[{"abstract":[{"text":"Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex.","lang":"eng"}],"author":[{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter"},{"full_name":"Brenner, Michael P.","first_name":"Michael P.","last_name":"Brenner"},{"last_name":"Ribbeck","first_name":"Katharina","full_name":"Ribbeck, Katharina"}],"article_number":"4348","year":"2018","month":"10","status":"public","_id":"7754","publication":"Nature Communications","title":"Enhanced diffusion by binding to the crosslinks of a polymer gel","oa":1,"article_processing_charge":"No","publisher":"Springer Nature","doi":"10.1038/s41467-018-06851-5","fulldoi":"https://doi.org/10.1038/s41467-018-06851-5","day":"19","publication_identifier":{"issn":["2041-1723"]},"volume":9,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-018-06851-5"}],"citation":{"ama":"Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. <i>Nature Communications</i>. 2018;9. doi:<a href=\"https://doi.org/10.1038/s41467-018-06851-5\">10.1038/s41467-018-06851-5</a>","ista":"Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348.","apa":"Goodrich, C. P., Brenner, M. P., &#38; Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-06851-5\">https://doi.org/10.1038/s41467-018-06851-5</a>","mla":"Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” <i>Nature Communications</i>, vol. 9, 4348, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06851-5\">10.1038/s41467-018-06851-5</a>.","ieee":"C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” <i>Nature Communications</i>, vol. 9. Springer Nature, 2018.","short":"C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018).","chicago":"Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06851-5\">https://doi.org/10.1038/s41467-018-06851-5</a>."},"date_published":"2018-10-19T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"         9","oa_version":"Published Version","date_created":"2020-04-30T11:38:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_type":"original","extern":"1","publication_status":"published","date_updated":"2021-01-12T08:15:18Z"},{"main_file_link":[{"url":"https://doi.org/10.1101/466771 ","open_access":"1"}],"citation":{"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.” <i>BioRxiv</i>. 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).","ieee":"R. P. J. Bevers <i>et al.</i>, “Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2018.","mla":"Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2018.","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. <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. <i>bioRxiv</i>. 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, ."},"page":"49","author":[{"last_name":"Bevers","full_name":"Bevers, Roel P.J.","first_name":"Roel P.J."},{"last_name":"Litovchenko","full_name":"Litovchenko, Maria","first_name":"Maria"},{"last_name":"Kapopoulou","first_name":"Adamandia","full_name":"Kapopoulou, Adamandia"},{"last_name":"Braman","first_name":"Virginie S.","full_name":"Braman, Virginie S."},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"full_name":"Auwerx, Johan","first_name":"Johan","last_name":"Auwerx"},{"full_name":"Hollis, Brian","first_name":"Brian","last_name":"Hollis"},{"first_name":"Bart","full_name":"Deplancke, Bart","last_name":"Deplancke"}],"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."}],"extern":"1","publication_status":"published","day":"09","date_updated":"2021-01-12T08:15:30Z","publisher":"Cold Spring Harbor Laboratory","title":"Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2020-04-30T13:09:37Z","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2018","_id":"7783","date_published":"2018-11-09T00:00:00Z","month":"11","status":"public","publication":"bioRxiv","type":"preprint"},{"date_published":"2018-08-26T00:00:00Z","type":"conference","has_accepted_license":"1","quality_controlled":"1","intvolume":"     11022","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:31Z","oa_version":"Submitted Version","file":[{"file_size":374851,"creator":"dernst","date_created":"2020-05-14T11:34:34Z","access_level":"open_access","file_id":"7831","relation":"main_file","checksum":"436b7574934324cfa7d1d3986fddc65b","date_updated":"2020-07-14T12:48:03Z","content_type":"application/pdf","file_name":"2018_LNCS_Bakhirkin.pdf"}],"publication_status":"published","department":[{"_id":"ToHe"}],"date_updated":"2025-04-15T06:26:03Z","publist_id":"7976","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"volume":11022,"citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">https://doi.org/10.1007/978-3-030-00151-3_13</a>.","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","mla":"Bakhirkin, Alexey, et al. <i>Online Timed Pattern Matching Using Automata</i>. Vol. 11022, Springer, 2018, pp. 215–32, doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">10.1007/978-3-030-00151-3_13</a>.","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., &#38; Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">https://doi.org/10.1007/978-3-030-00151-3_13</a>","ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">10.1007/978-3-030-00151-3_13</a>","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232."},"page":"215 - 232","external_id":{"isi":["000884993200013"]},"status":"public","_id":"78","month":"08","year":"2018","alternative_title":["LNCS"],"conference":{"start_date":"2018-09-04","location":"Bejing, China","end_date":"2018-09-06","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"scopus_import":"1","title":"Online timed pattern matching using automata","article_processing_charge":"No","oa":1,"doi":"10.1007/978-3-030-00151-3_13","file_date_updated":"2020-07-14T12:48:03Z","publisher":"Springer","ddc":["000"],"fulldoi":"https://doi.org/10.1007/978-3-030-00151-3_13","day":"26","publication_identifier":{"isbn":["978-3-030-00150-6"]},"abstract":[{"lang":"eng","text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated."