--- _id: '715' abstract: - lang: eng text: D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome. article_number: aao4218 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218 apa: Novarino, G. (2017). More excitation for Rett syndrome. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218 chicago: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218. ieee: G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218. mla: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aao4218. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:48:06Z date_published: 2017-08-30T00:00:00Z date_updated: 2021-01-12T08:12:04Z day: '30' department: - _id: GaNo doi: 10.1126/scitranslmed.aao4218 intvolume: ' 9' issue: '405' language: - iso: eng month: '08' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6968' quality_controlled: '1' scopus_import: 1 status: public title: More excitation for Rett syndrome type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '716' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.' article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408 apa: Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408 chicago: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408. ieee: K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017. ista: Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34. mla: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408. short: K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34. date_created: 2018-12-11T11:48:06Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:12:08Z day: '01' department: - _id: KrCh doi: 10.1145/3121408 ec_funded: 1 external_id: arxiv: - '1201.2829' intvolume: ' 64' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1201.2829 month: '09' oa: 1 oa_version: Preprint page: '34' project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Journal of the ACM publication_identifier: issn: - '00045411' publication_status: published publisher: ACM publist_id: '6964' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of mean-payoff pushdown games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2017' ... --- _id: '717' abstract: - lang: eng text: 'We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard.' acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259. doi:10.1016/j.jcss.2017.04.005 apa: Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005 chicago: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences. Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005. ieee: K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic Press, pp. 236–259, 2017. ista: Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259. mla: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences, vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005. short: K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259. date_created: 2018-12-11T11:48:07Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-23T10:38:15Z day: '01' department: - _id: KrCh doi: 10.1016/j.jcss.2017.04.005 ec_funded: 1 intvolume: ' 88' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1210.3141 month: '09' oa: 1 oa_version: Preprint page: 236 - 259 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Computer and System Sciences publication_status: published publisher: Academic Press publist_id: '6963' quality_controlled: '1' related_material: record: - id: '2329' relation: earlier_version status: public scopus_import: 1 status: public title: Hyperplane separation technique for multidimensional mean-payoff games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 88 year: '2017' ... --- _id: '719' abstract: - lang: eng text: 'The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rüdiger full_name: Ehlers, Rüdiger last_name: Ehlers citation: ama: 'Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica. 2017;54(6):543-544. doi:10.1007/s00236-017-0299-0' apa: 'Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0' chicago: 'Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.' ieee: 'K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.' ista: 'Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.' mla: 'Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:10.1007/s00236-017-0299-0.' short: K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544. date_created: 2018-12-11T11:48:07Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:12:18Z day: '01' department: - _id: KrCh doi: 10.1007/s00236-017-0299-0 intvolume: ' 54' issue: '6' language: - iso: eng month: '09' oa_version: None page: 543 - 544 publication: Acta Informatica publication_identifier: issn: - '00015903' publication_status: published publisher: Springer publist_id: '6961' quality_controlled: '1' scopus_import: 1 status: public title: 'Special issue: Synthesis and SYNT 2014' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2017' ... --- _id: '720' abstract: - lang: eng text: 'Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.' article_number: e1005763 article_processing_charge: Yes author: - first_name: Jan full_name: Humplik, Jan id: 2E9627A8-F248-11E8-B48F-1D18A9856A87 last_name: Humplik - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763 apa: Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763 chicago: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763. ieee: J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017. ista: Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763. mla: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763. short: J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017). date_created: 2018-12-11T11:48:08Z date_published: 2017-09-19T00:00:00Z date_updated: 2021-01-12T08:12:21Z day: '19' ddc: - '530' - '571' department: - _id: GaTk doi: 10.1371/journal.pcbi.1005763 file: - access_level: open_access checksum: 81107096c19771c36ddbe6f0282a3acb content_type: application/pdf creator: system date_created: 2018-12-12T10:18:30Z date_updated: 2020-07-14T12:47:53Z file_id: '5352' file_name: IST-2017-884-v1+1_journal.pcbi.1005763.pdf file_size: 14167050 relation: main_file file_date_updated: 2020-07-14T12:47:53Z has_accepted_license: '1' intvolume: ' 13' issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '09' oa: 1 oa_version: Published Version project: - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PLoS Computational Biology publication_identifier: issn: - 1553734X publication_status: published publisher: Public Library of Science publist_id: '6960' pubrep_id: '884' quality_controlled: '1' scopus_import: 1 status: public title: Probabilistic models for neural populations that naturally capture global coupling and criticality 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '721' abstract: - lang: eng text: 'Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur.' author: - first_name: Oskari H full_name: Ajanki, Oskari H id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87 last_name: Ajanki - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639 apa: Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639 chicago: Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639. ieee: O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” Communications on Pure and Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017. ista: Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705. mla: Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639. short: O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705. date_created: 2018-12-11T11:48:08Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:12:24Z day: '01' department: - _id: LaEr doi: 10.1002/cpa.21639 ec_funded: 1 intvolume: ' 70' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1512.03703 month: '09' oa: 1 oa_version: Submitted Version page: 1672 - 1705 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Communications on Pure and Applied Mathematics publication_identifier: issn: - '00103640' publication_status: published publisher: Wiley-Blackwell publist_id: '6959' quality_controlled: '1' scopus_import: 1 status: public title: Singularities of solutions to quadratic vector equations on the complex upper half plane type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '722' abstract: - lang: eng text: Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises. author: - first_name: Emily full_name: Morris, Emily last_name: Morris - first_name: Marcus full_name: Griffiths, Marcus last_name: Griffiths - first_name: Agata full_name: Golebiowska, Agata last_name: Golebiowska - first_name: Stefan full_name: Mairhofer, Stefan last_name: Mairhofer - first_name: Jasmine full_name: Burr Hersey, Jasmine last_name: Burr Hersey - first_name: Tatsuaki full_name: Goh, Tatsuaki last_name: Goh - first_name: Daniel full_name: Von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Brian full_name: Atkinson, Brian last_name: Atkinson - first_name: Craig full_name: Sturrock, Craig last_name: Sturrock - first_name: Jonathan full_name: Lynch, Jonathan last_name: Lynch - first_name: Kris full_name: Vissenberg, Kris last_name: Vissenberg - first_name: Karl full_name: Ritz, Karl last_name: Ritz - first_name: Darren full_name: Wells, Darren last_name: Wells - first_name: Sacha full_name: Mooney, Sacha last_name: Mooney - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett citation: ama: Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043 apa: Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043 chicago: Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043. ieee: E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017. ista: Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930. mla: Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043. short: E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930. date_created: 2018-12-11T11:48:08Z date_published: 2017-09-11T00:00:00Z date_updated: 2021-01-12T08:12:29Z day: '11' ddc: - '581' department: - _id: JiFr doi: 10.1016/j.cub.2017.06.043 ec_funded: 1 external_id: pmid: - '28898665' file: - access_level: open_access checksum: e45588b21097b408da6276a3e5eedb2e content_type: application/pdf creator: dernst date_created: 2019-04-17T07:46:40Z date_updated: 2020-07-14T12:47:54Z file_id: '6332' file_name: 2017_CurrentBiology_Morris.pdf file_size: 1576593 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 27' issue: '17' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Submitted Version page: R919 - R930 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press publist_id: '6956' pubrep_id: '982' quality_controlled: '1' scopus_import: 1 status: public title: Shaping 3D root system architecture tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2017' ... --- _id: '725' abstract: - lang: eng text: Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species. author: - first_name: Roy full_name: Harpaz, Roy last_name: Harpaz - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman citation: ama: Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114 apa: Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114 chicago: Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114. ieee: R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017. ista: Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154. mla: Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114. short: R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154. date_created: 2018-12-11T11:48:10Z date_published: 2017-09-19T00:00:00Z date_updated: 2021-01-12T08:12:36Z day: '19' department: - _id: GaTk doi: 10.1073/pnas.1703817114 external_id: pmid: - '28874581' intvolume: ' 114' issue: '38' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/ month: '09' oa: 1 oa_version: Submitted Version page: 10149 - 10154 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '6953' quality_controlled: '1' scopus_import: 1 status: public title: Discrete modes of social information processing predict individual behavior of fish in a group type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '724' abstract: - lang: eng text: We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic. acknowledgement: "We would like to thank Dmitry Abanin, Christophe De\r\nBeule, \ Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions. \ Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft \ (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate \ School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1." article_number: '104203' author: - first_name: Daniel full_name: Hetterich, Daniel last_name: Hetterich - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Fernando full_name: Domínguez, Fernando last_name: Domínguez - first_name: Frank full_name: Pollmann, Frank last_name: Pollmann - first_name: Björn full_name: Trauzettel, Björn last_name: Trauzettel citation: ama: Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203 apa: Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203 chicago: Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104203. ieee: D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” Physical Review B, vol. 96, no. 10. American Physical Society, 2017. ista: Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203. mla: Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203. short: D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017). date_created: 2018-12-11T11:48:09Z date_published: 2017-09-13T00:00:00Z date_updated: 2021-01-12T08:12:35Z day: '13' department: - _id: MaSe doi: 10.1103/PhysRevB.96.104203 intvolume: ' 96' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1701.02744 month: '09' oa: 1 oa_version: Submitted Version publication: Physical Review B publication_identifier: issn: - '24699950' publication_status: published publisher: American Physical Society publist_id: '6955' quality_controlled: '1' scopus_import: 1 status: public title: Noninteracting central site model localization and logarithmic entanglement growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ... --- _id: '7289' abstract: - lang: eng text: Aprotic sodium–O2 batteries require the reversible formation/dissolution of sodium superoxide (NaO2) on cycling. Poor cycle life has been associated with parasitic chemistry caused by the reactivity of electrolyte and electrode with NaO2, a strong nucleophile and base. Its reactivity can, however, not consistently explain the side reactions and irreversibility. Herein we show that singlet oxygen (1O2) forms at all stages of cycling and that it is a main driver for parasitic chemistry. It was detected in‐ and ex‐situ via a 1O2 trap that selectively and rapidly forms a stable adduct with 1O2. The 1O2 formation mechanism involves proton‐mediated superoxide disproportionation on discharge, rest, and charge below ca. 3.3 V, and direct electrochemical 1O2 evolution above ca. 3.3 V. Trace water, which is needed for high capacities also drives parasitic chemistry. Controlling the highly reactive singlet oxygen is thus crucial for achieving highly reversible cell operation. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Bettina full_name: Schafzahl, Bettina last_name: Schafzahl - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Schafzahl L, Mahne N, Schafzahl B, et al. Singlet oxygen during cycling of the aprotic sodium-O2 battery. Angewandte Chemie International Edition. 2017;56(49):15728-15732. doi:10.1002/anie.201709351 apa: Schafzahl, L., Mahne, N., Schafzahl, B., Wilkening, M., Slugovc, C., Borisov, S. M., & Freunberger, S. A. (2017). Singlet oxygen during cycling of the aprotic sodium-O2 battery. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201709351 chicago: Schafzahl, Lukas, Nika Mahne, Bettina Schafzahl, Martin Wilkening, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “Singlet Oxygen during Cycling of the Aprotic Sodium-O2 Battery.” Angewandte Chemie International Edition. Wiley, 2017. https://doi.org/10.1002/anie.201709351. ieee: L. Schafzahl et al., “Singlet oxygen during cycling of the aprotic sodium-O2 battery,” Angewandte Chemie International Edition, vol. 56, no. 49. Wiley, pp. 15728–15732, 2017. ista: Schafzahl L, Mahne N, Schafzahl B, Wilkening M, Slugovc C, Borisov SM, Freunberger SA. 2017. Singlet oxygen during cycling of the aprotic sodium-O2 battery. Angewandte Chemie International Edition. 56(49), 15728–15732. mla: Schafzahl, Lukas, et al. “Singlet Oxygen during Cycling of the Aprotic Sodium-O2 Battery.” Angewandte Chemie International Edition, vol. 56, no. 49, Wiley, 2017, pp. 15728–32, doi:10.1002/anie.201709351. short: L. Schafzahl, N. Mahne, B. Schafzahl, M. Wilkening, C. Slugovc, S.M. Borisov, S.A. Freunberger, Angewandte Chemie International Edition 56 (2017) 15728–15732. date_created: 2020-01-15T12:15:05Z date_published: 2017-12-04T00:00:00Z date_updated: 2021-01-12T08:12:47Z day: '04' ddc: - '540' doi: 10.1002/anie.201709351 extern: '1' file: - access_level: open_access checksum: 3c5b1e51954554dffb13c7d58f69836c content_type: application/pdf creator: dernst date_created: 2020-01-26T14:58:07Z date_updated: 2020-07-14T12:47:55Z file_id: '7362' file_name: 2017_AngChemieInternat_Schafzahl.pdf file_size: 1013492 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 56' issue: '49' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version page: 15728-15732 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Singlet oxygen during cycling of the aprotic sodium-O2 battery tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 56 year: '2017' ... --- _id: '7288' abstract: - lang: eng text: Nowadays commercial supercapacitors are based on purely capacitive storage at the porous carbons that are used for the electrodes. However, the limits that capacitive storage imposes on energy density calls to investigate new materials to improve the capacitance of the device. This new type of electrodes (e.g., RuO2, MnO2…) involves pseudo-capacitive faradaic redox processes with the solid material. Ion exchange with solid materials is, however, much slower than the adsorption process in capacitive storage and inevitably leads to significant loss of power. Faradaic process in the liquid state, in contrast can be similarly fast as capacitive processes due to the fast ion transport. Designing new devices with liquid like dynamics and improved specific capacitance is challenging. We present a new approach to increase the specific capacitance using biredox ionic liquids, where redox moieties are tethered to the electrolyte ions, allowing high redox concentrations and significant pseudo-capacitive storage in the liquid state. Anions and cations are functionalized with anthraquinone (AQ) and 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO) moieties, respectively. Glassy carbon, carbon-onion, and commercial activated carbon electrodes that exhibit different double layer structures and thus different diffusion dynamics were used to simultaneously study the electrochemical response of biredox ionic liquids at the positive and negative electrode. article_processing_charge: No article_type: original author: - first_name: C. full_name: Bodin, C. last_name: Bodin - first_name: E. full_name: Mourad, E. last_name: Mourad - first_name: D. full_name: Zigah, D. last_name: Zigah - first_name: S. full_name: Le Vot, S. last_name: Le Vot - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: F. full_name: Favier, F. last_name: Favier - first_name: O. full_name: Fontaine, O. last_name: Fontaine citation: ama: 'Bodin C, Mourad E, Zigah D, et al. Biredox ionic liquids: New opportunities toward high performance supercapacitors. Faraday Discussions. 2017;206:393-404. doi:10.1039/c7fd00174f' apa: 'Bodin, C., Mourad, E., Zigah, D., Le Vot, S., Freunberger, S. A., Favier, F., & Fontaine, O. (2017). Biredox ionic liquids: New opportunities toward high performance supercapacitors. