created":"2018-12-11T11:44:33Z","volume":10760,"month":"07","oa":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"doi":"10.1007/978-3-319-95246-8_9","language":[{"iso":"eng"}]},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-11-01T00:00:00Z","citation":{"mla":"Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:10.1038/s41567-018-0227-4.","short":"A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118.","chicago":"Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0227-4.","ama":"Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 2018;14(11):1114-1118. doi:10.1038/s41567-018-0227-4","ista":"Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118.","ieee":"A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” Nature Physics, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018.","apa":"Aubret, A., Youssef, M., Sacanna, S., & Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0227-4"},"publication":"Nature Physics","page":"1114-1118","article_type":"original","issue":"11","abstract":[{"text":"Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9062","intvolume":" 14","status":"public","title":"Targeted assembly and synchronization of self-spinning microgears","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"11","doi":"10.1038/s41567-018-0227-4","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1810.01033","open_access":"1"}],"external_id":{"arxiv":["1810.01033"]},"quality_controlled":"1","extern":"1","author":[{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"full_name":"Youssef, Mena","last_name":"Youssef","first_name":"Mena"},{"last_name":"Sacanna","first_name":"Stefano","full_name":"Sacanna, Stefano"},{"full_name":"Palacci, Jérémie A","first_name":"Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"}],"volume":14,"date_updated":"2023-02-23T13:48:02Z","date_created":"2021-02-02T13:52:49Z","year":"2018","publisher":"Springer Nature","publication_status":"published"},{"scopus_import":"1","day":"30","article_processing_charge":"No","article_type":"letter_note","page":"11","publication":"Opera Medica et Physiologica","citation":{"chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001"},"date_published":"2018-06-30T00:00:00Z","alternative_title":["Molecular and cellular neuroscience"],"type":"journal_article","issue":"S1","status":"public","title":"Diffraction-unlimited optical imaging for synaptic physiology","intvolume":" 4","_id":"9229","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","month":"06","publication_identifier":{"eissn":["2500-2295"],"issn":["2500-2287"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience"}],"language":[{"iso":"eng"}],"doi":"10.20388/omp2018.00s1.001","publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Lobachevsky State University of Nizhny Novgorod","year":"2018","date_created":"2021-03-07T23:01:25Z","date_updated":"2021-12-03T07:31:05Z","volume":4,"author":[{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}]},{"year":"2018","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"author":[{"full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"963"}]},"date_created":"2019-02-14T14:12:09Z","date_updated":"2023-02-23T14:02:58Z","volume":117,"article_number":"23","file_date_updated":"2020-07-14T12:47:15Z","license":"https://creativecommons.org/licenses/by/4.0/","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"}],"conference":{"location":"Liverpool, United Kingdom","start_date":"2018-08-27","end_date":"2018-08-31","name":"MFCS: Mathematical Foundations of Computer Science"},"doi":"10.4230/LIPICS.MFCS.2018.23","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["1868-8969"]},"_id":"6005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Timed network games with clocks","status":"public","ddc":["000"],"intvolume":" 117","file":[{"file_name":"2018_LIPIcs_Avni.pdf","access_level":"open_access","creator":"dernst","file_size":542889,"content_type":"application/pdf","file_id":"6007","relation":"main_file","date_created":"2019-02-14T14:22:04Z","date_updated":"2020-07-14T12:47:15Z","checksum":"41ab2ae9b63f5eb49fa995250c0ba128"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23"},"date_published":"2018-08-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"publication_identifier":{"issn":["1463-9076"],"eissn":["1463-9084"]},"month":"12","quality_controlled":"1","external_id":{"pmid":["30412211"],"arxiv":["1807.05551"]},"main_file_link":[{"url":"https://arxiv.org/abs/1807.05551","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1039/c8cp04561e","extern":"1","publisher":"Royal Society of Chemistry","publication_status":"published","pmid":1,"year":"2018","volume":20,"date_updated":"2021-08-09T12:36:47Z","date_created":"2021-07-15T12:51:44Z","author":[{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"first_name":"Christoph","last_name":"Dellago","full_name":"Dellago, Christoph"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"scopus_import":"1","article_processing_charge":"No","day":"07","page":"28732-28740","article_type":"original","citation":{"mla":"Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40, doi:10.1039/c8cp04561e.","short":"B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20 (2018) 28732–28740.","chicago":"Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2018. https://doi.org/10.1039/c8cp04561e.","ama":"Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e","ista":"Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 20(45), 28732–28740.","apa":"Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e","ieee":"B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740, 2018."},"publication":"Physical Chemistry Chemical Physics","date_published":"2018-12-07T00:00:00Z","type":"journal_article","issue":"45","abstract":[{"text":"Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods.","lang":"eng"}],"intvolume":" 20","status":"public","title":"Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9668","oa_version":"Preprint"},{"article_type":"original","citation":{"ama":"Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 2018;97(5). doi:10.1103/physrevb.97.054102","ista":"Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.","ieee":"B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids,” Physical Review B, vol. 97, no. 5. American Physical Society, 2018.","apa":"Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102","mla":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102.","short":"B. Cheng, M. Ceriotti, Physical Review B 97 (2018).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102."},"publication":"Physical Review B","date_published":"2018-02-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 97","status":"public","title":"Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9687","oa_version":"Preprint","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures."}],"quality_controlled":"1","external_id":{"arxiv":["1710.02815"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02815"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.97.054102","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"02","publisher":"American Physical Society","publication_status":"published","year":"2018","volume":97,"date_created":"2021-07-19T09:39:48Z","date_updated":"2021-08-09T12:38:26Z","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"article_number":"054102","extern":"1"},{"type":"journal_article","issue":"6","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"intvolume":" 16","ddc":["576"],"title":"Is the sky the limit? On the expansion threshold of a species’ range","status":"public","_id":"315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5870","checksum":"908c52751bba30c55ed36789e5e4c84d","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","access_level":"open_access","file_name":"2017_PLOS_Polechova.pdf","file_size":6968201,"content_type":"application/pdf","creator":"dernst"}],"scopus_import":1,"has_accepted_license":"1","day":"15","citation":{"chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018).","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372"},"publication":"PLoS Biology","date_published":"2018-06-15T00:00:00Z","article_number":"e2005372","publist_id":"7550","file_date_updated":"2020-07-14T12:46:01Z","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","year":"2018","volume":16,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9839"}]},"author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"}],"publication_identifier":{"issn":["15449173"]},"month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005372"}]