}],"author":[{"first_name":"Alexey","full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin"},{"first_name":"Thomas","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"},{"first_name":"Oded","full_name":"Maler, Oded","last_name":"Maler"},{"last_name":"Asarin","full_name":"Asarin, Eugene","first_name":"Eugene"}],"isi":1},{"day":"01","file_date_updated":"2020-07-14T12:48:03Z","ddc":["000"],"scopus_import":"1","title":"Model compression via distillation and quantization","article_processing_charge":"No","oa":1,"_id":"7812","month":"05","status":"public","year":"2018","publication":"6th International Conference on Learning Representations","conference":{"start_date":"2018-04-30","location":"Vancouver, Canada","name":"ICLR: International Conference on Learning Representations","end_date":"2018-05-03"},"author":[{"last_name":"Polino","full_name":"Polino, Antonio","first_name":"Antonio"},{"last_name":"Pascanu","full_name":"Pascanu, Razvan","first_name":"Razvan"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"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."}],"publication_status":"published","department":[{"_id":"DaAl"}],"date_updated":"2025-06-30T10:04:44Z","file":[{"date_created":"2020-05-26T13:02:00Z","creator":"dernst","file_size":308339,"access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","checksum":"a4336c167978e81891970e4e4517a8c3","file_id":"7894","file_name":"2018_ICLR_Polino.pdf","content_type":"application/pdf"}],"quality_controlled":"1","arxiv":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-05-10T22:00:51Z","oa_version":"Published Version","date_published":"2018-05-01T00:00:00Z","type":"conference","has_accepted_license":"1","citation":{"chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In <i>6th International Conference on Learning Representations</i>, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in <i>6th International Conference on Learning Representations</i>, Vancouver, Canada, 2018.","apa":"Polino, A., Pascanu, R., &#38; Alistarh, D.-A. (2018). Model compression via distillation and quantization. In <i>6th International Conference on Learning Representations</i>. Vancouver, Canada.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” <i>6th International Conference on Learning Representations</i>, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: <i>6th International Conference on Learning Representations</i>. ; 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."},"external_id":{"arxiv":["1802.05668"]},"acknowledgement":"We would like to thank Ce Zhang (ETH Zurich), Hantian Zhang (ETH Zurich) and Martin Jaggi ´\r\n(EPFL) for their support with experiments and valuable feedback.\r\n"},{"day":"15","doi":"10.1007/978-3-319-99154-2_4","publisher":"Springer","fulldoi":"https://doi.org/10.1007/978-3-319-99154-2_4","scopus_import":"1","title":"Parameter-independent strategies for pMDPs via POMDPs","article_processing_charge":"No","oa":1,"status":"public","_id":"79","month":"08","year":"2018","alternative_title":["LNCS"],"conference":{"location":"Beijing, China","end_date":"2018-09-07","name":"QEST: Quantitative Evaluation of Systems","start_date":"2018-09-04"},"isi":1,"author":[{"full_name":"Arming, Sebastian","first_name":"Sebastian","last_name":"Arming"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Joost P","full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"}],"abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol."}],"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-13T09:38:28Z","intvolume":"     11024","quality_controlled":"1","arxiv":1,"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","date_created":"2018-12-11T11:44:31Z","date_published":"2018-08-15T00:00:00Z","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}],"citation":{"ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>","mla":"Arming, Sebastian, et al. <i>Parameter-Independent Strategies for PMDPs via POMDPs</i>. Vol. 11024, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>.","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., &#38; Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>."},"page":"53-70","external_id":{"isi":["000548912200004"],"arxiv":["1806.05126"]},"volume":11024,"publist_id":"7975"},{"file":[{"access_level":"open_access","creator":"dernst","file_size":674789,"date_created":"2020-06-19T11:58:06Z","file_name":"2018_AngChemieDT_Mahne.pdf","content_type":"application/pdf","checksum":"81506e0f7079e1e3591f3cd9f626bf67","relation":"main_file","file_id":"7988","date_updated":"2020-07-14T12:48:06Z"}],"tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"article_type":"original","date_updated":"2021-01-12T08:16:21Z","publication_status":"published","extern":"1","has_accepted_license":"1","type":"journal_article","date_published":"2018-05-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-06-19T08:33:24Z","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       130","page":"5627-5631","citation":{"chicago":"Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” <i>Angewandte Chemie</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/ange.201802277\">https://doi.org/10.1002/ange.201802277</a>.","ama":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. <i>Angewandte Chemie</i>. 2018;130(19):5627-5631. doi:<a href=\"https://doi.org/10.1002/ange.201802277\">10.1002/ange.201802277</a>","ista":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 130(19), 5627–5631.","apa":"Mahne, N., Renfrew, S. E., McCloskey, B. D., &#38; Freunberger, S. A. (2018). Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.201802277\">https://doi.org/10.1002/ange.201802277</a>","mla":"Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” <i>Angewandte Chemie</i>, vol. 130, no. 19, Wiley, 2018, pp. 5627–31, doi:<a href=\"https://doi.org/10.1002/ange.201802277\">10.1002/ange.201802277</a>.","ieee":"N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” <i>Angewandte Chemie</i>, vol. 130, no. 19. Wiley, pp. 5627–5631, 2018.","short":"N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie 130 (2018) 5627–5631."},"issue":"19","volume":130,"ddc":["540"],"fulldoi":"https://doi.org/10.1002/ange.201802277","publisher":"Wiley","file_date_updated":"2020-07-14T12:48:06Z","doi":"10.1002/ange.201802277","publication_identifier":{"issn":["0044-8249"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"04","publication":"Angewandte Chemie","year":"2018","status":"public","_id":"7983","month":"05","oa":1,"article_processing_charge":"No","title":"Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff","abstract":[{"lang":"ger","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."