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c7fd00174f' chicago: 'Bodin, C., E. Mourad, D. Zigah, S. Le Vot, Stefan Alexander Freunberger, F. Favier, and O. Fontaine. “Biredox Ionic Liquids: New Opportunities toward High Performance Supercapacitors.” Faraday Discussions. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7fd00174f.' ieee: 'C. Bodin et al., “Biredox ionic liquids: New opportunities toward high performance supercapacitors,” Faraday Discussions, vol. 206. Royal Society of Chemistry, pp. 393–404, 2017.' ista: 'Bodin C, Mourad E, Zigah D, Le Vot S, Freunberger SA, Favier F, Fontaine O. 2017. Biredox ionic liquids: New opportunities toward high performance supercapacitors. Faraday Discussions. 206, 393–404.' mla: 'Bodin, C., et al. “Biredox Ionic Liquids: New Opportunities toward High Performance Supercapacitors.” Faraday Discussions, vol. 206, Royal Society of Chemistry, 2017, pp. 393–404, doi:10.1039/c7fd00174f.' short: C. Bodin, E. Mourad, D. Zigah, S. Le Vot, S.A. Freunberger, F. Favier, O. Fontaine, Faraday Discussions 206 (2017) 393–404. date_created: 2020-01-15T12:14:04Z date_published: 2017-06-29T00:00:00Z date_updated: 2021-06-10T06:17:17Z day: '29' doi: 10.1039/c7fd00174f extern: '1' intvolume: ' 206' language: - iso: eng month: '06' oa_version: None page: 393-404 publication: Faraday Discussions publication_identifier: issn: - 1359-6640 - 1364-5498 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Biredox ionic liquids: New opportunities toward high performance supercapacitors' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 206 year: '2017' ... --- _id: '7290' abstract: - lang: eng text: 'We report a family of Pt and Pd benzoporphyrin dyes with versatile photophysical properties and easy access from cheap and abundant chemicals. Attaching 4 or 8 alkylsulfone groups onto a meso-tetraphenyltetrabenzoporphyrin (TPTBP) macrocylcle renders the dyes highly soluble in organic solvents, photostable, and electron-deficient with the redox potential raised up to 0.65 V versus the parent porphyrin. The new dyes intensively absorb in the blue (Soret band, 440–480 nm) and in the red (Q-band, 620–650 nm) parts of the electromagnetic spectrum and show bright phosphorescence at room-temperature in the NIR with quantum yields up to 30% in solution. The small singlet–triplet energy gap yields unusually efficient thermally activated delayed fluorescence (TADF) at elevated temperatures in solution and in polymeric matrices with quantum yields as high as 27% at 120 °C, which is remarkable for benzoporphyrins. Apart from oxygen sensing, these properties enable unprecedented simultaneous, self-referenced oxygen and temperature sensing with a single indicator dye: whereas oxygen can be determined either via the decay time of phosphorescence or TADF, the temperature is accessed via the ratio of the two emissions. Moreover, the dyes are efficient sensitizers for triplet–triplet annihilation (TTA)-based upconversion making possible longer sensitization wavelength than the conventional benzoporphyrin complexes. The Pt-octa-sulfone dye also features interesting semireversible transformation in basic media, which generates new NIR absorbing species.' article_processing_charge: No article_type: original author: - first_name: Peter W. full_name: Zach, Peter W. last_name: Zach - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Ingo full_name: Klimant, Ingo last_name: Klimant - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov citation: ama: 'Zach PW, Freunberger SA, Klimant I, Borisov SM. Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and unusually efficient thermally activated delayed fluorescence: First demonstration of simultaneous oxygen and temperature sensing with a single emitter. ACS Applied Materials & Interfaces. 2017;9(43):38008-38023. doi:10.1021/acsami.7b10669' apa: 'Zach, P. W., Freunberger, S. A., Klimant, I., & Borisov, S. M. (2017). Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and unusually efficient thermally activated delayed fluorescence: First demonstration of simultaneous oxygen and temperature sensing with a single emitter. ACS Applied Materials & Interfaces. ACS. https://doi.org/10.1021/acsami.7b10669' chicago: 'Zach, Peter W., Stefan Alexander Freunberger, Ingo Klimant, and Sergey M. Borisov. “Electron-Deficient near-Infrared Pt(II) and Pd(II) Benzoporphyrins with Dual Phosphorescence and Unusually Efficient Thermally Activated Delayed Fluorescence: First Demonstration of Simultaneous Oxygen and Temperature Sensing with a Single Emitter.” ACS Applied Materials & Interfaces. ACS, 2017. https://doi.org/10.1021/acsami.7b10669.' ieee: 'P. W. Zach, S. A. Freunberger, I. Klimant, and S. M. Borisov, “Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and unusually efficient thermally activated delayed fluorescence: First demonstration of simultaneous oxygen and temperature sensing with a single emitter,” ACS Applied Materials & Interfaces, vol. 9, no. 43. ACS, pp. 38008–38023, 2017.' ista: 'Zach PW, Freunberger SA, Klimant I, Borisov SM. 2017. Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and unusually efficient thermally activated delayed fluorescence: First demonstration of simultaneous oxygen and temperature sensing with a single emitter. ACS Applied Materials & Interfaces. 9(43), 38008–38023.' mla: 'Zach, Peter W., et al. “Electron-Deficient near-Infrared Pt(II) and Pd(II) Benzoporphyrins with Dual Phosphorescence and Unusually Efficient Thermally Activated Delayed Fluorescence: First Demonstration of Simultaneous Oxygen and Temperature Sensing with a Single Emitter.” ACS Applied Materials & Interfaces, vol. 9, no. 43, ACS, 2017, pp. 38008–23, doi:10.1021/acsami.7b10669.' short: P.W. Zach, S.A. Freunberger, I. Klimant, S.M. Borisov, ACS Applied Materials & Interfaces 9 (2017) 38008–38023. date_created: 2020-01-15T12:15:16Z date_published: 2017-10-10T00:00:00Z date_updated: 2021-01-12T08:12:48Z day: '10' ddc: - '540' - '543' doi: 10.1021/acsami.7b10669 extern: '1' file: - access_level: open_access checksum: 0461c990eb910f19a70c6e5349ec35ed content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:49:32Z date_updated: 2020-07-14T12:47:55Z file_id: '8051' file_name: Paper_Manuscript_submitted.pdf file_size: 2072792 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 9' issue: '43' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 38008-38023 publication: ACS Applied Materials & Interfaces publication_identifier: eissn: - 1944-8252 issn: - 1944-8244 publication_status: published publisher: ACS quality_controlled: '1' status: public title: 'Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and unusually efficient thermally activated delayed fluorescence: First demonstration of simultaneous oxygen and temperature sensing with a single emitter' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '7292' abstract: - lang: eng text: 'Rechargeable Li–O2 batteries have amongst the highest formal energy and could store significantly more energy than other rechargeable batteries in practice if at least a large part of their promise could be realized. Realization, however, still faces many challenges than can only be overcome by fundamental understanding of the processes taking place. Here, we review recent advances in understanding the chemistry of the Li–O2 cathode and provide a perspective on dominant research needs. We put particular emphasis on issues that are often grossly misunderstood: realistic performance metrics and their reporting as well as identifying reversibility and quantitative measures to do so. Parasitic reactions are the prime obstacle for reversible cell operation and have recently been identified to be predominantly caused by singlet oxygen and not by reduced oxygen species as thought before. We discuss the far reaching implications of this finding on electrolyte and cathode stability, electrocatalysis, and future research needs.' article_processing_charge: No article_type: original author: - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Musthafa Ottakam full_name: Thotiyl, Musthafa Ottakam last_name: Thotiyl - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mahne N, Fontaine O, Thotiyl MO, Wilkening M, Freunberger SA. Mechanism and performance of lithium–oxygen batteries – a perspective. Chemical Science. 2017;8(10):6716-6729. doi:10.1039/c7sc02519j apa: Mahne, N., Fontaine, O., Thotiyl, M. O., Wilkening, M., & Freunberger, S. A. (2017). Mechanism and performance of lithium–oxygen batteries – a perspective. Chemical Science. RSC. https://doi.org/10.1039/c7sc02519j chicago: Mahne, Nika, Olivier Fontaine, Musthafa Ottakam Thotiyl, Martin Wilkening, and Stefan Alexander Freunberger. “Mechanism and Performance of Lithium–Oxygen Batteries – a Perspective.” Chemical Science. RSC, 2017. https://doi.org/10.1039/c7sc02519j. ieee: N. Mahne, O. Fontaine, M. O. Thotiyl, M. Wilkening, and S. A. Freunberger, “Mechanism and performance of lithium–oxygen batteries – a perspective,” Chemical Science, vol. 8, no. 10. RSC, pp. 6716–6729, 2017. ista: Mahne N, Fontaine O, Thotiyl MO, Wilkening M, Freunberger SA. 2017. Mechanism and performance of lithium–oxygen batteries – a perspective. Chemical Science. 8(10), 6716–6729. mla: Mahne, Nika, et al. “Mechanism and Performance of Lithium–Oxygen Batteries – a Perspective.” Chemical Science, vol. 8, no. 10, RSC, 2017, pp. 6716–29, doi:10.1039/c7sc02519j. short: N. Mahne, O. Fontaine, M.O. Thotiyl, M. Wilkening, S.A. Freunberger, Chemical Science 8 (2017) 6716–6729. date_created: 2020-01-15T12:15:42Z date_published: 2017-07-31T00:00:00Z date_updated: 2021-01-12T08:12:49Z day: '31' ddc: - '540' doi: 10.1039/c7sc02519j extern: '1' file: - access_level: open_access checksum: 70c7c2ce5430b6e8605ccbf0275f1e80 content_type: application/pdf creator: dernst date_created: 2020-01-26T15:04:44Z date_updated: 2020-07-14T12:47:55Z file_id: '7363' file_name: 2017_ChemicalScience_Mahne.pdf file_size: 992106 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 8' issue: '10' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 6716-6729 publication: Chemical Science publication_identifier: eissn: - 2041-6539 issn: - 2041-6520 publication_status: published publisher: RSC quality_controlled: '1' status: public title: Mechanism and performance of lithium–oxygen batteries – a perspective 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '7291' abstract: - lang: eng text: Na battery chemistries show poor passivation behavior of low voltage Na storage compounds and Na metal with organic carbonate‐based electrolytes adopted from Li‐ion batteries. Therefore, a suitable electrolyte remains a major challenge for establishing Na batteries. Here we report highly concentrated sodium bis(fluorosulfonyl)imide (NaFSI) in dimethoxyethane (DME) electrolytes and investigate them for Na metal and hard carbon anodes and intercalation cathodes. For a DME/NaFSI ratio of 2, a stable passivation of anode materials was found owing to the formation of a stable solid electrolyte interface, which was characterized spectroscopically. This permitted non‐dentritic Na metal cycling with approximately 98 % coulombic efficiency as shown for up to 300 cycles. The NaFSI/DME electrolyte may enable Na‐metal anodes and allows for more reliable assessment of electrode materials in Na‐ion half‐cells, as is demonstrated by comparing half‐cell cycling of hard carbon anodes and Na3V2(PO4)3 cathodes with a widely used carbonate and the NaFSI/DME electrolyte. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Ilie full_name: Hanzu, Ilie last_name: Hanzu - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Schafzahl L, Hanzu I, Wilkening M, Freunberger SA. An electrolyte for reversible cycling of sodium metal and intercalation compounds. ChemSusChem. 2017;10(2):401-408. doi:10.1002/cssc.201601222 apa: Schafzahl, L., Hanzu, I., Wilkening, M., & Freunberger, S. A. (2017). An electrolyte for reversible cycling of sodium metal and intercalation compounds. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.201601222 chicago: Schafzahl, Lukas, Ilie Hanzu, Martin Wilkening, and Stefan Alexander Freunberger. “An Electrolyte for Reversible Cycling of Sodium Metal and Intercalation Compounds.” ChemSusChem. Wiley, 2017. https://doi.org/10.1002/cssc.201601222. ieee: L. Schafzahl, I. Hanzu, M. Wilkening, and S. A. Freunberger, “An electrolyte for reversible cycling of sodium metal and intercalation compounds,” ChemSusChem, vol. 10, no. 2. Wiley, pp. 401–408, 2017. ista: Schafzahl L, Hanzu I, Wilkening M, Freunberger SA. 2017. An electrolyte for reversible cycling of sodium metal and intercalation compounds. ChemSusChem. 10(2), 401–408. mla: Schafzahl, Lukas, et al. “An Electrolyte for Reversible Cycling of Sodium Metal and Intercalation Compounds.” ChemSusChem, vol. 10, no. 2, Wiley, 2017, pp. 401–08, doi:10.1002/cssc.201601222. short: L. Schafzahl, I. Hanzu, M. Wilkening, S.A. Freunberger, ChemSusChem 10 (2017) 401–408. date_created: 2020-01-15T12:15:29Z date_published: 2017-01-20T00:00:00Z date_updated: 2021-01-12T08:12:48Z day: '20' doi: 10.1002/cssc.201601222 extern: '1' intvolume: ' 10' issue: '2' language: - iso: eng month: '01' oa_version: None page: 401-408 publication: ChemSusChem publication_identifier: issn: - 1864-5631 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: An electrolyte for reversible cycling of sodium metal and intercalation compounds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2017' ... --- _id: '731' abstract: - lang: eng text: Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently. article_number: eaap8168 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. The science of love in ASD and ADHD. Science Translational Medicine. 2017;9(411). doi:10.1126/scitranslmed.aap8168 apa: Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168 chicago: Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168. ieee: G. Novarino, “The science of love in ASD and ADHD,” Science Translational Medicine, vol. 9, no. 411. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168. mla: Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aap8168. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:48:12Z date_published: 2017-10-11T00:00:00Z date_updated: 2021-01-12T08:12:57Z day: '11' department: - _id: GaNo doi: 10.1126/scitranslmed.aap8168 intvolume: ' 9' issue: '411' language: - iso: eng month: '10' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6938' quality_controlled: '1' scopus_import: 1 status: public title: The science of love in ASD and ADHD type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '7360' abstract: - lang: eng text: Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy. article_processing_charge: No article_type: original author: - first_name: Anže full_name: Smole, Anže last_name: Smole - first_name: Duško full_name: Lainšček, Duško last_name: Lainšček - first_name: Urban full_name: Bezeljak, Urban id: 2A58201A-F248-11E8-B48F-1D18A9856A87 last_name: Bezeljak orcid: 0000-0003-1365-5631 - first_name: Simon full_name: Horvat, Simon last_name: Horvat - first_name: Roman full_name: Jerala, Roman last_name: Jerala citation: ama: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005 apa: Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005 chicago: Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005. ieee: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017. ista: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 25(1), 102–119. mla: Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005. short: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119. date_created: 2020-01-25T15:55:39Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:13:14Z day: '01' ddc: - '570' department: - _id: MaLo doi: 10.1016/j.ymthe.2016.10.005 external_id: pmid: - '28129106' file: - access_level: open_access checksum: ea8b1b28606dd1edab7379ba4fa3641f content_type: application/pdf creator: dernst date_created: 2020-03-03T10:55:13Z date_updated: 2020-07-14T12:47:56Z file_id: '7561' file_name: 2017_MolecularTherapy_Smole.pdf file_size: 3404806 relation: main_file file_date_updated: 2020-07-14T12:47:56Z has_accepted_license: '1' intvolume: ' 25' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 102-119 pmid: 1 publication: Molecular Therapy publication_identifier: issn: - 1525-0016 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2017' ... --- _id: '748' abstract: - lang: eng text: The essay focuses on individual and collective forms of liminality in John Marlyn’s Under the Ribs of Death. Set in early twentieth-century Winnipeg, the 1957 immigrant novel explores liminal experiences related to ethnic identity, male sexuality, social class, urban spaces and turbulent economic times. As the son of a poor working-class family from Hungary, Sandor Hunyadi makes every effort to become a true Canadian and a successful businessman, but, no matter how hard he tries to overcome contemporary ethnic prejudices and economic hardships, his personal and professional life remains in liminality. In other words, the protagonist undergoes separation, fails at incorporation, and becomes stuck in transition. alternative_title: - Canadiana author: - first_name: Bernhard full_name: Bernhard Wenzl id: 479E9046-F248-11E8-B48F-1D18A9856A87 last_name: Wenzl citation: ama: 'Wenzl B. “...beyond the invisible barrier at Portage and Main”: Liminality in John Marlyn’s Under the Ribs of Death. In: Brandt S, ed. In-Between - Liminal Spaces in Canadian Literature and Culture. Peter Lang GmbH; 2017:91-100. doi:10.3726/b11899' apa: 'Wenzl, B. (2017). “...beyond the invisible barrier at Portage and Main”: Liminality in John Marlyn’s Under the Ribs of Death. In S. Brandt (Ed.), In-Between - Liminal Spaces in Canadian Literature and Culture (pp. 91–100). Peter Lang GmbH. https://doi.org/10.3726/b11899' chicago: 'Wenzl, Bernhard. “‘...Beyond the Invisible Barrier at Portage and Main’: Liminality in John Marlyn’s Under the Ribs of Death.” In In-Between - Liminal Spaces in Canadian Literature and Culture, edited by Stefan Brandt, 91–100. Peter Lang GmbH, 2017. https://doi.org/10.3726/b11899.' ieee: 'B. Wenzl, “‘...beyond the invisible barrier at Portage and Main’: Liminality in John Marlyn’s Under the Ribs of Death,” in In-Between - Liminal Spaces in Canadian Literature and Culture, S. Brandt, Ed. Peter Lang GmbH, 2017, pp. 91–100.' ista: 'Wenzl B. 2017.‘...beyond the invisible barrier at Portage and Main’: Liminality in John Marlyn’s Under the Ribs of Death. In: In-Between - Liminal Spaces in Canadian Literature and Culture. Canadiana, , 91–100.' mla: 'Wenzl, Bernhard. “‘...Beyond the Invisible Barrier at Portage and Main’: Liminality in John Marlyn’s Under the Ribs of Death.” In-Between - Liminal Spaces in Canadian Literature and Culture, edited by Stefan Brandt, Peter Lang GmbH, 2017, pp. 91–100, doi:10.3726/b11899.' short: B. Wenzl, in:, S. Brandt (Ed.), In-Between - Liminal Spaces in Canadian Literature and Culture, Peter Lang GmbH, 2017, pp. 91–100. date_created: 2018-12-11T11:48:18Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:13:49Z day: '01' doi: 10.3726/b11899 editor: - first_name: Stefan full_name: Brandt, Stefan L. last_name: Brandt extern: 1 month: '12' page: 91 - 100 publication: In-Between - Liminal Spaces in Canadian Literature and Culture publication_status: published publisher: Peter Lang GmbH publist_id: '6909' quality_controlled: 0 status: public title: '''...beyond the invisible barrier at Portage and Main'': Liminality in John Marlyn''s Under the Ribs of Death' type: book_chapter year: '2017' ... --- _id: '750' abstract: - lang: eng text: Modern communication technologies allow first responders to contact thousands of potential volunteers simultaneously for support during a crisis or disaster event. However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation. author: - first_name: Jasmin full_name: Pielorz, Jasmin id: 49BC895A-F248-11E8-B48F-1D18A9856A87 last_name: Pielorz - first_name: Matthias full_name: Prandtstetter, Matthias last_name: Prandtstetter - first_name: Markus full_name: Straub, Markus last_name: Straub - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: 2017 IEEE International Conference on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375' apa: 'Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In 2017 IEEE International Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375' chicago: Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017 IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375. ieee: J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in 2017 IEEE International Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763. ista: Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial volunteer allocation needs realistic distances. 2017 IEEE International Conference on Big Data. Big Data, 3760–3763. mla: Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–63, doi:10.1109/BigData.2017.8258375. short: J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763. conference: end_date: 2017-12-14 location: Boston, MA, United States name: Big Data start_date: 2017-12-11 date_created: 2018-12-11T11:48:18Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:13:55Z day: '01' department: - _id: ChLa doi: 10.1109/BigData.2017.8258375 language: - iso: eng month: '12' oa_version: None page: 3760 - 3763 publication: 2017 IEEE International Conference on Big Data publication_identifier: isbn: - 978-153862714-3 publication_status: published publisher: IEEE publist_id: '6906' quality_controlled: '1' scopus_import: 1 status: public title: Optimal geospatial volunteer allocation needs realistic distances type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '7728' abstract: - lang: eng text: 'Meta-analyses of genome-wide association studies, which dominate genetic discovery, are based on data from diverse historical time periods and populations. Genetic scores derived from genome-wide association studies explain only a fraction of the heritability estimates obtained from whole-genome studies on single populations, known as the ‘hidden heritability’ puzzle. Using seven sampling populations (n = 35,062), we test whether hidden heritability is attributed to heterogeneity across sampling populations and time, showing that estimates are substantially smaller across populations compared with within populations. We show that the hidden heritability varies substantially: from zero for height to 20% for body mass index, 37% for education, 40% for age at first birth and up to 75% for number of children. Simulations demonstrate that our results are more likely to reflect heterogeneity in phenotypic measurement or gene–environment interactions than genetic heterogeneity. These findings have substantial implications for genetic discovery, suggesting that large homogenous datasets are required for behavioural phenotypes and that gene–environment interaction may be a central challenge for genetic discovery.' article_processing_charge: No article_type: original author: - first_name: Felix C. full_name: Tropf, Felix C. last_name: Tropf - first_name: S. Hong full_name: Lee, S. Hong last_name: Lee - first_name: Renske M. full_name: Verweij, Renske M. last_name: Verweij - first_name: Gert full_name: Stulp, Gert last_name: Stulp - first_name: Peter J. full_name: van der Most, Peter J. last_name: van der Most - first_name: Ronald full_name: de Vlaming, Ronald last_name: de Vlaming - first_name: Andrew full_name: Bakshi, Andrew last_name: Bakshi - first_name: Daniel A. full_name: Briley, Daniel A. last_name: Briley - first_name: Charles full_name: Rahal, Charles last_name: Rahal - first_name: Robert full_name: Hellpap, Robert last_name: Hellpap - first_name: Anastasia N. full_name: Iliadou, Anastasia N. last_name: Iliadou - first_name: Tõnu full_name: Esko, Tõnu last_name: Esko - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Sarah E. full_name: Medland, Sarah E. last_name: Medland - first_name: Nicholas G. full_name: Martin, Nicholas G. last_name: Martin - first_name: Nicola full_name: Barban, Nicola last_name: Barban - first_name: Harold full_name: Snieder, Harold last_name: Snieder - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Melinda C. full_name: Mills, Melinda C. last_name: Mills citation: ama: Tropf FC, Lee SH, Verweij RM, et al. Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. 2017;1(10):757-765. doi:10.1038/s41562-017-0195-1 apa: Tropf, F. C., Lee, S. H., Verweij, R. M., Stulp, G., van der Most, P. J., de Vlaming, R., … Mills, M. C. (2017). Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-017-0195-1 chicago: Tropf, Felix C., S. Hong Lee, Renske M. Verweij, Gert Stulp, Peter J. van der Most, Ronald de Vlaming, Andrew Bakshi, et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” Nature Human Behaviour. Springer Nature, 2017. https://doi.org/10.1038/s41562-017-0195-1. ieee: F. C. Tropf et al., “Hidden heritability due to heterogeneity across seven populations,” Nature Human Behaviour, vol. 1, no. 10. Springer Nature, pp. 757–765, 2017. ista: Tropf FC, Lee SH, Verweij RM, Stulp G, van der Most PJ, de Vlaming R, Bakshi A, Briley DA, Rahal C, Hellpap R, Iliadou AN, Esko T, Metspalu A, Medland SE, Martin NG, Barban N, Snieder H, Robinson MR, Mills MC. 2017. Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. 1(10), 757–765. mla: Tropf, Felix C., et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” Nature Human Behaviour, vol. 1, no. 10, Springer Nature, 2017, pp. 757–65, doi:10.1038/s41562-017-0195-1. short: F.C. Tropf, S.H. Lee, R.M. Verweij, G. Stulp, P.J. van der Most, R. de Vlaming, A. Bakshi, D.A. Briley, C. Rahal, R. Hellpap, A.N. Iliadou, T. Esko, A. Metspalu, S.E. Medland, N.G. Martin, N. Barban, H. Snieder, M.R. Robinson, M.C. Mills, Nature Human Behaviour 1 (2017) 757–765. date_created: 2020-04-30T10:47:02Z date_published: 2017-09-11T00:00:00Z date_updated: 2021-01-12T08:15:08Z day: '11' doi: 10.1038/s41562-017-0195-1 extern: '1' intvolume: ' 1' issue: '10' language: - iso: eng month: '09' oa_version: None page: 757-765 publication: Nature Human Behaviour publication_identifier: issn: - 2397-3374 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Hidden heritability due to heterogeneity across seven populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2017' ... --- _id: '7727' abstract: - lang: eng text: Genes of the major histocompatibility complex (MHC) have been shown to influence social signalling and mate preferences in many species, including humans. First observations suggest that MHC signalling may also affect female fertility. To test this hypothesis, we exposed 191 female horses (Equus caballus) to either an MHC-similar or an MHC-dissimilar stimulus male around the time of ovulation and conception. A within-subject experimental design controlled for non-MHC-linked male characteristics, and instrumental insemination with semen of other males (n = 106) controlled for potential confounding effects of semen or embryo characteristics. We found that females were more likely to become pregnant if exposed to an MHC-dissimilar than to an MHC-similar male, while overall genetic distance to the stimulus males (based on microsatellite markers on 20 chromosomes) had no effect. Our results demonstrate that early pregnancy failures can be due to maternal life-history decisions (cryptic female choice) influenced by MHC-linked social signalling. article_number: '20171824' article_processing_charge: No article_type: original author: - first_name: D. full_name: Burger, D. last_name: Burger - first_name: S. full_name: Thomas, S. last_name: Thomas - first_name: H. full_name: Aepli, H. last_name: Aepli - first_name: M. full_name: Dreyer, M. last_name: Dreyer - first_name: G. full_name: Fabre, G. last_name: Fabre - first_name: E. full_name: Marti, E. last_name: Marti - first_name: H. full_name: Sieme, H. last_name: Sieme - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: C. full_name: Wedekind, C. last_name: Wedekind citation: ama: 'Burger D, Thomas S, Aepli H, et al. Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. 2017;284(1868). doi:10.1098/rspb.2017.1824' apa: 'Burger, D., Thomas, S., Aepli, H., Dreyer, M., Fabre, G., Marti, E., … Wedekind, C. (2017). Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2017.1824' chicago: 'Burger, D., S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, Matthew Richard Robinson, and C. Wedekind. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2017. https://doi.org/10.1098/rspb.2017.1824.' ieee: 'D. Burger et al., “Major histocompatibility complex-linked social signalling affects female fertility,” Proceedings of the Royal Society B: Biological Sciences, vol. 284, no. 1868. The Royal Society, 2017.' ista: 'Burger D, Thomas S, Aepli H, Dreyer M, Fabre G, Marti E, Sieme H, Robinson MR, Wedekind C. 2017. Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. 284(1868), 20171824.' mla: 'Burger, D., et al. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences, vol. 284, no. 1868, 20171824, The Royal Society, 2017, doi:10.1098/rspb.2017.1824.' short: 'D. Burger, S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, M.R. Robinson, C. Wedekind, Proceedings of the Royal Society B: Biological Sciences 284 (2017).' date_created: 2020-04-30T10:46:43Z date_published: 2017-12-06T00:00:00Z date_updated: 2021-01-12T08:15:08Z day: '06' doi: 10.1098/rspb.2017.1824 extern: '1' external_id: pmid: - '29212724' intvolume: ' 284' issue: '1868' language: - iso: eng month: '12' oa_version: None pmid: 1 publication: 'Proceedings of the Royal Society B: Biological Sciences' publication_identifier: issn: - 0962-8452 - 1471-2954 publication_status: published publisher: The Royal Society quality_controlled: '1' status: public title: Major histocompatibility complex-linked social signalling affects female fertility type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 284 year: '2017' ... --- _id: '7729' abstract: - lang: eng text: Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000 participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs for complete inbreeding; P<0.001). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data. article_processing_charge: No article_type: original author: - first_name: Loic full_name: Yengo, Loic last_name: Yengo - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Bruce S. full_name: Weir, Bruce S. last_name: Weir - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 2017;114(32):8602-8607. doi:10.1073/pnas.1621096114 apa: Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., & Visscher, P. M. (2017). Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1621096114 chicago: Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621096114. ieee: L. Yengo et al., “Detection and quantification of inbreeding depression for complex traits from SNP data,” Proceedings of the National Academy of Sciences, vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607, 2017. ista: Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607. mla: Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences, vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07, doi:10.1073/pnas.1621096114. short: L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher, Proceedings of the National Academy of Sciences 114 (2017) 8602–8607. date_created: 2020-04-30T10:47:19Z date_published: 2017-08-08T00:00:00Z date_updated: 2021-01-12T08:15:09Z day: '08' doi: 10.1073/pnas.1621096114 extern: '1' intvolume: ' 114' issue: '32' language: - iso: eng month: '08' oa_version: None page: 8602-8607 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - relation: other url: https://doi.org/10.1073/pnas.1718598115 status: public title: Detection and quantification of inbreeding depression for complex traits from SNP data type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '7725' abstract: - lang: eng text: Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is plausible. Existing studies on the adaptation of plasticity typically focus on single traits and a few populations, while theory about interactions among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale (for example, multiple populations) perspective is required. We present data from a landscape scale, replicated, multi-trait experiment using a classic predator–prey system centred on the water flea Daphnia pulex. We find predator regime-driven differences in genetic variation of multivariate plasticity. These differences are associated with strong divergent selection linked to a predation regime. Our findings are evidence for local adaptation of plasticity, suggesting that responses of populations to environmental variation depend on the conditions in which they evolved in the past. article_processing_charge: No article_type: original author: - first_name: Julia full_name: Reger, Julia last_name: Reger - first_name: Martin I. full_name: Lind, Martin I. last_name: Lind - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Andrew P. full_name: Beckerman, Andrew P. last_name: Beckerman citation: ama: Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2017;2:100-107. doi:10.1038/s41559-017-0373-6 apa: Reger, J., Lind, M. I., Robinson, M. R., & Beckerman, A. P. (2017). Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0373-6 chicago: Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution. Springer Nature, 2017. https://doi.org/10.1038/s41559-017-0373-6. ieee: J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives local adaptation of phenotypic plasticity,” Nature Ecology & Evolution, vol. 2. Springer Nature, pp. 100–107, 2017. ista: Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2, 100–107. mla: Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution, vol. 2, Springer Nature, 2017, pp. 100–07, doi:10.1038/s41559-017-0373-6. short: J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology & Evolution 2 (2017) 100–107. date_created: 2020-04-30T10:46:02Z date_published: 2017-11-27T00:00:00Z date_updated: 2021-01-12T08:15:07Z day: '27' doi: 10.1038/s41559-017-0373-6 extern: '1' intvolume: ' 2' language: - iso: eng month: '11' oa_version: None page: 100-107 publication: Nature Ecology & Evolution publication_identifier: issn: - 2397-334X publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Predation drives local adaptation of phenotypic plasticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2017' ... --- _id: '7733' abstract: - lang: eng text: "Sections\r\nPDFPDF\r\nTools\r\nShare\r\nAbstract\r\nBackground: Gene discovery has provided remarkable biological insights into amyotrophic lateral sclerosis (ALS). One challenge for clinical application of genetic testing is critical evaluation of the significance of reported variants.\r\nMethods: We use whole exome sequencing (WES) to develop a clinically relevant approach to identify a subset of ALS patients harboring likely pathogenic mutations. In parallel, we assess if DNA methylation can be used to screen for pathogenicity of novel variants since a methylation signature has been shown to associate with the pathogenic C9orf72 expansion, but has not been explored for other ALS mutations. Australian patients identified with ALS‐relevant variants were cross‐checked with population databases and case reports to critically assess whether they were “likely causal,” “uncertain significance,” or “unlikely causal.”\r\nResults: Published ALS variants were identified in >10% of patients; however, in only 3% of patients (4/120) could these be confidently considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential DNA methylation signature in these mutation carriers.\r\nConclusions: The use of WES in a typical ALS clinic demonstrates a critical approach to variant assessment with the capability to combine cohorts to enhance the largely unknown genetic basis of ALS." article_processing_charge: No article_type: original author: - first_name: Fleur C. full_name: Garton, Fleur C. last_name: Garton - first_name: Beben full_name: Benyamin, Beben last_name: Benyamin - first_name: Qiongyi full_name: Zhao, Qiongyi last_name: Zhao - first_name: Zhijun full_name: Liu, Zhijun last_name: Liu - first_name: Jacob full_name: Gratten, Jacob last_name: Gratten - first_name: Anjali K. full_name: Henders, Anjali K. last_name: Henders - first_name: Zong-Hong full_name: Zhang, Zong-Hong last_name: Zhang - first_name: Janette full_name: Edson, Janette last_name: Edson - first_name: Sarah full_name: Furlong, Sarah last_name: Furlong - first_name: Sarah full_name: Morgan, Sarah last_name: Morgan - first_name: Susan full_name: Heggie, Susan last_name: Heggie - first_name: Kathryn full_name: Thorpe, Kathryn last_name: Thorpe - first_name: Casey full_name: Pfluger, Casey last_name: Pfluger - first_name: Karen A. full_name: Mather, Karen A. last_name: Mather - first_name: Perminder S. full_name: Sachdev, Perminder S. last_name: Sachdev - first_name: Allan F. full_name: McRae, Allan F. last_name: McRae - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Sonia full_name: Shah, Sonia last_name: Shah - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Marie full_name: Mangelsdorf, Marie last_name: Mangelsdorf - first_name: Robert D. full_name: Henderson, Robert D. last_name: Henderson - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Pamela A. full_name: McCombe, Pamela A. last_name: McCombe citation: ama: Garton FC, Benyamin B, Zhao Q, et al. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 2017;5(4):418-428. doi:10.1002/mgg3.302 apa: Garton, F. C., Benyamin, B., Zhao, Q., Liu, Z., Gratten, J., Henders, A. K., … McCombe, P. A. (2017). Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. Wiley. https://doi.org/10.1002/mgg3.302 chicago: Garton, Fleur C., Beben Benyamin, Qiongyi Zhao, Zhijun Liu, Jacob Gratten, Anjali K. Henders, Zong-Hong Zhang, et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine. Wiley, 2017. https://doi.org/10.1002/mgg3.302. ieee: F. C. Garton et al., “Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort,” Molecular Genetics & Genomic Medicine, vol. 5, no. 4. Wiley, pp. 418–428, 2017. ista: Garton FC, Benyamin B, Zhao Q, Liu Z, Gratten J, Henders AK, Zhang Z-H, Edson J, Furlong S, Morgan S, Heggie S, Thorpe K, Pfluger C, Mather KA, Sachdev PS, McRae AF, Robinson MR, Shah S, Visscher PM, Mangelsdorf M, Henderson RD, Wray NR, McCombe PA. 2017. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 5(4), 418–428. mla: Garton, Fleur C., et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine, vol. 5, no. 4, Wiley, 2017, pp. 418–28, doi:10.1002/mgg3.302. short: F.C. Garton, B. Benyamin, Q. Zhao, Z. Liu, J. Gratten, A.K. Henders, Z.-H. Zhang, J. Edson, S. Furlong, S. Morgan, S. Heggie, K. Thorpe, C. Pfluger, K.A. Mather, P.S. Sachdev, A.F. McRae, M.R. Robinson, S. Shah, P.M. Visscher, M. Mangelsdorf, R.D. Henderson, N.R. Wray, P.A. McCombe, Molecular Genetics & Genomic Medicine 5 (2017) 418–428. date_created: 2020-04-30T10:48:25Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:15:10Z day: '01' doi: 10.1002/mgg3.302 extern: '1' intvolume: ' 5' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/mgg3.302 month: '07' oa: 1 oa_version: Published Version page: 418-428 publication: Molecular Genetics & Genomic Medicine publication_identifier: issn: - 2324-9269 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2017' ... --- _id: '7731' abstract: - lang: eng text: 'Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n = 625) and skin (n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).' article_processing_charge: No article_type: original author: - first_name: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Gerhard full_name: Moser, Gerhard last_name: Moser - first_name: Jian full_name: Zeng, Jian last_name: Zeng - first_name: Sandra full_name: Beleza, Sandra last_name: Beleza - first_name: Gregory S. full_name: Barsh, Gregory S. last_name: Barsh - first_name: Hua full_name: Tang, Hua last_name: Tang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Lloyd-Jones LR, Robinson MR, Moser G, et al. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 2017;206(2):1113-1126. doi:10.1534/genetics.116.193383 apa: Lloyd-Jones, L. R., Robinson, M. R., Moser, G., Zeng, J., Beleza, S., Barsh, G. S., … Visscher, P. M. (2017). Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193383 chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Gerhard Moser, Jian Zeng, Sandra Beleza, Gregory S. Barsh, Hua Tang, and Peter M. Visscher. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193383. ieee: L. R. Lloyd-Jones et al., “Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models,” Genetics, vol. 206, no. 2. Genetics Society of America, pp. 1113–1126, 2017. ista: Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, Tang H, Visscher PM. 2017. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 206(2), 1113–1126. mla: Lloyd-Jones, Luke R., et al. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics, vol. 206, no. 2, Genetics Society of America, 2017, pp. 1113–26, doi:10.1534/genetics.116.193383. short: L.R. Lloyd-Jones, M.R. Robinson, G. Moser, J. Zeng, S. Beleza, G.S. Barsh, H. Tang, P.M. Visscher, Genetics 206 (2017) 1113–1126. date_created: 2020-04-30T10:47:50Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:15:10Z day: '01' doi: 10.1534/genetics.116.193383 extern: '1' intvolume: ' 206' issue: '2' language: - iso: eng month: '06' oa_version: None page: 1113-1126 publication: Genetics publication_identifier: issn: - 0016-6731 - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 206 year: '2017' ... --- _id: '7755' abstract: - lang: eng text: We give a bird's-eye view of the plastic deformation of crystals aimed at the statistical physics community, as well as a broad introduction to the statistical theories of forced rigid systems aimed at the plasticity community. Memory effects in magnets, spin glasses, charge density waves, and dilute colloidal suspensions are discussed in relation to the onset of plastic yielding in crystals. Dislocation avalanches and complex dislocation tangles are discussed via a brief introduction to the renormalization group and scaling. Analogies to emergent scale invariance in fracture, jamming, coarsening, and a variety of depinning transitions are explored. Dislocation dynamics in crystals challenge nonequilibrium statistical physics. Statistical physics provides both cautionary tales of subtle memory effects in nonequilibrium systems and systematic tools designed to address complex scale-invariant behavior on multiple length scales and timescales. article_processing_charge: No article_type: original author: - first_name: James P. full_name: Sethna, James P. last_name: Sethna - first_name: Matthew K. full_name: Bierbaum, Matthew K. last_name: Bierbaum - first_name: Karin A. full_name: Dahmen, Karin A. last_name: Dahmen - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Julia R. full_name: Greer, Julia R. last_name: Greer - first_name: Lorien X. full_name: Hayden, Lorien X. last_name: Hayden - first_name: Jaron P. full_name: Kent-Dobias, Jaron P. last_name: Kent-Dobias - first_name: Edward D. full_name: Lee, Edward D. last_name: Lee - first_name: Danilo B. full_name: Liarte, Danilo B. last_name: Liarte - first_name: Xiaoyue full_name: Ni, Xiaoyue last_name: Ni - first_name: Katherine N. full_name: Quinn, Katherine N. last_name: Quinn - first_name: Archishman full_name: Raju, Archishman last_name: Raju - first_name: D. Zeb full_name: Rocklin, D. Zeb last_name: Rocklin - first_name: Ashivni full_name: Shekhawat, Ashivni last_name: Shekhawat - first_name: Stefano full_name: Zapperi, Stefano last_name: Zapperi citation: ama: 'Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 2017;47:217-246. doi:10.1146/annurev-matsci-070115-032036' apa: 'Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J. R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. Annual Reviews. https://doi.org/10.1146/annurev-matsci-070115-032036' chicago: 'Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich, Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research. Annual Reviews, 2017. https://doi.org/10.1146/annurev-matsci-070115-032036.' ieee: 'J. P. Sethna et al., “Deformation of crystals: Connections with statistical physics,” Annual Review of Materials Research, vol. 47. Annual Reviews, pp. 217–246, 2017.' ista: 'Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi S. 2017. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 47, 217–246.' mla: 'Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research, vol. 47, Annual Reviews, 2017, pp. 217–46, doi:10.1146/annurev-matsci-070115-032036.' short: J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X. Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z. Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017) 217–246. date_created: 2020-04-30T11:38:24Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:15:18Z day: '01' doi: 10.1146/annurev-matsci-070115-032036 extern: '1' intvolume: ' 47' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1146/annurev-matsci-070115-032036 month: '07' oa: 1 oa_version: Published Version page: 217-246 publication: Annual Review of Materials Research publication_identifier: issn: - 1531-7331 - 1545-4118 publication_status: published publisher: Annual Reviews quality_controlled: '1' status: public title: 'Deformation of crystals: Connections with statistical physics' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2017' ... --- _id: '7757' abstract: - lang: eng text: Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks. article_processing_charge: No article_type: original author: - first_name: Jason W. full_name: Rocks, Jason W. last_name: Rocks - first_name: Nidhi full_name: Pashine, Nidhi last_name: Pashine - first_name: Irmgard full_name: Bischofberger, Irmgard last_name: Bischofberger - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 2017;114(10):2520-2525. doi:10.1073/pnas.1612139114 apa: Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2017). Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612139114 chicago: Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1612139114. ieee: J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” Proceedings of the National Academy of Sciences, vol. 114, no. 10. Proceedings of the National Academy of Sciences, pp. 2520–2525, 2017. ista: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 114(10), 2520–2525. mla: Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences, vol. 114, no. 10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:10.1073/pnas.1612139114. short: J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel, Proceedings of the National Academy of Sciences 114 (2017) 2520–2525. date_created: 2020-04-30T11:38:53Z date_published: 2017-03-07T00:00:00Z date_updated: 2021-01-12T08:15:19Z day: '07' doi: 10.1073/pnas.1612139114 extern: '1' intvolume: ' 114' issue: '10' language: - iso: eng month: '03' oa_version: None page: 2520-2525 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Designing allostery-inspired response in mechanical networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '7758' abstract: - lang: eng text: Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles. article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner citation: ama: Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 2017;114(2):257-262. doi:10.1073/pnas.1608838114 apa: Goodrich, C. P., & Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1608838114 chicago: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1608838114. ieee: C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” Proceedings of the National Academy of Sciences, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017. ista: Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262. mla: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:10.1073/pnas.1608838114. short: C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262. date_created: 2020-04-30T11:39:09Z date_published: 2017-01-10T00:00:00Z date_updated: 2021-01-12T08:15:20Z day: '10' doi: 10.1073/pnas.1608838114 extern: '1' intvolume: ' 114' issue: '2' language: - iso: eng month: '01' oa_version: None page: 257-262 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Using active colloids as machines to weave and braid on the micrometer scale type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '7756' abstract: - lang: eng text: We study the shear jamming of athermal frictionless soft spheres, and find that in the thermodynamic limit, a shear-jammed state exists with different elastic properties from the isotropically-jammed state. For example, shear-jammed states can have a non-zero residual shear stress in the thermodynamic limit that arises from long-range stress-stress correlations. As a result, the ratio of the shear and bulk moduli, which in isotropically-jammed systems vanishes as the jamming transition is approached from above, instead approaches a constant. Despite these striking differences, we argue that in a deeper sense, the shear jamming and isotropic jamming transitions actually have the same symmetry, and that the differences can be fully understood by rotating the six-dimensional basis of the elastic modulus tensor. article_processing_charge: No article_type: original author: - first_name: Marco full_name: Baity-Jesi, Marco last_name: Baity-Jesi - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel - first_name: James P. full_name: Sethna, James P. last_name: Sethna citation: ama: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 2017;167(3-4):735-748. doi:10.1007/s10955-016-1703-9 apa: Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., & Sethna, J. P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-016-1703-9 chicago: Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel, and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics. Springer Nature, 2017. https://doi.org/10.1007/s10955-016-1703-9. ieee: M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent SO(3) symmetry of the frictionless shear jamming transition,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017. ista: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 167(3–4), 735–748. mla: Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer Nature, 2017, pp. 735–48, doi:10.1007/s10955-016-1703-9. short: M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal of Statistical Physics 167 (2017) 735–748. date_created: 2020-04-30T11:38:38Z date_published: 2017-01-03T00:00:00Z date_updated: 2021-01-12T08:15:19Z day: '03' doi: 10.1007/s10955-016-1703-9 extern: '1' intvolume: ' 167' issue: 3-4 language: - iso: eng month: '01' oa_version: None page: 735-748 publication: Journal of Statistical Physics publication_identifier: issn: - 0022-4715 - 1572-9613 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Emergent SO(3) symmetry of the frictionless shear jamming transition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 167 year: '2017' ... --- _id: '788' abstract: - lang: eng text: In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed with an appropriate error model in mind. Here we consider the model of chemical reaction networks that preserve molecular count (population protocols), and ask whether computation can be made robust to a natural model of unintended “leak” reactions. Our definition of leak is motivated by both the particular spurious behavior seen when implementing chemical reaction networks with DNA strand displacement cascades, as well as the unavoidable side reactions in any implementation due to the basic laws of chemistry. We develop a new “Robust Detection” algorithm for the problem of fast (logarithmic time) single molecule detection, and prove that it is robust to this general model of leaks. Besides potential applications in single molecule detection, the error-correction ideas developed here might enable a new class of robust-by-design chemical algorithms. Our analysis is based on a non-standard hybrid argument, combining ideas from discrete analysis of population protocols with classic Markov chain techniques. acknowledgement: "D. Alistarh - Supported by an SNF Ambizione Fellowship. A. Kosowski — Supported by Inria project GANG, ANR project DESCARTES, and\r\nNCN grant 2015/17/B/ST6/01897. D. Soloveichik — Supported by NSF grants CCF-1618895 and CCF-1652824.\r\n\r\n" alternative_title: - LNCS article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Bartłomiej full_name: Dudek, Bartłomiej last_name: Dudek - first_name: Adrian full_name: Kosowski, Adrian last_name: Kosowski - first_name: David full_name: Soloveichik, David last_name: Soloveichik - first_name: Przemysław full_name: Uznański, Przemysław last_name: Uznański citation: ama: 'Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. Robust detection in leak-prone population protocols. In: Vol 10467 LNCS. Springer; 2017:155-171. doi:10.1007/978-3-319-66799-7_11' apa: Alistarh, D.-A., Dudek, B., Kosowski, A., Soloveichik, D., & Uznański, P. (2017). Robust detection in leak-prone population protocols (Vol. 10467 LNCS, pp. 155–171). Presented at the DNA Computing and Molecular Programming, Springer. https://doi.org/10.1007/978-3-319-66799-7_11 chicago: Alistarh, Dan-Adrian, Bartłomiej Dudek, Adrian Kosowski, David Soloveichik, and Przemysław Uznański. “Robust Detection in Leak-Prone Population Protocols,” 10467 LNCS:155–71. Springer, 2017. https://doi.org/10.1007/978-3-319-66799-7_11. ieee: D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, and P. Uznański, “Robust detection in leak-prone population protocols,” presented at the DNA Computing and Molecular Programming, 2017, vol. 10467 LNCS, pp. 155–171. ista: Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. 2017. Robust detection in leak-prone population protocols. DNA Computing and Molecular Programming, LNCS, vol. 10467 LNCS, 155–171. mla: Alistarh, Dan-Adrian, et al. Robust Detection in Leak-Prone Population Protocols. Vol. 10467 LNCS, Springer, 2017, pp. 155–71, doi:10.1007/978-3-319-66799-7_11. short: D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, P. Uznański, in:, Springer, 2017, pp. 155–171. conference: name: DNA Computing and Molecular Programming date_created: 2018-12-11T11:48:30Z date_published: 2017-01-01T00:00:00Z date_updated: 2022-03-18T12:48:02Z day: '01' doi: 10.1007/978-3-319-66799-7_11 extern: '1' external_id: arxiv: - '1706.09937' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.09937 month: '01' oa: 1 oa_version: None page: 155 - 171 publication_status: published publisher: Springer publist_id: '6868' quality_controlled: '1' scopus_import: '1' status: public title: Robust detection in leak-prone population protocols type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10467 LNCS year: '2017' ... --- _id: '787' abstract: - lang: eng text: 'Population protocols are a popular model of distributed computing, in which randomly-interacting agents with little computational power cooperate to jointly perform computational tasks. Inspired by developments in molecular computation, and in particular DNA computing, recent algorithmic work has focused on the complexity of solving simple yet fundamental tasks in the population model, such as leader election (which requires convergence to a single agent in a special "leader" state), and majority (in which agents must converge to a decision as to which of two possible initial states had higher initial count). Known results point towards an inherent trade-off between the time complexity of such algorithms, and the space complexity, i.e. size of the memory available to each agent. In this paper, we explore this trade-off and provide new upper and lower bounds for majority and leader election. First, we prove a unified lower bound, which relates the space available per node with the time complexity achievable by a protocol: for instance, our result implies that any protocol solving either of these tasks for n agents using O(log log n) states must take (n=polylogn) expected time. This is the first result to characterize time complexity for protocols which employ super-constant number of states per node, and proves that fast, poly-logarithmic running times require protocols to have relatively large space costs. On the positive side, we give algorithms showing that fast, poly-logarithmic convergence time can be achieved using O(log2 n) space per node, in the case of both tasks. Overall, our results highlight a time complexity separation between O(log log n) and (log2 n) state space size for both majority and leader election in population protocols, and introduce new techniques, which should be applicable more broadly.' acknowledgement: "Dan Alistarh was supported by a Swiss National Science\r\nFoundation Ambizione Fellowship. James Aspnes was supported by the National Science Foundation \ under grants\r\nCCF-1637385 and CCF-1650596. Rati Gelashvili was supported by \ the National Science Foundation under grants\r\nCCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and\r\nOracle and Intel corporations.\r\nThe authors would like to thank David Doty, David\r\nSoloveichik, \ and Milan Vojnovic for insightful discussions\r\nand feedback during the development of this work." author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: David full_name: Eisenstat, David last_name: Eisenstat - first_name: Ronald full_name: Rivest, Ronald last_name: Rivest - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili citation: ama: 'Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. Time-space trade-offs in population protocols. In: SIAM; 2017:2560-2579. doi:doi.org/10.1137/1.9781611974782.169' apa: 'Alistarh, D.-A., Aspnes, J., Eisenstat, D., Rivest, R., & Gelashvili, R. (2017). Time-space trade-offs in population protocols (pp. 2560–2579). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/doi.org/10.1137/1.9781611974782.169' chicago: Alistarh, Dan-Adrian, James Aspnes, David Eisenstat, Ronald Rivest, and Rati Gelashvili. “Time-Space Trade-Offs in Population Protocols,” 2560–79. SIAM, 2017. https://doi.org/doi.org/10.1137/1.9781611974782.169. ieee: 'D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, and R. Gelashvili, “Time-space trade-offs in population protocols,” presented at the SODA: Symposium on Discrete Algorithms, 2017, pp. 2560–2579.' ista: 'Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. 2017. Time-space trade-offs in population protocols. SODA: Symposium on Discrete Algorithms, 2560–2579.' mla: Alistarh, Dan-Adrian, et al. Time-Space Trade-Offs in Population Protocols. SIAM, 2017, pp. 2560–79, doi:doi.org/10.1137/1.9781611974782.169. short: D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, R. Gelashvili, in:, SIAM, 2017, pp. 2560–2579. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T11:48:30Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-23T13:19:13Z day: '01' doi: doi.org/10.1137/1.9781611974782.169 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.08032 month: '01' oa: 1 oa_version: None page: 2560 - 2579 publication_status: published publisher: SIAM publist_id: '6869' status: public title: Time-space trade-offs in population protocols type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '789' abstract: - lang: eng text: 'The problem of efficient concurrent memory reclamation in unmanaged languages such as C or C++ is one of the major challenges facing the parallelization of billions of lines of legacy code. Garbage collectors for C/C++ can be inefficient; thus, programmers are often forced to use finely-crafted concurrent memory reclamation techniques. These techniques can provide good performance, but require considerable programming effort to deploy, and have strict requirements, allowing the programmer very little room for error. In this work, we present Forkscan, a new conservative concurrent memory reclamation scheme which is fully automatic and surprisingly scalable. Forkscan''s semantics place it between automatic garbage collectors (it requires the programmer to explicitly retire nodes before they can be reclaimed), and concurrent memory reclamation techniques (as it does not assume that nodes are completely unlinked from the data structure for correctness). Forkscan''s implementation exploits these new semantics for efficiency: we leverage parallelism and optimized implementations of signaling and copy-on-write in modern operating systems to efficiently obtain and process consistent snapshots of memory that can be scanned concurrently with the normal program operation. Empirical evaluation on a range of classical concurrent data structure microbenchmarks shows that Forkscan can preserve the scalability of the original code, while maintaining an order of magnitude lower latency than automatic garbage collection, and demonstrating competitive performance with finely crafted memory reclamation techniques.' acknowledgement: William Leiserson, Alexander Matveev, and Nir Shavit were supported by the NSF under grants IIS-1447786 and CCF-1563880, and Dan Alistarh was supported by a Swiss National Fund Ambizione Fellowship. article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: William full_name: Leiserson, William last_name: Leiserson - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. Forkscan: Conservative memory reclamation for modern operating systems. In: ACM; 2017:483-498. doi:10.1145/3064176.3064214' apa: 'Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2017). Forkscan: Conservative memory reclamation for modern operating systems (pp. 483–498). Presented at the EuroSys: European Conference on Computer Systems, ACM. https://doi.org/10.1145/3064176.3064214' chicago: 'Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “Forkscan: Conservative Memory Reclamation for Modern Operating Systems,” 483–98. ACM, 2017. https://doi.org/10.1145/3064176.3064214.' ieee: 'D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “Forkscan: Conservative memory reclamation for modern operating systems,” presented at the EuroSys: European Conference on Computer Systems, 2017, pp. 483–498.' ista: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2017. Forkscan: Conservative memory reclamation for modern operating systems. EuroSys: European Conference on Computer Systems, 483–498.' mla: 'Alistarh, Dan-Adrian, et al. Forkscan: Conservative Memory Reclamation for Modern Operating Systems. ACM, 2017, pp. 483–98, doi:10.1145/3064176.3064214.' short: D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, in:, ACM, 2017, pp. 483–498. conference: name: 'EuroSys: European Conference on Computer Systems' date_created: 2018-12-11T11:48:30Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-23T13:19:44Z day: '01' doi: 10.1145/3064176.3064214 extern: '1' language: - iso: eng month: '01' oa_version: None page: 483 - 498 publication_status: published publisher: ACM publist_id: '6867' status: public title: 'Forkscan: Conservative memory reclamation for modern operating systems' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '790' abstract: - lang: eng text: Stochastic gradient descent (SGD) is a commonly used algorithm for training linear machine learning models. Based on vector algebra, it benefits from the inherent parallelism available in an FPGA. In this paper, we first present a single-precision floating-point SGD implementation on an FPGA that provides similar performance as a 10-core CPU. We then adapt the design to make it capable of processing low-precision data. The low-precision data is obtained from a novel compression scheme - called stochastic quantization, specifically designed for machine learning applications. We test both full-precision and low-precision designs on various regression and classification data sets. We achieve up to an order of magnitude training speedup when using low-precision data compared to a full-precision SGD on the same FPGA and a state-of-the-art multi-core solution, while maintaining the quality of training. We open source the designs presented in this paper. article_processing_charge: No author: - first_name: Kaan full_name: Kara, Kaan last_name: Kara - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Gustavo full_name: Alonso, Gustavo last_name: Alonso - first_name: Onur full_name: Mutlu, Onur last_name: Mutlu - first_name: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. FPGA-accelerated dense linear machine learning: A precision-convergence trade-off. In: IEEE; 2017:160-167. doi:10.1109/FCCM.2017.39' apa: 'Kara, K., Alistarh, D.-A., Alonso, G., Mutlu, O., & Zhang, C. (2017). FPGA-accelerated dense linear machine learning: A precision-convergence trade-off (pp. 160–167). Presented at the FCCM: Field-Programmable Custom Computing Machines, IEEE. https://doi.org/10.1109/FCCM.2017.39' chicago: 'Kara, Kaan, Dan-Adrian Alistarh, Gustavo Alonso, Onur Mutlu, and Ce Zhang. “FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence Trade-Off,” 160–67. IEEE, 2017. https://doi.org/10.1109/FCCM.2017.39.' ieee: 'K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, and C. Zhang, “FPGA-accelerated dense linear machine learning: A precision-convergence trade-off,” presented at the FCCM: Field-Programmable Custom Computing Machines, 2017, pp. 160–167.' ista: 'Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. 2017. FPGA-accelerated dense linear machine learning: A precision-convergence trade-off. FCCM: Field-Programmable Custom Computing Machines, 160–167.' mla: 'Kara, Kaan, et al. FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence Trade-Off. IEEE, 2017, pp. 160–67, doi:10.1109/FCCM.2017.39.' short: K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, C. Zhang, in:, IEEE, 2017, pp. 160–167. conference: name: 'FCCM: Field-Programmable Custom Computing Machines' date_created: 2018-12-11T11:48:31Z date_published: 2017-06-30T00:00:00Z date_updated: 2023-02-23T13:19:52Z day: '30' doi: 10.1109/FCCM.2017.39 extern: '1' language: - iso: eng month: '06' oa_version: None page: 160 - 167 publication_status: published publisher: IEEE publist_id: '6865' status: public title: 'FPGA-accelerated dense linear machine learning: A precision-convergence trade-off' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '795' abstract: - lang: eng text: 'We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof.' article_number: P3.18 article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Dömötör full_name: Pálvölgyi, Dömötör last_name: Pálvölgyi citation: ama: Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 2017;24(3). doi:10.37236/6663 apa: Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663 chicago: Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics. International Press, 2017. https://doi.org/10.37236/6663. ieee: R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, 2017. ista: Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18. mla: Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663. short: R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017). date_created: 2018-12-11T11:48:32Z date_published: 2017-07-28T00:00:00Z date_updated: 2022-03-18T12:58:53Z day: '28' ddc: - '000' department: - _id: UlWa doi: 10.37236/6663 ec_funded: 1 file: - access_level: open_access checksum: ef320cff0f062051e858f929be6a3581 content_type: application/pdf creator: dernst date_created: 2019-01-18T14:04:08Z date_updated: 2020-07-14T12:48:06Z file_id: '5853' file_name: 2017_ElectrCombi_Fulek.pdf file_size: 236944 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 24' issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Electronic Journal of Combinatorics publication_identifier: issn: - '10778926' publication_status: published publisher: International Press publist_id: '6859' quality_controlled: '1' scopus_import: '1' status: public title: Unified Hanani Tutte theorem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2017' ... --- _id: '7981' abstract: - lang: ger text: Aprotische Natrium‐O2‐Batterien basieren auf der reversiblen Bildung und Auflösung von Natriumsuperoxid (NaO2) während des Zellbetriebs. Nebenreaktionen des Elektrolyten und der Elektrode mit dem stark nukleophilen und basischen NaO2 führen zu mangelhafter Zyklenstabilität. Seine Reaktivität allein kann die Nebenreaktionen und schlechte Reversibilität jedoch nicht schlüssig erklären. Hier wird gezeigt, dass Singulett‐Sauerstoff (1O2) in allen Phasen des Betriebs entsteht und eine Hauptursache für Nebenreaktionen ist. 1O2 wurde in situ und ex situ mit einem 1O2‐Fänger detektiert, der schnell und selektiv ein Addukt mit 1O2 bildet. Mechanistisch betrachtet entsteht 1O2 entweder durch protonenunterstützte Disproportionierung von Superoxid während des Entladens, Lagerns und Ladens unter ca. 3.3 V oder durch direkte elektrochemische 1O2‐Entwicklung über ca. 3.3 V. Spuren von Wasser ermöglichen hohe Kapazitäten, beschleunigen aber auch Nebenreaktionen. Daher muss das hochreaktive 1O2 unbedingt kontrolliert werden, um die Zelle reversibel zu betreiben. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Bettina full_name: Schafzahl, Bettina last_name: Schafzahl - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Schafzahl L, Mahne N, Schafzahl B, et al. Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. Angewandte Chemie. 2017;129(49):15934-15938. doi:10.1002/ange.201709351 apa: Schafzahl, L., Mahne, N., Schafzahl, B., Wilkening, M., Slugovc, C., Borisov, S. M., & Freunberger, S. A. (2017). Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201709351 chicago: Schafzahl, Lukas, Nika Mahne, Bettina Schafzahl, Martin Wilkening, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “Singulett-Sauerstoff in Der Aprotischen Natrium-O2-Batterie.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201709351. ieee: L. Schafzahl et al., “Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie,” Angewandte Chemie, vol. 129, no. 49. Wiley, pp. 15934–15938, 2017. ista: Schafzahl L, Mahne N, Schafzahl B, Wilkening M, Slugovc C, Borisov SM, Freunberger SA. 2017. Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. Angewandte Chemie. 129(49), 15934–15938. mla: Schafzahl, Lukas, et al. “Singulett-Sauerstoff in Der Aprotischen Natrium-O2-Batterie.” Angewandte Chemie, vol. 129, no. 49, Wiley, 2017, pp. 15934–38, doi:10.1002/ange.201709351. short: L. Schafzahl, N. Mahne, B. Schafzahl, M. Wilkening, C. Slugovc, S.M. Borisov, S.A. Freunberger, Angewandte Chemie 129 (2017) 15934–15938. date_created: 2020-06-19T08:22:06Z date_published: 2017-12-04T00:00:00Z date_updated: 2021-01-12T08:16:20Z day: '04' ddc: - '540' doi: 10.1002/ange.201709351 extern: '1' file: - access_level: open_access checksum: 38f2c2383bc9573f6770c1dba72d7a9a content_type: application/pdf creator: dernst date_created: 2020-06-19T11:39:09Z date_updated: 2020-07-14T12:48:06Z file_id: '7987' file_name: 2017_AngChemieDT_Schafzahl.pdf file_size: 988125 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 129' issue: '49' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 15934-15938 publication: Angewandte Chemie publication_identifier: issn: - 0044-8249 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2017' ... --- _id: '7980' abstract: - lang: eng text: In this part, the use of polysaccharides, either directly through composite approaches, or by carbonization will be described. In many cases, materials are obtained which are competitive in terms of capacitance and cycle lifetime. In this part, the use of polysaccharides, either directly through composite approaches, or by carbonization will be described. In many cases, materials are obtained which are competitive in terms of capacitance and cycle lifetime. The following part will focus mainly on cellulosic composites with conductive polymers since cellulose is most abundant and therefore has attracted much more research interest in this field whereas in the second part also other polysaccharides, such as chitin, xylans, alginates, pectins, dextrans and caragenaans have been used in carbonization experiments. alternative_title: - SpringerBriefs in Molecular Science article_processing_charge: No author: - first_name: Soon full_name: Yee Liew, Soon last_name: Yee Liew - first_name: Wim full_name: Thielemans, Wim last_name: Thielemans - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Stefan full_name: Spirk, Stefan last_name: Spirk citation: ama: 'Yee Liew S, Thielemans W, Freunberger SA, Spirk S. Polysaccharides in supercapacitors. In: Yee Liew S, Thielemans W, Freunberger SA, Spirk S, eds. Polysaccharide Based Supercapacitors. Springer Nature; 2017:15-53. doi:10.1007/978-3-319-50754-5_2' apa: Yee Liew, S., Thielemans, W., Freunberger, S. A., & Spirk, S. (2017). Polysaccharides in supercapacitors. In S. Yee Liew, W. Thielemans, S. A. Freunberger, & S. Spirk (Eds.), Polysaccharide Based Supercapacitors (pp. 15–53). Springer Nature. https://doi.org/10.1007/978-3-319-50754-5_2 chicago: Yee Liew, Soon, Wim Thielemans, Stefan Alexander Freunberger, and Stefan Spirk. “Polysaccharides in Supercapacitors.” In Polysaccharide Based Supercapacitors, edited by Soon Yee Liew, Wim Thielemans, Stefan Alexander Freunberger, and Stefan Spirk, 15–53. Springer Nature, 2017. https://doi.org/10.1007/978-3-319-50754-5_2. ieee: S. Yee Liew, W. Thielemans, S. A. Freunberger, and S. Spirk, “Polysaccharides in supercapacitors,” in Polysaccharide Based Supercapacitors, S. Yee Liew, W. Thielemans, S. A. Freunberger, and S. Spirk, Eds. Springer Nature, 2017, pp. 15–53. ista: 'Yee Liew S, Thielemans W, Freunberger SA, Spirk S. 2017.Polysaccharides in supercapacitors. In: Polysaccharide Based Supercapacitors. SpringerBriefs in Molecular Science, , 15–53.' mla: Yee Liew, Soon, et al. “Polysaccharides in Supercapacitors.” Polysaccharide Based Supercapacitors, edited by Soon Yee Liew et al., Springer Nature, 2017, pp. 15–53, doi:10.1007/978-3-319-50754-5_2. short: S. Yee Liew, W. Thielemans, S.A. Freunberger, S. Spirk, in:, S. Yee Liew, W. Thielemans, S.A. Freunberger, S. Spirk (Eds.), Polysaccharide Based Supercapacitors, Springer Nature, 2017, pp. 15–53. date_created: 2020-06-19T08:11:08Z date_published: 2017-03-26T00:00:00Z date_updated: 2021-01-12T08:16:19Z day: '26' ddc: - '540' - '541' doi: 10.1007/978-3-319-50754-5_2 editor: - first_name: Soon full_name: Yee Liew, Soon last_name: Yee Liew - first_name: Wim full_name: Thielemans, Wim last_name: Thielemans - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Stefan full_name: Spirk, Stefan last_name: Spirk extern: '1' file: - access_level: open_access checksum: 4182aeee32c9263a626a7e522f1934f5 content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:13:44Z date_updated: 2020-07-14T12:48:06Z file_id: '8048' file_name: Final_EPNOE.pdf file_size: 3339826 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 15-53 publication: Polysaccharide Based Supercapacitors publication_identifier: isbn: - '9783319507538' - '9783319507545' issn: - 2191-5407 - 2191-5415 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Polysaccharides in supercapacitors type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '7982' abstract: - lang: eng text: Beyond-intercalation batteries promise a step-change in energy storage compared to intercalation-based lithium-ion and sodium-ion batteries. However, only performance metrics that include all cell components and operation parameters can tell whether a true advance over intercalation batteries has been achieved. article_number: '17091' article_processing_charge: No article_type: original author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Freunberger SA. True performance metrics in beyond-intercalation batteries. Nature Energy. 2017;2(7). doi:10.1038/nenergy.2017.91 apa: Freunberger, S. A. (2017). True performance metrics in beyond-intercalation batteries. Nature Energy. Springer Nature. https://doi.org/10.1038/nenergy.2017.91 chicago: Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation Batteries.” Nature Energy. Springer Nature, 2017. https://doi.org/10.1038/nenergy.2017.91. ieee: S. A. Freunberger, “True performance metrics in beyond-intercalation batteries,” Nature Energy, vol. 2, no. 7. Springer Nature, 2017. ista: Freunberger SA. 2017. True performance metrics in beyond-intercalation batteries. Nature Energy. 2(7), 17091. mla: Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation Batteries.” Nature Energy, vol. 2, no. 7, 17091, Springer Nature, 2017, doi:10.1038/nenergy.2017.91. short: S.A. Freunberger, Nature Energy 2 (2017). date_created: 2020-06-19T08:23:47Z date_published: 2017-06-05T00:00:00Z date_updated: 2021-01-12T08:16:20Z day: '05' ddc: - '540' - '546' - '541' doi: 10.1038/nenergy.2017.91 extern: '1' external_id: arxiv: - '2002.00712' file: - access_level: open_access checksum: 2564255b76f5346a32e764dbfd17fa2f content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T13:26:55Z date_updated: 2020-07-14T12:48:06Z file_id: '8046' file_name: NEnergy_Comment_final.pdf file_size: 817665 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 2' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.00712 month: '06' oa: 1 oa_version: Submitted Version publication: Nature Energy publication_identifier: issn: - 2058-7546 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: True performance metrics in beyond-intercalation batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2017' ... --- _id: '7986' article_number: '17036 ' article_processing_charge: No article_type: original author: - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Bettina full_name: Schafzahl, Bettina last_name: Schafzahl - first_name: Christian full_name: Leypold, Christian last_name: Leypold - first_name: Mario full_name: Leypold, Mario last_name: Leypold - first_name: Sandra full_name: Grumm, Sandra last_name: Grumm - first_name: Anita full_name: Leitgeb, Anita last_name: Leitgeb - first_name: Gernot A. full_name: Strohmeier, Gernot A. last_name: Strohmeier - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Denis full_name: Kramer, Denis last_name: Kramer - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mahne N, Schafzahl B, Leypold C, et al. Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries. Nature Energy. 2017;2(5). doi:10.1038/nenergy.2017.36 apa: Mahne, N., Schafzahl, B., Leypold, C., Leypold, M., Grumm, S., Leitgeb, A., … Freunberger, S. A. (2017). Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries. Nature Energy. Springer Nature. https://doi.org/10.1038/nenergy.2017.36 chicago: Mahne, Nika, Bettina Schafzahl, Christian Leypold, Mario Leypold, Sandra Grumm, Anita Leitgeb, Gernot A. Strohmeier, et al. “Singlet Oxygen Generation as a Major Cause for Parasitic Reactions during Cycling of Aprotic Lithium–Oxygen Batteries.” Nature Energy. Springer Nature, 2017. https://doi.org/10.1038/nenergy.2017.36. ieee: N. Mahne et al., “Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries,” Nature Energy, vol. 2, no. 5. Springer Nature, 2017. ista: Mahne N, Schafzahl B, Leypold C, Leypold M, Grumm S, Leitgeb A, Strohmeier GA, Wilkening M, Fontaine O, Kramer D, Slugovc C, Borisov SM, Freunberger SA. 2017. Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries. Nature Energy. 