}],"author":[{"last_name":"Mahne","first_name":"Nika","full_name":"Mahne, Nika"},{"full_name":"Renfrew, Sara E.","first_name":"Sara E.","last_name":"Renfrew"},{"last_name":"McCloskey","full_name":"McCloskey, Bryan D.","first_name":"Bryan D."},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"}]},{"volume":98,"issue":"1","external_id":{"pmid":["29621492"]},"citation":{"chicago":"Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” <i>Neuron</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.neuron.2018.03.028\">https://doi.org/10.1016/j.neuron.2018.03.028</a>.","ista":"Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify, transmit. Neuron. 98(1), 8–9.","ama":"Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit. <i>Neuron</i>. 2018;98(1):8-9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.03.028\">10.1016/j.neuron.2018.03.028</a>","apa":"Stroud, J. P., &#38; Vogels, T. P. (2018). Cortical signal propagation: Balance, amplify, transmit. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2018.03.028\">https://doi.org/10.1016/j.neuron.2018.03.028</a>","mla":"Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” <i>Neuron</i>, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.03.028\">10.1016/j.neuron.2018.03.028</a>.","ieee":"J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify, transmit,” <i>Neuron</i>, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.","short":"J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9."},"page":"8-9","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2018.03.028","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2020-06-25T12:53:39Z","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        98","type":"journal_article","date_published":"2018-04-04T00:00:00Z","date_updated":"2021-01-12T08:16:31Z","publication_status":"published","extern":"1","article_type":"original","pmid":1,"author":[{"first_name":"Jake P.","full_name":"Stroud, Jake P.","last_name":"Stroud"},{"last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"}],"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. "}],"oa":1,"article_processing_charge":"No","title":"Cortical signal propagation: Balance, amplify, transmit","publication":"Neuron","year":"2018","status":"public","_id":"8015","month":"04","publication_identifier":{"issn":["0896-6273"]},"day":"04","fulldoi":"https://doi.org/10.1016/j.neuron.2018.03.028","publisher":"Elsevier","doi":"10.1016/j.neuron.2018.03.028"},{"volume":63,"publist_id":"6844","external_id":{"isi":["000424633700008"]},"page":"105 - 123","citation":{"ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. 2018;63:105-123. doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.","apa":"Cremer, S., Pull, C., &#38; Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>","mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>.","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” <i>Annual Review of Entomology</i>, vol. 63. Annual Reviews, pp. 105–123, 2018.","short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>. Annual Reviews, 2018. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>."},"date_created":"2018-12-11T11:48:36Z","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"intvolume":"        63","quality_controlled":"1","type":"journal_article","date_published":"2018-01-07T00:00:00Z","date_updated":"2026-04-08T14:19:10Z","department":[{"_id":"SyCr"}],"publication_status":"published","author":[{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"},{"last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","first_name":"Matthias"}],"abstract":[{"lang":"eng","text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology."}],"related_material":{"record":[{"id":"819","relation":"dissertation_contains","status":"public"}]},"corr_author":"1","isi":1,"article_processing_charge":"No","title":"Social immunity: Emergence and evolution of colony-level disease protection","scopus_import":"1","publication":"Annual Review of Entomology","year":"2018","_id":"806","month":"01","status":"public","publication_identifier":{"issn":["1545-4487"]},"day":"07","fulldoi":"https://doi.org/10.1146/annurev-ento-020117-043110","publisher":"Annual Reviews","doi":"10.1146/annurev-ento-020117-043110"},{"type":"journal_article","date_published":"2018-12-01T00:00:00Z","date_created":"2020-06-30T13:18:02Z","oa_version":"Submitted Version","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        21","article_type":"original","date_updated":"2021-01-12T08:16:46Z","publication_status":"published","extern":"1","volume":21,"external_id":{"pmid":["30482949"]},"page":"1774-1783","citation":{"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.","ama":"Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and time via targeted gain modulation in cortical networks. <i>Nature Neuroscience</i>. 2018;21(12):1774-1783. doi:<a href=\"https://doi.org/10.1038/s41593-018-0276-0\">10.1038/s41593-018-0276-0</a>","apa":"Stroud, J. P., Porter, M. A., Hennequin, G., &#38; Vogels, T. P. (2018). Motor primitives in space and time via targeted gain modulation in cortical networks. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-018-0276-0\">https://doi.org/10.1038/s41593-018-0276-0</a>","mla":"Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” <i>Nature Neuroscience</i>, vol. 21, no. 12, Springer Nature, 2018, pp. 1774–83, doi:<a href=\"https://doi.org/10.1038/s41593-018-0276-0\">10.1038/s41593-018-0276-0</a>.","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,” <i>Nature Neuroscience</i>, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018.","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.” <i>Nature Neuroscience</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41593-018-0276-0\">https://doi.org/10.1038/s41593-018-0276-0</a>."},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/"}],"issue":"12","publication":"Nature Neuroscience","year":"2018","_id":"8073","status":"public","month":"12","oa":1,"article_processing_charge":"No","title":"Motor primitives in space and time via targeted gain modulation in cortical networks","fulldoi":"https://doi.org/10.1038/s41593-018-0276-0","publisher":"Springer Nature","doi":"10.1038/s41593-018-0276-0","publication_identifier":{"issn":["1097-6256","1546-1726"]},"day":"01","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"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41593-018-0307-x","relation":"erratum"}]},"pmid":1,"author":[{"last_name":"Stroud","full_name":"Stroud, Jake P.","first_name":"Jake P."},{"first_name":"Mason A.","full_name":"Porter, Mason A.","last_name":"Porter"},{"full_name":"Hennequin, Guillaume","first_name":"Guillaume","last_name":"Hennequin"},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","first_name":"Tim P","orcid":"0000-0003-3295-6181"}]},{"file":[{"file_size":537219,"creator":"dernst","date_created":"2020-10-09T06:24:21Z","access_level":"open_access","file_id":"8638","relation":"main_file","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","date_updated":"2020-10-09T06:24:21Z","success":1,"content_type":"application/pdf","file_name":"2018_LNCS_Elgyuett.pdf"}],"department":[{"_id":"ToHe"}],"publication_status":"published","date_updated":"2025-04-15T06:26:03Z","date_published":"2018-08-26T00:00:00Z","type":"conference","has_accepted_license":"1","intvolume":"     11022","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:31Z","citation":{"chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>.","mla":"Elgyütt, Adrian, et al. <i>Monitoring Temporal Logic with Clock Variables</i>. Vol. 11022, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>.","apa":"Elgyütt, A., Ferrere, T., &#38; Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70."},"page":"53 - 70","external_id":{"isi":["000884993200004"]},"publist_id":"7973","project":[{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"volume":11022,"file_date_updated":"2020-10-09T06:24:21Z","doi":"10.1007/978-3-030-00151-3_4","publisher":"Springer","ddc":["000"],"fulldoi":"https://doi.org/10.1007/978-3-030-00151-3_4","day":"26","month":"08","_id":"81","status":"public","year":"2018","alternative_title":["LNCS"],"conference":{"location":"Beijing, China","end_date":"2018-09-06","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2018-09-04"},"scopus_import":"1","title":"Monitoring temporal logic with clock variables","article_processing_charge":"No","oa":1,"isi":1,"abstract":[{"text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,","lang":"eng"}],"author":[{"first_name":"Adrian","full_name":"Elgyütt, Adrian","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","last_name":"Elgyütt"},{"first_name":"Thomas","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}]},{"author":[{"last_name":"Chaudhry","first_name":"Waqas","full_name":"Chaudhry, Waqas"},{"first_name":"Maros","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska"},{"last_name":"Shah","first_name":"Nilang","full_name":"Shah, Nilang"},{"first_name":"Howard","full_name":"Weiss, Howard","last_name":"Weiss"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"last_name":"Gupta","full_name":"Gupta, Animesh","first_name":"Animesh"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"last_name":"Levin","full_name":"Levin, Bruce","first_name":"Bruce"}],"related_material":{"record":[{"id":"9810","relation":"research_data","status":"public"}]},"abstract":[{"text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term &quot;leaky resistance.&quot; We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.","lang":"eng"}],"isi":1,"article_number":"2005971","scopus_import":"1","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","article_processing_charge":"Yes","oa":1,"month":"08","_id":"82","status":"public","year":"2018","publication":"PLoS Biology","day":"16","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:48:10Z","doi":"10.1371/journal.pbio.2005971","publisher":"Public Library of Science","fulldoi":"https://doi.org/10.1371/journal.pbio.2005971","ddc":["570"],"volume":16,"publist_id":"7972","issue":"8","citation":{"chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. 2018;16(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ieee":"W. Chaudhry <i>et al.</i>, “Leaky resistance and the conditions for the existence of lytic bacteriophage,” <i>PLoS Biology</i>, vol. 16, no. 8. Public Library of Science, 2018."},"external_id":{"isi":["000443383300024"]},"quality_controlled":"1","intvolume":"        16","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","date_created":"2018-12-11T11:44:32Z","date_published":"2018-08-16T00:00:00Z","type":"journal_article","has_accepted_license":"1","department":[{"_id":"CaGu"}],"publication_status":"published","date_updated":"2023-09-13T08:45:41Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","file_name":"2018_Plos_Chaudhry.pdf","file_id":"5706","checksum":"527076f78265cd4ea192cd1569851587","relation":"main_file","date_updated":"2020-07-14T12:48:10Z","access_level":"open_access","file_size":4007095,"creator":"dernst","date_created":"2018-12-17T12:55:31Z"}]},{"author":[{"first_name":"Judit","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas-Singer"},{"last_name":"Singer","full_name":"Singer, Josef","first_name":"Josef"},{"last_name":"Ilieva","first_name":"Kristina M.","full_name":"Ilieva, Kristina M."},{"last_name":"Matz","first_name":"Miroslawa","full_name":"Matz, Miroslawa"},{"full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"first_name":"Edzard","full_name":"Spillner, Edzard","last_name":"Spillner"},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"}],"fulldoi":"https://doi.org/10.1016/j.jaci.2018.04.021","publisher":"Elsevier","doi":"10.1016/j.jaci.2018.04.021","publication_identifier":{"issn":["0091-6749"]},"day":"01","publication":"Journal of Allergy and Clinical Immunology","year":"2018","month":"09","status":"public","_id":"8231","oa":1,"article_processing_charge":"No","title":"AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor","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.","ama":"Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. <i>Journal of Allergy and Clinical Immunology</i>. 