2(5), 17036. mla: Mahne, Nika, et al. “Singlet Oxygen Generation as a Major Cause for Parasitic Reactions during Cycling of Aprotic Lithium–Oxygen Batteries.” Nature Energy, vol. 2, no. 5, 17036, Springer Nature, 2017, doi:10.1038/nenergy.2017.36. short: N. Mahne, B. Schafzahl, C. Leypold, M. Leypold, S. Grumm, A. Leitgeb, G.A. Strohmeier, M. Wilkening, O. Fontaine, D. Kramer, C. Slugovc, S.M. Borisov, S.A. Freunberger, Nature Energy 2 (2017). date_created: 2020-06-19T10:42:33Z date_published: 2017-03-20T00:00:00Z date_updated: 2021-01-12T08:16:21Z day: '20' doi: 10.1038/nenergy.2017.36 extern: '1' external_id: arxiv: - '1711.10340' intvolume: ' 2' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.10340 month: '03' oa: 1 oa_version: Preprint publication: Nature Energy publication_identifier: issn: - 2058-7546 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2017' ... --- _id: '797' abstract: - lang: ger text: Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden. article_processing_charge: No article_type: original author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305 apa: Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. Wiley. https://doi.org/10.1002/piuz.201770305 chicago: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305. ieee: J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol. 48, no. 3. Wiley, pp. 111–113, 2017. ista: Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113. mla: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305. short: J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113. date_created: 2018-12-11T11:48:33Z date_published: 2017-05-01T00:00:00Z date_updated: 2022-03-24T09:16:20Z day: '01' department: - _id: JoFi doi: 10.1002/piuz.201770305 intvolume: ' 48' issue: '3' language: - iso: eng month: '05' oa_version: None page: 111 - 113 publication: Physik in unserer Zeit publication_status: published publisher: Wiley publist_id: '6856' quality_controlled: '1' status: public title: Photonenblockade aufgelöst type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2017' ... --- _id: '8016' abstract: - lang: eng text: Long-term modifications of neuronal connections are critical for reliable memory storage in the brain. However, their locus of expression—pre- or postsynaptic—is highly variable. Here we introduce a theoretical framework in which long-term plasticity performs an optimization of the postsynaptic response statistics toward a given mean with minimal variance. Consequently, the state of the synapse at the time of plasticity induction determines the ratio of pre- and postsynaptic modifications. Our theory explains the experimentally observed expression loci of the hippocampal and neocortical synaptic potentiation studies we examined. Moreover, the theory predicts presynaptic expression of long-term depression, consistent with experimental observations. At inhibitory synapses, the theory suggests a statistically efficient excitatory-inhibitory balance in which changes in inhibitory postsynaptic response statistics specifically target the mean excitation. Our results provide a unifying theory for understanding the expression mechanisms and functions of long-term synaptic transmission plasticity. article_processing_charge: No article_type: original author: - first_name: Rui Ponte full_name: Costa, Rui Ponte last_name: Costa - first_name: Zahid full_name: Padamsey, Zahid last_name: Padamsey - first_name: James A. full_name: D’Amour, James A. last_name: D’Amour - first_name: Nigel J. full_name: Emptage, Nigel J. last_name: Emptage - first_name: Robert C. full_name: Froemke, Robert C. last_name: Froemke - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. Synaptic transmission optimization predicts expression loci of long-term plasticity. Neuron. 2017;96(1):177-189.e7. doi:10.1016/j.neuron.2017.09.021 apa: Costa, R. P., Padamsey, Z., D’Amour, J. A., Emptage, N. J., Froemke, R. C., & Vogels, T. P. (2017). Synaptic transmission optimization predicts expression loci of long-term plasticity. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.09.021 chicago: Costa, Rui Ponte, Zahid Padamsey, James A. D’Amour, Nigel J. Emptage, Robert C. Froemke, and Tim P Vogels. “Synaptic Transmission Optimization Predicts Expression Loci of Long-Term Plasticity.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.09.021. ieee: R. P. Costa, Z. Padamsey, J. A. D’Amour, N. J. Emptage, R. C. Froemke, and T. P. Vogels, “Synaptic transmission optimization predicts expression loci of long-term plasticity,” Neuron, vol. 96, no. 1. Elsevier, p. 177–189.e7, 2017. ista: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. 2017. Synaptic transmission optimization predicts expression loci of long-term plasticity. Neuron. 96(1), 177–189.e7. mla: Costa, Rui Ponte, et al. “Synaptic Transmission Optimization Predicts Expression Loci of Long-Term Plasticity.” Neuron, vol. 96, no. 1, Elsevier, 2017, p. 177–189.e7, doi:10.1016/j.neuron.2017.09.021. short: R.P. Costa, Z. Padamsey, J.A. D’Amour, N.J. Emptage, R.C. Froemke, T.P. Vogels, Neuron 96 (2017) 177–189.e7. date_created: 2020-06-25T12:54:46Z date_published: 2017-09-27T00:00:00Z date_updated: 2021-01-12T08:16:32Z day: '27' ddc: - '570' doi: 10.1016/j.neuron.2017.09.021 extern: '1' external_id: pmid: - '28957667' file: - access_level: open_access checksum: 49fbca2821066c0965bd5678b32b6b48 content_type: application/pdf creator: cziletti date_created: 2020-07-09T09:42:49Z date_updated: 2020-07-14T12:48:08Z file_id: '8103' file_name: 2017_Neuron_Costa.pdf file_size: 7140149 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 96' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 177-189.e7 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Synaptic transmission optimization predicts expression loci of long-term plasticity 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) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 96 year: '2017' ... --- _id: '8018' abstract: - lang: eng text: 'Nervous systems use excitatory cell assemblies to encode and represent sensory percepts. Similarly, synaptically connected cell assemblies or "engrams" are thought to represent memories of past experience. Multiple lines of recent evidence indicate that brain systems create and use inhibitory replicas of excitatory representations for important cognitive functions. Such matched "inhibitory engrams" can form through homeostatic potentiation of inhibition onto postsynaptic cells that show increased levels of excitation. Inhibitory engrams can reduce behavioral responses to familiar stimuli, thereby resulting in behavioral habituation. In addition, by preventing inappropriate activation of excitatory memory engrams, inhibitory engrams can make memories quiescent, stored in a latent form that is available for context-relevant activation. In neural networks with balanced excitatory and inhibitory engrams, the release of innate responses and recall of associative memories can occur through focused disinhibition. Understanding mechanisms that regulate the formation and expression of inhibitory engrams in vivo may help not only to explain key features of cognition but also to provide insight into transdiagnostic traits associated with psychiatric conditions such as autism, schizophrenia, and posttraumatic stress disorder. ' article_processing_charge: No article_type: original author: - first_name: Helen C. full_name: Barron, Helen C. last_name: Barron - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Timothy E. full_name: Behrens, Timothy E. last_name: Behrens - first_name: Mani full_name: Ramaswami, Mani last_name: Ramaswami citation: ama: Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. 2017;114(26):6666-6674. doi:10.1073/pnas.1701812114 apa: Barron, H. C., Vogels, T. P., Behrens, T. E., & Ramaswami, M. (2017). Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1701812114 chicago: Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami. “Inhibitory Engrams in Perception and Memory.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1701812114. ieee: H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams in perception and memory,” Proceedings of the National Academy of Sciences, vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674, 2017. ista: Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. 114(26), 6666–6674. mla: Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” Proceedings of the National Academy of Sciences, vol. 114, no. 26, Proceedings of the National Academy of Sciences, 2017, pp. 6666–74, doi:10.1073/pnas.1701812114. short: H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the National Academy of Sciences 114 (2017) 6666–6674. date_created: 2020-06-25T12:56:58Z date_published: 2017-06-27T00:00:00Z date_updated: 2021-01-12T08:16:33Z day: '27' doi: 10.1073/pnas.1701812114 extern: '1' external_id: pmid: - '28611219' intvolume: ' 114' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/ month: '06' oa: 1 oa_version: Published Version page: 6666-6674 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Inhibitory engrams in perception and memory type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 114 year: '2017' ... --- _id: '8019' abstract: - lang: eng text: Synaptic plasticity is essential for the function of neural systems. It sets up initial circuitry and adjusts connection strengths according to the maintenance requirements of its host networks. Like all things biological, synaptic plasticity must rely on genetic programs to provide the molecular components of its machinery to integrate ongoing, often multi-sensory experience without destabilising effects. Because of its fundamental importance to healthy behaviour, understanding plasticity is thought to hold the key to understanding the brain. There are innumerable ways to approach this topic and a complete review of its status quo would be impossible. In the current issue we dig into some of the finer points of synaptic plasticity, starting small, at the level of genes, and slowly zooming out to synapses, populations of synapses, and finally entire systems and brain regions. At each level, we tried to represent different perspectives, different systems, and approaches to the same questions to give a broad sampling of how synaptic plasticity is being studied. article_processing_charge: No article_type: letter_note author: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Leslie C full_name: Griffith, Leslie C last_name: Griffith citation: ama: 'Vogels TP, Griffith LC. Editorial overview: Neurobiology of learning and plasticity 2017. Current Opinion in Neurobiology. 2017;43:A1-A5. doi:10.1016/j.conb.2017.04.002' apa: 'Vogels, T. P., & Griffith, L. C. (2017). Editorial overview: Neurobiology of learning and plasticity 2017. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.04.002' chicago: 'Vogels, Tim P, and Leslie C Griffith. “Editorial Overview: Neurobiology of Learning and Plasticity 2017.” Current Opinion in Neurobiology. Elsevier, 2017. https://doi.org/10.1016/j.conb.2017.04.002.' ieee: 'T. P. Vogels and L. C. Griffith, “Editorial overview: Neurobiology of learning and plasticity 2017,” Current Opinion in Neurobiology, vol. 43. Elsevier, pp. A1–A5, 2017.' ista: 'Vogels TP, Griffith LC. 2017. Editorial overview: Neurobiology of learning and plasticity 2017. Current Opinion in Neurobiology. 43, A1–A5.' mla: 'Vogels, Tim P., and Leslie C. Griffith. “Editorial Overview: Neurobiology of Learning and Plasticity 2017.” Current Opinion in Neurobiology, vol. 43, Elsevier, 2017, pp. A1–5, doi:10.1016/j.conb.2017.04.002.' short: T.P. Vogels, L.C. Griffith, Current Opinion in Neurobiology 43 (2017) A1–A5. date_created: 2020-06-25T13:03:30Z date_published: 2017-04-17T00:00:00Z date_updated: 2021-01-12T08:16:33Z day: '17' doi: 10.1016/j.conb.2017.04.002 extern: '1' external_id: pmid: - '28427877' intvolume: ' 43' language: - iso: eng month: '04' oa_version: None page: A1-A5 pmid: 1 publication: Current Opinion in Neurobiology publication_identifier: issn: - 0959-4388 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Editorial overview: Neurobiology of learning and plasticity 2017' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2017' ... --- _id: '8017' abstract: - lang: eng text: nhibitory neurons, although relatively few in number, exert powerful control over brain circuits. They stabilize network activity in the face of strong feedback excitation and actively engage in computations. Recent studies reveal the importance of a precise balance of excitation and inhibition in neural circuits, which often requires exquisite fine-tuning of inhibitory connections. We review inhibitory synaptic plasticity and its roles in shaping both feedforward and feedback control. We discuss the necessity of complex, codependent plasticity mechanisms to build nontrivial, functioning networks, and we end by summarizing experimental evidence of such interactions. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Everton J. full_name: Agnes, Everton J. last_name: Agnes - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: 'Hennequin G, Agnes EJ, Vogels TP. Inhibitory plasticity: Balance, control, and codependence. Annual Review of Neuroscience. 2017;40(1):557-579. doi:10.1146/annurev-neuro-072116-031005' apa: 'Hennequin, G., Agnes, E. J., & Vogels, T. P. (2017). Inhibitory plasticity: Balance, control, and codependence. Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev-neuro-072116-031005' chicago: 'Hennequin, Guillaume, Everton J. Agnes, and Tim P Vogels. “Inhibitory Plasticity: Balance, Control, and Codependence.” Annual Review of Neuroscience. Annual Reviews, 2017. https://doi.org/10.1146/annurev-neuro-072116-031005.' ieee: 'G. Hennequin, E. J. Agnes, and T. P. Vogels, “Inhibitory plasticity: Balance, control, and codependence,” Annual Review of Neuroscience, vol. 40, no. 1. Annual Reviews, pp. 557–579, 2017.' ista: 'Hennequin G, Agnes EJ, Vogels TP. 2017. Inhibitory plasticity: Balance, control, and codependence. Annual Review of Neuroscience. 40(1), 557–579.' mla: 'Hennequin, Guillaume, et al. “Inhibitory Plasticity: Balance, Control, and Codependence.” Annual Review of Neuroscience, vol. 40, no. 1, Annual Reviews, 2017, pp. 557–79, doi:10.1146/annurev-neuro-072116-031005.' short: G. Hennequin, E.J. Agnes, T.P. Vogels, Annual Review of Neuroscience 40 (2017) 557–579. date_created: 2020-06-25T12:55:53Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:16:32Z day: '01' doi: 10.1146/annurev-neuro-072116-031005 extern: '1' external_id: pmid: - '28598717' intvolume: ' 40' issue: '1' language: - iso: eng month: '07' oa_version: None page: 557-579 pmid: 1 publication: Annual Review of Neuroscience publication_identifier: issn: - 0147-006X - 1545-4126 publication_status: published publisher: Annual Reviews quality_controlled: '1' status: public title: 'Inhibitory plasticity: Balance, control, and codependence' type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 40 year: '2017' ... --- _id: '8075' abstract: - lang: eng text: Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling. article_number: e22152 article_processing_charge: No article_type: original author: - first_name: William F full_name: Podlaski, William F last_name: Podlaski - first_name: Alexander full_name: Seeholzer, Alexander last_name: Seeholzer - first_name: Lukas N full_name: Groschner, Lukas N last_name: Groschner - first_name: Gero full_name: Miesenböck, Gero last_name: Miesenböck - first_name: Rajnish full_name: Ranjan, Rajnish last_name: Ranjan - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. Mapping the function of neuronal ion channels in model and experiment. eLife. 2017;6. doi:10.7554/elife.22152 apa: Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R., & Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model and experiment. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.22152 chicago: Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck, Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” ELife. eLife Sciences Publications, Ltd, 2017. https://doi.org/10.7554/elife.22152. ieee: W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,” eLife, vol. 6. eLife Sciences Publications, Ltd, 2017. ista: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. 2017. Mapping the function of neuronal ion channels in model and experiment. eLife. 6, e22152. mla: Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” ELife, vol. 6, e22152, eLife Sciences Publications, Ltd, 2017, doi:10.7554/elife.22152. short: W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P. Vogels, ELife 6 (2017). date_created: 2020-06-30T13:32:18Z date_published: 2017-03-06T00:00:00Z date_updated: 2021-01-12T08:16:46Z day: '06' ddc: - '570' doi: 10.7554/elife.22152 extern: '1' external_id: pmid: - '28267430' file: - access_level: open_access checksum: e5c5a33bcb3ac38ad62df1010ab29040 content_type: application/pdf creator: cziletti date_created: 2020-07-16T12:08:40Z date_updated: 2020-07-16T12:08:40Z file_id: '8124' file_name: 2017_elife_Podlaski.pdf file_size: 16034505 relation: main_file success: 1 file_date_updated: 2020-07-16T12:08:40Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications, Ltd quality_controlled: '1' status: public title: Mapping the function of neuronal ion channels in model and experiment 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) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 6 year: '2017' ... --- _id: '807' abstract: - lang: eng text: 'On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.' author: - first_name: Magdalena full_name: Andrae, Magdalena last_name: Andrae - first_name: Márton full_name: Villányi, Márton id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87 last_name: Villányi orcid: 0000-0001-8126-0426 citation: ama: Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898 apa: Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898 chicago: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898. ieee: M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017. ista: Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280. mla: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898. short: M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280. date_created: 2018-12-11T11:48:36Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:16:45Z day: '01' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v70i2.1898 file: - access_level: open_access checksum: 558c18bcf5580d87dd371ec626d52075 content_type: application/pdf creator: dernst date_created: 2019-01-18T13:39:26Z date_updated: 2020-07-14T12:48:09Z file_id: '5851' file_name: 2017_VOEB_Andrae.pdf file_size: 125065 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 70' issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 274 - 280 popular_science: '1' publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare publication_identifier: issn: - '10222588' publication_status: published publisher: VÖB publist_id: '6843' scopus_import: 1 status: public title: Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '8129' abstract: - lang: eng text: "Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function.\r\nOverall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts." article_processing_charge: No author: - first_name: Rui Ponte full_name: Costa, Rui Ponte last_name: Costa - first_name: Yannis M. full_name: Assael, Yannis M. last_name: Assael - first_name: Brendan full_name: Shillingford, Brendan last_name: Shillingford - first_name: Nando de full_name: Freitas, Nando de last_name: Freitas - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits as gated-recurrent neural networks. In: Advances in Neural Information Processing Systems. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.' apa: 'Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, & Vogels, T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In Advances in Neural Information Processing Systems (Vol. 30, pp. 272–283). Long Beach, CA, United States: Neural Information Processing Systems Foundation.' chicago: Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas, and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” In Advances in Neural Information Processing Systems, 30:272–83. Neural Information Processing Systems Foundation, 2017. ieee: R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels, “Cortical microcircuits as gated-recurrent neural networks,” in Advances in Neural Information Processing Systems, Long Beach, CA, United States, 2017, vol. 30, pp. 272–283. ista: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical microcircuits as gated-recurrent neural networks. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.' mla: Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” Advances in Neural Information Processing Systems, vol. 30, Neural Information Processing Systems Foundation, 2017, pp. 272–83. short: R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2017, pp. 272–283. conference: end_date: 2017-12-09 location: Long Beach, CA, United States name: 'NIPS: Neural Information Processing System' start_date: 2017-12-04 date_created: 2020-07-16T19:13:10Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:17:03Z day: '01' extern: '1' external_id: arxiv: - '1711.02448' intvolume: ' 30' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.02448 month: '12' oa: 1 oa_version: Preprint page: 272-283 publication: Advances in Neural Information Processing Systems publication_identifier: issn: - '10495258' publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' status: public title: Cortical microcircuits as gated-recurrent neural networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2017' ... --- _id: '817' abstract: - lang: eng text: Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4. Å resolution structure determined by subtomogram averaging. author: - first_name: Beata full_name: Turoňová, Beata last_name: Turoňová - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: William full_name: Wan, William last_name: Wan - first_name: John full_name: Briggs, John last_name: Briggs citation: ama: Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. 2017;199(3):187-195. doi:10.1016/j.jsb.2017.07.007 apa: Turoňová, B., Schur, F. K., Wan, W., & Briggs, J. (2017). Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2017.07.007 chicago: Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of Structural Biology. Academic Press, 2017. https://doi.org/10.1016/j.jsb.2017.07.007. ieee: B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å,” Journal of Structural Biology, vol. 199, no. 3. Academic Press, pp. 187–195, 2017. ista: Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. 199(3), 187–195. mla: Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of Structural Biology, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:10.1016/j.jsb.2017.07.007. short: B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology 199 (2017) 187–195. date_created: 2018-12-11T11:48:40Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:17:16Z day: '01' ddc: - '570' doi: 10.1016/j.jsb.2017.07.007 extern: '1' file: - access_level: open_access checksum: 7f2d4bbac767f9acc254d1a4114d181a content_type: application/pdf creator: kschuh date_created: 2019-03-22T09:29:44Z date_updated: 2020-07-14T12:48:09Z file_id: '6168' file_name: 2017_Elsevier_Turonova.pdf file_size: 1310009 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 199' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 187-195 publication: Journal of Structural Biology publication_status: published publisher: Academic Press publist_id: '6832' quality_controlled: '1' status: public title: Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 199 year: '2017' ... --- _id: '8237' abstract: - lang: eng text: Monoclonal antibodies find broad application as therapy for various types of cancer by employing multiple mechanisms of action against tumors. Manipulating the Fc-mediated functions of antibodies that engage immune effector cells, such as NK cells, represents a strategy to influence effector cell activation and to enhance antibody potency and potentially efficacy. We developed a novel approach to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies. This entailed coupling single expression vector (pVitro1) antibody cloning, using polymerase incomplete primer extension (PIPE) polymerase chain reaction, together with simultaneous Fc region point mutagenesis and high yield transient expression in human mammalian cells. Employing this, we engineered wild type, low (N297Q, NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan 4. Antibodies were generated with universal mutagenic primers applicable to any IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in small culture volumes, at high yields and within 12 days from design to purified material. Antibody variants conserved their Fab-mediated recognition of target antigens and their direct anti-proliferative effects against cancer cells. Fc mutations had a significant impact on antibody interactions with Fc receptors (FcRs) on human NK cells, and consequently on the potency of NK cell activation, quantified by immune complex-mediated calcium mobilization and by antibody-dependent cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and testing of Fc region engagement with cognate FcRs can facilitate the design of antibodies with defined effector functions and potentially enhanced efficacy against tumor cells. article_number: '1112' article_processing_charge: No article_type: original author: - first_name: Kristina M. full_name: Ilieva, Kristina M. last_name: Ilieva - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Daniela Y. full_name: Achkova, Daniela Y. last_name: Achkova - first_name: Tihomir S. full_name: Dodev, Tihomir S. last_name: Dodev - first_name: Silvia full_name: Mele, Silvia last_name: Mele - first_name: Silvia full_name: Crescioli, Silvia last_name: Crescioli - first_name: Heather J. full_name: Bax, Heather J. last_name: Bax - first_name: Anthony full_name: Cheung, Anthony last_name: Cheung - first_name: Panagiotis full_name: Karagiannis, Panagiotis last_name: Karagiannis - first_name: Isabel full_name: Correa, Isabel last_name: Correa - first_name: Mariangela full_name: Figini, Mariangela last_name: Figini - first_name: Rebecca full_name: Marlow, Rebecca last_name: Marlow - first_name: Debra H. full_name: Josephs, Debra H. last_name: Josephs - first_name: Andrew J. full_name: Beavil, Andrew J. last_name: Beavil - first_name: John full_name: Maher, John last_name: Maher - first_name: James F. full_name: Spicer, James F. last_name: Spicer - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Andrew N. full_name: Tutt, Andrew N. last_name: Tutt - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis citation: ama: Ilieva KM, Singer J, Achkova DY, et al. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. 2017;8. doi:10.3389/fimmu.2017.01112 apa: Ilieva, K. M., Singer, J., Achkova, D. Y., Dodev, T. S., Mele, S., Crescioli, S., … Karagiannis, S. N. (2017). Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2017.01112 chicago: Ilieva, Kristina M., Judit Singer, Daniela Y. Achkova, Tihomir S. Dodev, Silvia Mele, Silvia Crescioli, Heather J. Bax, et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” Frontiers in Immunology. Frontiers, 2017. https://doi.org/10.3389/fimmu.2017.01112. ieee: K. M. Ilieva et al., “Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields,” Frontiers in Immunology, vol. 8. Frontiers, 2017. ista: Ilieva KM, Singer J, Achkova DY, Dodev TS, Mele S, Crescioli S, Bax HJ, Cheung A, Karagiannis P, Correa I, Figini M, Marlow R, Josephs DH, Beavil AJ, Maher J, Spicer JF, Jensen-Jarolim E, Tutt AN, Karagiannis SN. 2017. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. 8, 1112. mla: Ilieva, Kristina M., et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” Frontiers in Immunology, vol. 8, 1112, Frontiers, 2017, doi:10.3389/fimmu.2017.01112. short: K.M. Ilieva, J. Singer, D.Y. Achkova, T.S. Dodev, S. Mele, S. Crescioli, H.J. Bax, A. Cheung, P. Karagiannis, I. Correa, M. Figini, R. Marlow, D.H. Josephs, A.J. Beavil, J. Maher, J.F. Spicer, E. Jensen-Jarolim, A.N. Tutt, S.N. Karagiannis, Frontiers in Immunology 8 (2017). date_created: 2020-08-10T11:53:32Z date_published: 2017-09-11T00:00:00Z date_updated: 2021-01-12T08:17:39Z day: '11' doi: 10.3389/fimmu.2017.01112 extern: '1' intvolume: ' 8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3389/fimmu.2017.01112 month: '09' oa: 1 oa_version: Published Version publication: Frontiers in Immunology publication_identifier: issn: - 1664-3224 publication_status: published publisher: Frontiers quality_controlled: '1' status: public title: Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '8236' abstract: - lang: eng text: Th2 immunity and allergic immune surveillance play critical roles in host responses to pathogens, parasites and allergens. Numerous studies have reported significant links between Th2 responses and cancer, including insights into the functions of IgE antibodies and associated effector cells in both antitumour immune surveillance and therapy. The interdisciplinary field of AllergoOncology was given Task Force status by the European Academy of Allergy and Clinical Immunology in 2014. Affiliated expert groups focus on the interface between allergic responses and cancer, applied to immune surveillance, immunomodulation and the functions of IgE‐mediated immune responses against cancer, to derive novel insights into more effective treatments. Coincident with rapid expansion in clinical application of cancer immunotherapies, here we review the current state‐of‐the‐art and future translational opportunities, as well as challenges in this relatively new field. Recent developments include improved understanding of Th2 antibodies, intratumoral innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation by dendritic cells, as well as immunotherapeutic strategies such as vaccines and recombinant antibodies, and finally, the management of allergy in daily clinical oncology. Shedding light on the crosstalk between allergic response and cancer is paving the way for new avenues of treatment. article_processing_charge: No article_type: original author: - first_name: E. full_name: Jensen-Jarolim, E. last_name: Jensen-Jarolim orcid: 0000-0003-4019-5765 - first_name: H. J. full_name: Bax, H. J. last_name: Bax - first_name: R. full_name: Bianchini, R. last_name: Bianchini - first_name: M. full_name: Capron, M. last_name: Capron - first_name: C. full_name: Corrigan, C. last_name: Corrigan - first_name: M. full_name: Castells, M. last_name: Castells - first_name: D. full_name: Dombrowicz, D. last_name: Dombrowicz - first_name: T. R. full_name: Daniels-Wells, T. R. last_name: Daniels-Wells - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: E. full_name: Fiebiger, E. last_name: Fiebiger - first_name: S. full_name: Gatault, S. last_name: Gatault - first_name: H. J. full_name: Gould, H. J. last_name: Gould - first_name: J. full_name: Janda, J. last_name: Janda - first_name: D. H. full_name: Josephs, D. H. last_name: Josephs - first_name: P. full_name: Karagiannis, P. last_name: Karagiannis - first_name: F. full_name: Levi-Schaffer, F. last_name: Levi-Schaffer - first_name: A. full_name: Meshcheryakova, A. last_name: Meshcheryakova - first_name: D. full_name: Mechtcheriakova, D. last_name: Mechtcheriakova - first_name: Y. full_name: Mekori, Y. last_name: Mekori - first_name: F. full_name: Mungenast, F. last_name: Mungenast - first_name: E. A. full_name: Nigro, E. A. last_name: Nigro - first_name: M. L. full_name: Penichet, M. L. last_name: Penichet - first_name: F. full_name: Redegeld, F. last_name: Redegeld - first_name: L. full_name: Saul, L. last_name: Saul - first_name: J. full_name: Singer, J. last_name: Singer - first_name: J. F. full_name: Spicer, J. F. last_name: Spicer - first_name: A. G. full_name: Siccardi, A. G. last_name: Siccardi - first_name: E. full_name: Spillner, E. last_name: Spillner - first_name: M. C. full_name: Turner, M. C. last_name: Turner - first_name: E. full_name: Untersmayr, E. last_name: Untersmayr - first_name: L. full_name: Vangelista, L. last_name: Vangelista - first_name: S. N. full_name: Karagiannis, S. N. last_name: Karagiannis citation: ama: 'Jensen-Jarolim E, Bax HJ, Bianchini R, et al. AllergoOncology - the impact of allergy in oncology: EAACI position paper. Allergy. 2017;72(6):866-887. doi:10.1111/all.13119' apa: 'Jensen-Jarolim, E., Bax, H. J., Bianchini, R., Capron, M., Corrigan, C., Castells, M., … Karagiannis, S. N. (2017). AllergoOncology - the impact of allergy in oncology: EAACI position paper. Allergy. Wiley. https://doi.org/10.1111/all.13119' chicago: 'Jensen-Jarolim, E., H. J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells, D. Dombrowicz, et al. “AllergoOncology - the Impact of Allergy in Oncology: EAACI Position Paper.” Allergy. Wiley, 2017. https://doi.org/10.1111/all.13119.' ieee: 'E. Jensen-Jarolim et al., “AllergoOncology - the impact of allergy in oncology: EAACI position paper,” Allergy, vol. 72, no. 6. Wiley, pp. 866–887, 2017.' ista: 'Jensen-Jarolim E, Bax HJ, Bianchini R, Capron M, Corrigan C, Castells M, Dombrowicz D, Daniels-Wells TR, Singer J, Fiebiger E, Gatault S, Gould HJ, Janda J, Josephs DH, Karagiannis P, Levi-Schaffer F, Meshcheryakova A, Mechtcheriakova D, Mekori Y, Mungenast F, Nigro EA, Penichet ML, Redegeld F, Saul L, Singer J, Spicer JF, Siccardi AG, Spillner E, Turner MC, Untersmayr E, Vangelista L, Karagiannis SN. 2017. AllergoOncology - the impact of allergy in oncology: EAACI position paper. Allergy. 72(6), 866–887.' mla: 'Jensen-Jarolim, E., et al. “AllergoOncology - the Impact of Allergy in Oncology: EAACI Position Paper.” Allergy, vol. 72, no. 6, Wiley, 2017, pp. 866–87, doi:10.1111/all.13119.' short: E. Jensen-Jarolim, H.J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells, D. Dombrowicz, T.R. Daniels-Wells, J. Singer, E. Fiebiger, S. Gatault, H.J. Gould, J. Janda, D.H. Josephs, P. Karagiannis, F. Levi-Schaffer, A. Meshcheryakova, D. Mechtcheriakova, Y. Mekori, F. Mungenast, E.A. Nigro, M.L. Penichet, F. Redegeld, L. Saul, J. Singer, J.F. Spicer, A.G. Siccardi, E. Spillner, M.C. Turner, E. Untersmayr, L. Vangelista, S.N. Karagiannis, Allergy 72 (2017) 866–887. date_created: 2020-08-10T11:53:26Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:17:39Z day: '01' doi: 10.1111/all.13119 extern: '1' intvolume: ' 72' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/all.13119 month: '06' oa: 1 oa_version: Published Version page: 866-887 publication: Allergy publication_identifier: issn: - 0105-4538 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'AllergoOncology - the impact of allergy in oncology: EAACI position paper' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 72 year: '2017' ... --- _id: '8239' abstract: - lang: eng text: Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts during smoking and is best known for its genotoxic capacity. Here, we aimed to assess whether acrolein at concentrations relevant for smokers may also exert immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c allergy model repeated nasal exposure to acrolein abrogated allergen-specific antibody and cytokine formation, and led to a relative accumulation of regulatory T cells in the lungs. Only the acrolein-treated mice were protected from bronchial hyperreactivity as well as from anaphylactic reactions upon challenge with the specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls. Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which could be antagonized by resveratrol. Our mouse and human data thus revealed that acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells. This provides a novel explanation why smokers have a lower allergy, but higher cancer risk. article_number: '45067' article_processing_charge: No article_type: original author: - first_name: Franziska full_name: Roth-Walter, Franziska last_name: Roth-Walter - first_name: Cornelia full_name: Bergmayr, Cornelia last_name: Bergmayr - first_name: Sarah full_name: Meitz, Sarah last_name: Meitz - first_name: Stefan full_name: Buchleitner, Stefan last_name: Buchleitner - first_name: Caroline full_name: Stremnitzer, Caroline last_name: Stremnitzer - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Anna full_name: Moskovskich, Anna last_name: Moskovskich - first_name: Mario A. full_name: Müller, Mario A. last_name: Müller - first_name: Georg A. full_name: Roth, Georg A. last_name: Roth - first_name: Krisztina full_name: Manzano-Szalai, Krisztina last_name: Manzano-Szalai - first_name: Zdenek full_name: Dvorak, Zdenek last_name: Dvorak - first_name: Alina full_name: Neunkirchner, Alina last_name: Neunkirchner - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: 'Roth-Walter F, Bergmayr C, Meitz S, et al. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. 2017;7. doi:10.1038/srep45067' apa: 'Roth-Walter, F., Bergmayr, C., Meitz, S., Buchleitner, S., Stremnitzer, C., Singer, J., … Jensen-Jarolim, E. (2017). Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. Springer Nature. https://doi.org/10.1038/srep45067' chicago: 'Roth-Walter, Franziska, Cornelia Bergmayr, Sarah Meitz, Stefan Buchleitner, Caroline Stremnitzer, Judit Singer, Anna Moskovskich, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” Scientific Reports. Springer Nature, 2017. https://doi.org/10.1038/srep45067.' ieee: 'F. Roth-Walter et al., “Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure,” Scientific Reports, vol. 7. Springer Nature, 2017.' ista: 'Roth-Walter F, Bergmayr C, Meitz S, Buchleitner S, Stremnitzer C, Singer J, Moskovskich A, Müller MA, Roth GA, Manzano-Szalai K, Dvorak Z, Neunkirchner A, Jensen-Jarolim E. 2017. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. 7, 45067.' mla: 'Roth-Walter, Franziska, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” Scientific Reports, vol. 7, 45067, Springer Nature, 2017, doi:10.1038/srep45067.' short: F. Roth-Walter, C. Bergmayr, S. Meitz, S. Buchleitner, C. Stremnitzer, J. Singer, A. Moskovskich, M.A. Müller, G.A. Roth, K. Manzano-Szalai, Z. Dvorak, A. Neunkirchner, E. Jensen-Jarolim, Scientific Reports 7 (2017). date_created: 2020-08-10T11:53:46Z date_published: 2017-03-23T00:00:00Z date_updated: 2021-01-12T08:17:40Z day: '23' doi: 10.1038/srep45067 extern: '1' intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/srep45067 month: '03' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: issn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2017' ... --- _id: '8240' abstract: - lang: eng text: "Background/Aim: Cancer cell lines are indispensible surrogate models in cancer research, as they can be used off-the-shelf, expanded to the desired extent, easily modified and exchanged between research groups for affirmation, reproduction or follow-up experiments.\r\nAs malignant cells are prone to genomic instability, phenotypical changes may occur after certain passages in culture. Thus, cell lines have to be regularly authenticated to ensure data quality. In between experiments these cell lines are often stored in liquid nitrogen for extended time periods.\r\nAlthough freezing of cells is a necessary evil, little research is performed on how long-term storage affects cancer cell lines. Therefore, this study investigated the effects of a 28-year long liquid nitrogen storage period on BT474 cells with regard to phenotypical changes, differences in cell-surface receptor expression as well as cytokine and gene expressional variations.\r\nMethods: Two batches of BT474 cells, one frozen in 1986, the other directly purchased from ATCC were investigated by light microscopy, cell growth analysis, flow cytometry and cytokine as well as whole-transcriptome expression profiling.