2018;142(3):973-976.e11. doi:<a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">10.1016/j.jaci.2018.04.021</a>","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. <i>Journal of Allergy and Clinical Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">https://doi.org/10.1016/j.jaci.2018.04.021</a>","mla":"Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” <i>Journal of Allergy and Clinical Immunology</i>, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:<a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">10.1016/j.jaci.2018.04.021</a>.","ieee":"J. Singer <i>et al.</i>, “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” <i>Journal of Allergy and Clinical Immunology</i>, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.","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.","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.” <i>Journal of Allergy and Clinical Immunology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">https://doi.org/10.1016/j.jaci.2018.04.021</a>."},"page":"973-976.e11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jaci.2018.04.021"}],"issue":"3","volume":142,"article_type":"letter_note","date_updated":"2021-01-12T08:17:37Z","publication_status":"published","extern":"1","type":"journal_article","date_published":"2018-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2020-08-10T11:51:36Z","language":[{"iso":"eng"}],"intvolume":"       142","quality_controlled":"1"},{"year":"2018","status":"public","month":"04","_id":"8232","publication":"Oncotarget","title":"Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody","oa":1,"article_processing_charge":"No","publisher":"Impact Journals","doi":"10.18632/oncotarget.24876","fulldoi":"https://doi.org/10.18632/oncotarget.24876","day":"10","publication_identifier":{"eissn":["1949-2553"]},"abstract":[{"lang":"eng","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."}],"author":[{"first_name":"Tadanobu","full_name":"Nagaya, Tadanobu","last_name":"Nagaya"},{"last_name":"Okuyama","full_name":"Okuyama, Shuhei","first_name":"Shuhei"},{"last_name":"Ogata","first_name":"Fusa","full_name":"Ogata, Fusa"},{"last_name":"Maruoka","first_name":"Yasuhiro","full_name":"Maruoka, Yasuhiro"},{"last_name":"Knapp","first_name":"Deborah W.","full_name":"Knapp, Deborah W."},{"full_name":"Karagiannis, Sophia N.","first_name":"Sophia N.","last_name":"Karagiannis"},{"last_name":"Fazekas-Singer","first_name":"Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit"},{"last_name":"Choyke","first_name":"Peter L.","full_name":"Choyke, Peter L."},{"full_name":"LeBlanc, Amy K.","first_name":"Amy K.","last_name":"LeBlanc"},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"},{"first_name":"Hisataka","full_name":"Kobayashi, Hisataka","last_name":"Kobayashi"}],"date_published":"2018-04-10T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"         9","date_created":"2020-08-10T11:52:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","extern":"1","date_updated":"2021-01-12T08:17:37Z","volume":9,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.18632/oncotarget.24876"}],"citation":{"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.” <i>Oncotarget</i>. Impact Journals, 2018. <a href=\"https://doi.org/10.18632/oncotarget.24876\">https://doi.org/10.18632/oncotarget.24876</a>.","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. <i>Oncotarget</i>. Impact Journals. <a href=\"https://doi.org/10.18632/oncotarget.24876\">https://doi.org/10.18632/oncotarget.24876</a>","mla":"Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” <i>Oncotarget</i>, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:<a href=\"https://doi.org/10.18632/oncotarget.24876\">10.18632/oncotarget.24876</a>.","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.","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. <i>Oncotarget</i>. 2018;9:19026-19038. doi:<a href=\"https://doi.org/10.18632/oncotarget.24876\">10.18632/oncotarget.24876</a>","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.","ieee":"T. Nagaya <i>et al.</i>, “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” <i>Oncotarget</i>, vol. 9. Impact Journals, pp. 19026–19038, 2018."},"page":"19026-19038"},{"volume":82,"issue":"5","main_file_link":[{"url":"https://doi.org/10.1016/j.dci.2018.01.005","open_access":"1"}],"page":"118-127","citation":{"short":"I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental &#38; Comparative Immunology 82 (2018) 118–127.","ieee":"I. Herrmann <i>et al.</i>, “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” <i>Developmental &#38; Comparative Immunology</i>, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.","apa":"Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., &#38; Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. <i>Developmental &#38; Comparative Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">https://doi.org/10.1016/j.dci.2018.01.005</a>","mla":"Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” <i>Developmental &#38; Comparative Immunology</i>, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:<a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">10.1016/j.dci.2018.01.005</a>.","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. <i>Developmental &#38; Comparative Immunology</i>. 2018;82(5):118-127. doi:<a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">10.1016/j.dci.2018.01.005</a>","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 &#38; Comparative Immunology. 82(5), 118–127.","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.” <i>Developmental &#38; Comparative Immunology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">https://doi.org/10.1016/j.dci.2018.01.005</a>."},"intvolume":"        82","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2020-08-10T11:53:01Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-05-01T00:00:00Z","type":"journal_article","publication_status":"published","extern":"1","date_updated":"2021-01-12T08:17:38Z","article_type":"original","author":[{"full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"last_name":"Gotovina","full_name":"Gotovina, Jelena","first_name":"Jelena"},{"last_name":"Fazekas-Singer","first_name":"Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit"},{"first_name":"Michael B.","full_name":"Fischer, Michael B.","last_name":"Fischer"},{"full_name":"Hufnagl, Karin","first_name":"Karin","last_name":"Hufnagl"},{"full_name":"Bianchini, Rodolfo","first_name":"Rodolfo","last_name":"Bianchini"},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"}],"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"}],"title":"Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy","article_processing_charge":"No","oa":1,"_id":"8233","month":"05","status":"public","year":"2018","publication":"Developmental & Comparative Immunology","day":"01","publication_identifier":{"issn":["0145-305X"]},"doi":"10.1016/j.dci.2018.01.005","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.dci.2018.01.005"},{"volume":2018,"main_file_link":[{"url":"https://doi.org/10.1155/2018/1269830","open_access":"1"}],"citation":{"ieee":"T. Balber <i>et al.</i>, “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” <i>Contrast Media &#38; Molecular Imaging</i>, vol. 2018. Hindawi, 2018.","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 &#38; Molecular Imaging 2018 (2018).","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 &#38; Molecular Imaging. 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. <i>Contrast Media &#38; Molecular Imaging</i>. 2018;2018. doi:<a href=\"https://doi.org/10.1155/2018/1269830\">10.1155/2018/1269830</a>","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.” <i>Contrast Media &#38; Molecular Imaging</i>, vol. 2018, 1269830, Hindawi, 2018, doi:<a href=\"https://doi.org/10.1155/2018/1269830\">10.1155/2018/1269830</a>.","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. <i>Contrast Media &#38; Molecular Imaging</i>. Hindawi. <a href=\"https://doi.org/10.1155/2018/1269830\">https://doi.org/10.1155/2018/1269830</a>","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.” <i>Contrast Media &#38; Molecular Imaging</i>. Hindawi, 2018. <a href=\"https://doi.org/10.1155/2018/1269830\">https://doi.org/10.1155/2018/1269830</a>."},"intvolume":"      2018","quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-10T11:53:07Z","language":[{"iso":"eng"}],"date_published":"2018-02-13T00:00:00Z","type":"journal_article","publication_status":"published","extern":"1","date_updated":"2021-01-12T08:17:38Z","article_type":"original","author":[{"first_name":"T.","full_name":"Balber, T.","last_name":"Balber"},{"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.","first_name":"M.","last_name":"Dumanic"},{"first_name":"L.","full_name":"Fetty, L.","last_name":"Fetty"},{"last_name":"Fazekas-Singer","full_name":"Fazekas-Singer, J.","first_name":"J.","orcid":"0000-0002-8777-3502"},{"first_name":"C.","full_name":"Vraka, C.","last_name":"Vraka"},{"last_name":"Nics","full_name":"Nics, L.","first_name":"L."},{"last_name":"Bergmann","first_name":"M.","full_name":"Bergmann, M."},{"last_name":"Pallitsch","full_name":"Pallitsch, K.","first_name":"K."},{"first_name":"H.","full_name":"Spreitzer, H.","last_name":"Spreitzer"},{"orcid":"0000-0003-4479-8053","first_name":"W.","full_name":"Wadsak, W.","last_name":"Wadsak"},{"full_name":"Hacker, M.","first_name":"M.","last_name":"Hacker"},{"full_name":"Jensen-Jarolim, E.","first_name":"E.","last_name":"Jensen-Jarolim"},{"full_name":"Viernstein, H.","first_name":"H.","last_name":"Viernstein"},{"orcid":"0000-0003-3173-5272","first_name":"M.","full_name":"Mitterhauser, M.","last_name":"Mitterhauser"}],"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"}],"article_number":"1269830","title":"Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer","oa":1,"article_processing_charge":"No","year":"2018","_id":"8234","status":"public","month":"02","publication":"Contrast Media & Molecular Imaging","day":"13","publication_identifier":{"issn":["1555-4309","1555-4317"]},"publisher":"Hindawi","doi":"10.1155/2018/1269830","fulldoi":"https://doi.org/10.1155/2018/1269830"},{"citation":{"short":"O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).","ieee":"O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” <i>BMC Genomics</i>, vol. 19. Springer Nature, 2018.","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>, vol. 19, 965, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>.","apa":"Bochkareva, O., Moroz, E. V., Davydov, I. I., &#38; Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>","ama":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>","ista":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965.","chicago":"Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>."},"main_file_link":[{"url":"https://doi.org/10.1186/s12864-018-5245-1","open_access":"1"}],"volume":19,"article_type":"original","date_updated":"2023-02-23T13:28:52Z","extern":"1","publication_status":"published","type":"journal_article","date_published":"2018-12-27T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2020-08-15T11:02:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","intvolume":"        19","article_number":"965","abstract":[{"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.","lang":"eng"}],"author":[{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","first_name":"Olga","last_name":"Bochkareva"},{"last_name":"Moroz","full_name":"Moroz, Elena V.","first_name":"Elena V."},{"first_name":"Iakov I.","full_name":"Davydov, Iakov I.","last_name":"Davydov"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"fulldoi":"https://doi.org/10.1186/s12864-018-5245-1","doi":"10.1186/s12864-018-5245-1","publisher":"Springer Nature","publication_identifier":{"issn":["1471-2164"]},"day":"27","publication":"BMC Genomics","month":"12","_id":"8262","status":"public","year":"2018","article_processing_charge":"No","oa":1,"title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp."},{"article_number":"e4545","pmid":1,"author":[{"last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"last_name":"Dranenko","full_name":"Dranenko, Natalia O.","first_name":"Natalia O."},{"full_name":"Ocheredko, Elena S.","first_name":"Elena S.","last_name":"Ocheredko"},{"full_name":"Kanevsky, German M.","first_name":"German M.","last_name":"Kanevsky"},{"first_name":"Yaroslav N.","full_name":"Lozinsky, Yaroslav N.","last_name":"Lozinsky"},{"last_name":"Khalaycheva","first_name":"Vera A.","full_name":"Khalaycheva, Vera A."},{"full_name":"Artamonova, Irena I.","first_name":"Irena I.","last_name":"Artamonova"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"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."}],"publication_identifier":{"issn":["2167-8359"]},"day":"27","fulldoi":"https://doi.org/10.7717/peerj.4545","publisher":"PeerJ","doi":"10.7717/peerj.4545","oa":1,"article_processing_charge":"No","title":"Genome rearrangements and phylogeny reconstruction in Yersinia pestis","publication":"PeerJ","year":"2018","_id":"8265","month":"03","status":"public","external_id":{"pmid":["29607260"]},"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.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.4545\">https://doi.org/10.7717/peerj.4545</a>.","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.","ama":"Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. <i>PeerJ</i>. 2018;6. doi:<a href=\"https://doi.org/10.7717/peerj.4545\">10.7717/peerj.4545</a>","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” <i>PeerJ</i>, vol. 6, e4545, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.4545\">10.7717/peerj.4545</a>.","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. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.4545\">https://doi.org/10.7717/peerj.4545</a>","ieee":"O. Bochkareva <i>et al.</i>, “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” <i>PeerJ</i>, vol. 6. PeerJ, 2018.","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)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7717/peerj.4545"}],"volume":6,"date_updated":"2023-02-23T13:28:57Z","publication_status":"published","extern":"1","article_type":"original","date_created":"2020-08-15T11:08:23Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"         6","type":"journal_article","date_published":"2018-03-27T00:00:00Z"},{"fulldoi":"https://doi.org/10.21873/anticanres.12525","doi":"10.21873/anticanres.12525","article_type":"original","publisher":"International Institute of Anticancer Research","date_updated":"2021-01-12T08:17:52Z","publication_identifier":{"eissn":["1791-7530"],"issn":["0250-7005"]},"publication_status":"published","extern":"1","day":"01","publication":"Anticancer Research","type":"journal_article","status":"public","_id":"8274","date_published":"2018-05-01T00:00:00Z","month":"05","year":"2018","article_processing_charge":"No","language":[{"iso":"eng"}],"date_created":"2020-08-17T07:13:55Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        38","quality_controlled":"1","title":"Bidirectional regulation of COX-2 expression between cancer cells and macrophages","page":"2811-2817","citation":{"chicago":"Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” <i>Anticancer Research</i>. International Institute of Anticancer Research, 2018. <a href=\"https://doi.org/10.21873/anticanres.12525\">https://doi.org/10.21873/anticanres.12525</a>.","mla":"Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” <i>Anticancer Research</i>, vol. 38, no. 5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:<a href=\"https://doi.org/10.21873/anticanres.12525\">10.21873/anticanres.12525</a>.","apa":"Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer, J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression between cancer cells and macrophages. <i>Anticancer Research</i>. International Institute of Anticancer Research. <a href=\"https://doi.org/10.21873/anticanres.12525\">https://doi.org/10.21873/anticanres.12525</a>","ama":"Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. <i>Anticancer Research</i>. 2018;38(5):2811-2817. doi:<a href=\"https://doi.org/10.21873/anticanres.12525\">10.21873/anticanres.12525</a>","ista":"Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG, Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817.","short":"M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G. Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38 (2018) 2811–2817.","ieee":"M. I. Carvalho <i>et al.</i>, “Bidirectional regulation of COX-2 expression between cancer cells and macrophages,” <i>Anticancer Research</i>, vol. 38, no. 5. International Institute of Anticancer Research, pp. 2811–2817, 2018."},"issue":"5","abstract":[{"lang":"eng","text":"Background/Aim: Our aim was to investigate the crosstalk between tumor and immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes (dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2 overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages, was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29 human colon cancer cells and reduced production of COX2 in BT474 human mammary cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion: Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape a tolerogenic tumor microenvironment in CMT."}],"volume":38,"author":[{"last_name":"Carvalho","first_name":"Maria Isabel","full_name":"Carvalho, Maria Isabel"},{"last_name":"Bianchini","full_name":"Bianchini, Rodolfo","first_name":"Rodolfo"},{"full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer"},{"full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"last_name":"Flickinger","first_name":"Irene","full_name":"Flickinger, Irene"},{"last_name":"Thalhammer","full_name":"Thalhammer, Johann G.","first_name":"Johann G."},{"full_name":"Pires, Isabel","first_name":"Isabel","last_name":"Pires"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"},{"first_name":"Felisbina L.","full_name":"Queiroga, Felisbina L.","last_name":"Queiroga"}]},{"fulldoi":"https://doi.org/10.1109/sp.2018.000-5","publisher":"IEEE","doi":"10.1109/sp.2018.000-5","date_updated":"2021-01-12T08:17:56Z","publication_identifier":{"issn":["2375-1207"],"isbn":["9781538643532"]},"day":"26","extern":"1","publication_status":"published","conference":{"end_date":"2018-05-24","name":"SP: Symposium on Security and Privacy","location":"San Francisco, CA, United States","start_date":"2018-05-20"},"publication":"2018 IEEE Symposium on Security and Privacy","type":"conference","year":"2018","_id":"8297","date_published":"2018-07-26T00:00:00Z","month":"07","status":"public","date_created":"2020-08-26T11:46:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","title":"OmniLedger: A secure, scale-out, decentralized ledger via sharding","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 <i>2018 IEEE Symposium on Security and Privacy</i>, 583–98. IEEE, 2018. <a href=\"https://doi.org/10.1109/sp.2018.000-5\">https://doi.org/10.1109/sp.2018.000-5</a>.","apa":"Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., &#38; Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In <i>2018 IEEE Symposium on Security and Privacy</i> (pp. 583–598). San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/sp.2018.000-5\">https://doi.org/10.1109/sp.2018.000-5</a>","mla":"Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” <i>2018 IEEE Symposium on Security and Privacy</i>, IEEE, 2018, pp. 583–98, doi:<a href=\"https://doi.org/10.1109/sp.2018.000-5\">10.1109/sp.2018.000-5</a>.","ama":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: <i>2018 IEEE Symposium on Security and Privacy</i>. IEEE; 2018:583-598. doi:<a href=\"https://doi.org/10.1109/sp.2018.000-5\">10.1109/sp.2018.000-5</a>","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.","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.","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 <i>2018 IEEE Symposium on Security and Privacy</i>, San Francisco, CA, United States, 2018, pp. 583–598."},"page":"583-598","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/406"}],"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."}],"author":[{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"},{"full_name":"Gasser, Linus","first_name":"Linus","last_name":"Gasser"},{"full_name":"Gailly, Nicolas","first_name":"Nicolas","last_name":"Gailly"},{"last_name":"Syta","full_name":"Syta, Ewa","first_name":"Ewa"},{"first_name":"Bryan","full_name":"Ford, Bryan","last_name":"Ford"}]},{"day":"08","extern":"1","publication_status":"published","date_updated":"2021-01-12T08:17:57Z","publication_identifier":{"isbn":["9783319990729"],"eisbn":["9783319990736"],"issn":["0302-9743","1611-3349"]},"publisher":"Springer Nature","doi":"10.1007/978-3-319-99073-6_6","fulldoi":"https://doi.org/10.1007/978-3-319-99073-6_6","quality_controlled":"1","intvolume":"     11098","title":"Channels: Horizontal scaling and confidentiality on permissioned blockchains","date_created":"2020-08-26T11:47:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2018","status":"public","_id":"8298","date_published":"2018-08-08T00:00:00Z","month":"08","conference":{"start_date":"2018-09-03","name":"ESORICS: European Symposium on Research in Computer Security","end_date":"2018-09-07","location":"Barcelona, Spain"},"alternative_title":["LNCS"],"publication":"Computer Security","type":"conference","citation":{"apa":"Androulaki, E., Cachin, C., De Caro, A., &#38; Kokoris Kogias, E. (2018). Channels: Horizontal scaling and confidentiality on permissioned blockchains. In <i>Computer Security</i> (Vol. 11098, pp. 111–131). Barcelona, Spain: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-99073-6_6\">https://doi.org/10.1007/978-3-319-99073-6_6</a>","mla":"Androulaki, Elli, et al. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” <i>Computer Security</i>, vol. 11098, Springer Nature, 2018, pp. 111–31, doi:<a href=\"https://doi.org/10.1007/978-3-319-99073-6_6\">10.1007/978-3-319-99073-6_6</a>.","ista":"Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. 2018. Channels: Horizontal scaling and confidentiality on permissioned blockchains. Computer Security. ESORICS: European Symposium on Research in Computer Security, LNCS, vol. 11098, 111–131.","ama":"Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. Channels: Horizontal scaling and confidentiality on permissioned blockchains. In: <i>Computer Security</i>. Vol 11098. Springer Nature; 2018:111-131. doi:<a href=\"https://doi.org/10.1007/978-3-319-99073-6_6\">10.1007/978-3-319-99073-6_6</a>","short":"E. Androulaki, C. Cachin, A. De Caro, E. Kokoris Kogias, in:, Computer Security, Springer Nature, 2018, pp. 111–131.","ieee":"E. Androulaki, C. Cachin, A. De Caro, and E. Kokoris Kogias, “Channels: Horizontal scaling and confidentiality on permissioned blockchains,” in <i>Computer Security</i>, Barcelona, Spain, 2018, vol. 11098, pp. 111–131.","chicago":"Androulaki, Elli, Christian Cachin, Angelo De Caro, and Eleftherios Kokoris Kogias. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” In <i>Computer Security</i>, 11098:111–31. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-99073-6_6\">https://doi.org/10.1007/978-3-319-99073-6_6</a>."},"page":"111-131","author":[{"first_name":"Elli","full_name":"Androulaki, Elli","last_name":"Androulaki"},{"last_name":"Cachin","first_name":"Christian","full_name":"Cachin, Christian"},{"first_name":"Angelo","full_name":"De Caro, Angelo","last_name":"De Caro"},{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios"}],"volume":11098,"abstract":[{"lang":"eng","text":"Sharding, or partitioning the system’s state so that different subsets of participants handle it, is a proven approach to building distributed systems whose total capacity scales horizontally with the number of participants. Many distributed ledgers have adopted this approach to increase their performance, however, they focus on the permissionless setting that assumes the existence of a strong adversary. In this paper, we deploy channels for permissioned blockchains. Our first contribution is to adapt sharding on asset-management applications for the permissioned setting, while preserving liveness and safety even on transactions spanning across-channels. Our second contribution is to leverage channels as a confidentiality boundary, enabling different organizations and consortia to preserve their privacy within their channels and still be part of a bigger collaborative ecosystem. To make our system concrete we map it on top of Hyperledger Fabric."}]}]