\r\nResults: The cell lines were morphologically indifferent and showed similar growth rates and similar cell-surface receptor expression. Transcriptome analysis revealed significant differences in only 26 of 40,716 investigated RefSeq transcripts with 4 of them being up-regulated and 22 down-regulated.\r\nConclusion: This study demonstrates that even after very long periods of storage in liquid nitrogen, cancer cell lines display only minimal changes in their gene expression profiles. However, also such minor changes should be carefully assessed before continuation of experiments, especially if phenotypic alterations can be additionally observed." article_processing_charge: No article_type: original author: - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Thomas W. full_name: Grunt, Thomas W. last_name: Grunt - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Josef full_name: Singer, Josef last_name: Singer citation: ama: Singer J, Grunt TW, Jensen-Jarolim E, Singer J. Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. Oncotarget. 2017;8:35076-35087. doi:10.18632/oncotarget.16623 apa: Singer, J., Grunt, T. W., Jensen-Jarolim, E., & Singer, J. (2017). Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.16623 chicago: Singer, Judit, Thomas W. Grunt, Erika Jensen-Jarolim, and Josef Singer. “Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.16623. ieee: J. Singer, T. W. Grunt, E. Jensen-Jarolim, and J. Singer, “Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474,” Oncotarget, vol. 8. Impact Journals, pp. 35076–35087, 2017. ista: Singer J, Grunt TW, Jensen-Jarolim E, Singer J. 2017. Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. Oncotarget. 8, 35076–35087. mla: Singer, Judit, et al. “Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” Oncotarget, vol. 8, Impact Journals, 2017, pp. 35076–87, doi:10.18632/oncotarget.16623. short: J. Singer, T.W. Grunt, E. Jensen-Jarolim, J. Singer, Oncotarget 8 (2017) 35076–35087. date_created: 2020-08-10T11:53:53Z date_published: 2017-03-28T00:00:00Z date_updated: 2021-01-12T08:17:41Z day: '28' doi: 10.18632/oncotarget.16623 extern: '1' intvolume: ' 8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.18632/oncotarget.16623 month: '03' oa: 1 oa_version: Published Version page: 35076-35087 publication: Oncotarget publication_identifier: issn: - 1949-2553 publication_status: published publisher: Impact Journals quality_controlled: '1' status: public title: Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '8235' abstract: - lang: eng text: Due to large homology of human and canine EGFR, dogs suffering from spontaneous EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic compounds can be developed for both human and veterinary patients. This study describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc. Successful coupling of 10 DTPA molecules per antibody on average was proven by significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots. Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained its binding capacity towards human and canine EGFR in flow cytometry, immuno- and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma cells by a competition binding technique. Stability tests of the radiolabeled compound identified TRIS buffered saline as the ideal formulation for short-term storage with 87.11 ±6.04% intact compound being still detected 60 minutes post radiolabeling. High stability, specificity and EGFR binding affinity pinpoint towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the first proof-of-concept diagnostic and therapeutic applications in canine cancer patients. article_processing_charge: No article_type: original author: - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Neydher full_name: Berroterán-Infante, Neydher last_name: Berroterán-Infante - first_name: Christina full_name: Rami-Mark, Christina last_name: Rami-Mark - first_name: Monika full_name: Dumanic, Monika last_name: Dumanic - first_name: Miroslawa full_name: Matz, Miroslawa last_name: Matz - first_name: Michael full_name: Willmann, Michael last_name: Willmann - first_name: Fritz full_name: Andreae, Fritz last_name: Andreae - first_name: Josef full_name: Singer, Josef last_name: Singer - first_name: Wolfgang full_name: Wadsak, Wolfgang last_name: Wadsak - first_name: Markus full_name: Mitterhauser, Markus last_name: Mitterhauser - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: Singer J, Berroterán-Infante N, Rami-Mark C, et al. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. 2017;8:83128-83141. doi:10.18632/oncotarget.20914 apa: Singer, J., Berroterán-Infante, N., Rami-Mark, C., Dumanic, M., Matz, M., Willmann, M., … Jensen-Jarolim, E. (2017). Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.20914 chicago: Singer, Judit, Neydher Berroterán-Infante, Christina Rami-Mark, Monika Dumanic, Miroslawa Matz, Michael Willmann, Fritz Andreae, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20914. ieee: J. Singer et al., “Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials,” Oncotarget, vol. 8. Impact Journals, pp. 83128–83141, 2017. ista: Singer J, Berroterán-Infante N, Rami-Mark C, Dumanic M, Matz M, Willmann M, Andreae F, Singer J, Wadsak W, Mitterhauser M, Jensen-Jarolim E. 2017. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. 8, 83128–83141. mla: Singer, Judit, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” Oncotarget, vol. 8, Impact Journals, 2017, pp. 83128–41, doi:10.18632/oncotarget.20914. short: J. Singer, N. Berroterán-Infante, C. Rami-Mark, M. Dumanic, M. Matz, M. Willmann, F. Andreae, J. Singer, W. Wadsak, M. Mitterhauser, E. Jensen-Jarolim, Oncotarget 8 (2017) 83128–83141. date_created: 2020-08-10T11:53:18Z date_published: 2017-09-15T00:00:00Z date_updated: 2021-01-12T08:17:39Z day: '15' doi: 10.18632/oncotarget.20914 extern: '1' intvolume: ' 8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.18632/oncotarget.20914 month: '09' oa: 1 oa_version: Published Version page: 83128-83141 publication: Oncotarget publication_identifier: issn: - 1949-2553 publication_status: published publisher: Impact Journals quality_controlled: '1' status: public title: Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '825' abstract: - lang: eng text: What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep. author: - first_name: Barbara full_name: Petritsch, Barbara id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 citation: ama: Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678 apa: Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678 chicago: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678. ieee: B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017. ista: Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207. mla: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678. short: B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207. date_created: 2018-12-11T11:48:42Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:17:44Z day: '01' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v70i2.1678 file: - access_level: open_access checksum: 7c4544d07efa2c2add8612b489abb4e2 content_type: application/pdf creator: dernst date_created: 2019-01-18T13:32:17Z date_updated: 2020-07-14T12:48:11Z file_id: '5850' file_name: 2017_VOEB_Petritsch.pdf file_size: 7843975 relation: main_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' intvolume: ' 70' issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 200 - 207 publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare publication_identifier: issn: - '10222588' publication_status: published publisher: VÖB publist_id: '6823' scopus_import: 1 status: public title: Metadata for research data in practice 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '8299' abstract: - lang: eng text: 'Permissionless blockchain-based cryptocurrencies commonly use proof-of-work (PoW) or proof-of-stake (PoS) to ensure their security, e.g. to prevent double spending attacks. However, both approaches have disadvantages: PoW leads to massive amounts of wasted electricity and re-centralization, whereas major stakeholders in PoS might be able to create a monopoly. In this work, we propose proof-of-personhood (PoP), a mechanism that binds physical entities to virtual identities in a way that enables accountability while preserving anonymity. Afterwards we introduce PoPCoin, a new cryptocurrency, whose consensus mechanism leverages PoP to eliminate the dis-advantages of PoW and PoS while ensuring security. PoPCoin leads to a continuously fair and democratic wealth creation process which paves the way for an experimental basic income infrastructure.' article_number: '7966966' article_processing_charge: No author: - first_name: Maria full_name: Borge, Maria last_name: Borge - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic - first_name: Linus full_name: Gasser, Linus last_name: Gasser - first_name: Nicolas full_name: Gailly, Nicolas last_name: Gailly - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. In: 2017 IEEE European Symposium on Security and Privacy Workshops. IEEE; 2017. doi:10.1109/eurospw.2017.46' apa: 'Borge, M., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., & Ford, B. (2017). Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. In 2017 IEEE European Symposium on Security and Privacy Workshops. Paris, France: IEEE. https://doi.org/10.1109/eurospw.2017.46' chicago: 'Borge, Maria, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, and Bryan Ford. “Proof-of-Personhood: Redemocratizing Permissionless Cryptocurrencies.” In 2017 IEEE European Symposium on Security and Privacy Workshops. IEEE, 2017. https://doi.org/10.1109/eurospw.2017.46.' ieee: 'M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, and B. Ford, “Proof-of-personhood: Redemocratizing permissionless cryptocurrencies,” in 2017 IEEE European Symposium on Security and Privacy Workshops, Paris, France, 2017.' ista: 'Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. 2017. Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. 2017 IEEE European Symposium on Security and Privacy Workshops. EuroS&PW: European Symposium on Security and Privacy Workshops, 7966966.' mla: 'Borge, Maria, et al. “Proof-of-Personhood: Redemocratizing Permissionless Cryptocurrencies.” 2017 IEEE European Symposium on Security and Privacy Workshops, 7966966, IEEE, 2017, doi:10.1109/eurospw.2017.46.' short: M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, B. Ford, in:, 2017 IEEE European Symposium on Security and Privacy Workshops, IEEE, 2017. conference: end_date: 2017-04-28 location: Paris, France name: 'EuroS&PW: European Symposium on Security and Privacy Workshops' start_date: 2017-04-26 date_created: 2020-08-26T11:48:11Z date_published: 2017-06-30T00:00:00Z date_updated: 2021-01-12T08:17:57Z day: '30' doi: 10.1109/eurospw.2017.46 extern: '1' language: - iso: eng month: '06' oa_version: None publication: 2017 IEEE European Symposium on Security and Privacy Workshops publication_identifier: eisbn: - '9781538622445' publication_status: published publisher: IEEE quality_controlled: '1' status: public title: 'Proof-of-personhood: Redemocratizing permissionless cryptocurrencies' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '8306' abstract: - lang: eng text: Bias-resistant public randomness is a critical component in many (distributed) protocols. Generating public randomness is hard, however, because active adversaries may behave dishonestly to bias public random choices toward their advantage. Existing solutions do not scale to hundreds or thousands of participants, as is needed in many decentralized systems. We propose two large-scale distributed protocols, RandHound and RandHerd, which provide publicly-verifiable, unpredictable, and unbiasable randomness against Byzantine adversaries. RandHound relies on an untrusted client to divide a set of randomness servers into groups for scalability, and it depends on the pigeonhole principle to ensure output integrity, even for non-random, adversarial group choices. RandHerd implements an efficient, decentralized randomness beacon. RandHerd is structurally similar to a BFT protocol, but uses RandHound in a one-time setup to arrange participants into verifiably unbiased random secret-sharing groups, which then repeatedly produce random output at predefined intervals. Our prototype demonstrates that RandHound and RandHerd achieve good performance across hundreds of participants while retaining a low failure probability by properly selecting protocol parameters, such as a group size and secret-sharing threshold. For example, when sharding 512 nodes into groups of 32, our experiments show that RandHound can produce fresh random output after 240 seconds. RandHerd, after a setup phase of 260 seconds, is able to generate fresh random output in intervals of approximately 6 seconds. For this configuration, both protocols operate at a failure probability of at most 0.08% against a Byzantine adversary. article_processing_charge: No author: - first_name: E. full_name: Syta, E. last_name: Syta - first_name: P. full_name: Jovanovic, P. last_name: Jovanovic - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: N. full_name: Gailly, N. last_name: Gailly - first_name: L. full_name: Gasser, L. last_name: Gasser - first_name: I. full_name: Khoffi, I. last_name: Khoffi - first_name: M. J. full_name: Fischer, M. J. last_name: Fischer - first_name: B. full_name: Ford, B. last_name: Ford citation: ama: 'Syta E, Jovanovic P, Kokoris Kogias E, et al. Scalable bias-resistant distributed randomness. In: 2017 IEEE Symposium on Security and Privacy. IEEE; 2017:444-460. doi:10.1109/SP.2017.45' apa: 'Syta, E., Jovanovic, P., Kokoris Kogias, E., Gailly, N., Gasser, L., Khoffi, I., … Ford, B. (2017). Scalable bias-resistant distributed randomness. In 2017 IEEE Symposium on Security and Privacy (pp. 444–460). San Jose, CA, United States: IEEE. https://doi.org/10.1109/SP.2017.45' chicago: Syta, E., P. Jovanovic, Eleftherios Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M. J. Fischer, and B. Ford. “Scalable Bias-Resistant Distributed Randomness.” In 2017 IEEE Symposium on Security and Privacy, 444–60. IEEE, 2017. https://doi.org/10.1109/SP.2017.45. ieee: E. Syta et al., “Scalable bias-resistant distributed randomness,” in 2017 IEEE Symposium on Security and Privacy, San Jose, CA, United States, 2017, pp. 444–460. ista: 'Syta E, Jovanovic P, Kokoris Kogias E, Gailly N, Gasser L, Khoffi I, Fischer MJ, Ford B. 2017. Scalable bias-resistant distributed randomness. 2017 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 444–460.' mla: Syta, E., et al. “Scalable Bias-Resistant Distributed Randomness.” 2017 IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–60, doi:10.1109/SP.2017.45. short: E. Syta, P. Jovanovic, E. Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M.J. Fischer, B. Ford, in:, 2017 IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–460. conference: end_date: 2017-05-26 location: San Jose, CA, United States name: 'SP: Symposium on Security and Privacy' start_date: 2017-05-22 date_created: 2020-08-26T12:26:08Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:18:02Z day: '01' doi: 10.1109/SP.2017.45 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/1067 month: '06' oa: 1 oa_version: Preprint page: 444-460 publication: 2017 IEEE Symposium on Security and Privacy publication_identifier: isbn: - '9781509055340' issn: - 2375-1207 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Scalable bias-resistant distributed randomness type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '8301' abstract: - lang: eng text: Software-update mechanisms are critical to the security of modern systems, but their typically centralized design presents a lucrative and frequently attacked target. In this work, we propose CHAINIAC, a decentralized software-update framework that eliminates single points of failure, enforces transparency, and provides efficient verifiability of integrity and authenticity for software-release processes. Independent witness servers collectively verify conformance of software updates to release policies, build verifiers validate the source-to-binary correspondence, and a tamper-proof release log stores collectively signed updates, thus ensuring that no release is accepted by clients before being widely disclosed and validated. The release log embodies a skipchain, a novel data structure, enabling arbitrarily out-of-date clients to efficiently validate updates and signing keys. Evaluation of our CHAINIAC prototype on reproducible Debian packages shows that the automated update process takes the average of 5 minutes per release for individual packages, and only 20 seconds for the aggregate timeline. We further evaluate the framework using real-world data from the PyPI package repository and show that it offers clients security comparable to verifying every single update themselves while consuming only one-fifth of the bandwidth and having a minimal computational overhead. article_processing_charge: No author: - first_name: Kirill full_name: Nikitin, Kirill last_name: Nikitin - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic - first_name: Linus full_name: Gasser, Linus last_name: Gasser - first_name: Nicolas full_name: Gailly, Nicolas last_name: Gailly - first_name: Ismail full_name: Khoffi, Ismail last_name: Khoffi - first_name: Justin full_name: Cappos, Justin last_name: Cappos - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Nikitin K, Kokoris Kogias E, Jovanovic P, et al. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In: Proceedings of the 26th USENIX Conference on Security Symposium. USENIX Association; 2017:1271–1287.' apa: 'Nikitin, K., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Khoffi, I., … Ford, B. (2017). CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In Proceedings of the 26th USENIX Conference on Security Symposium (pp. 1271–1287). Vancouver, Canada: USENIX Association.' chicago: 'Nikitin, Kirill, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ismail Khoffi, Justin Cappos, and Bryan Ford. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” In Proceedings of the 26th USENIX Conference on Security Symposium, 1271–1287. USENIX Association, 2017.' ieee: 'K. Nikitin et al., “CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds,” in Proceedings of the 26th USENIX Conference on Security Symposium, Vancouver, Canada, 2017, pp. 1271–1287.' ista: 'Nikitin K, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Khoffi I, Cappos J, Ford B. 2017. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. Proceedings of the 26th USENIX Conference on Security Symposium. SEC: Security Symposium, 1271–1287.' mla: 'Nikitin, Kirill, et al. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” Proceedings of the 26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp. 1271–1287.' short: K. Nikitin, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, I. Khoffi, J. Cappos, B. Ford, in:, Proceedings of the 26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp. 1271–1287. conference: end_date: 2017-08-18 location: Vancouver, Canada name: 'SEC: Security Symposium' start_date: 2017-08-16 date_created: 2020-08-26T12:04:44Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:18:00Z day: '01' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.usenix.org/system/files/conference/usenixsecurity17/sec17-nikitin.pdf month: '09' oa: 1 oa_version: Published Version page: 1271–1287 publication: Proceedings of the 26th USENIX Conference on Security Symposium publication_identifier: isbn: - '9781931971409' publication_status: published publisher: USENIX Association quality_controlled: '1' status: public title: 'CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '8446' abstract: - lang: eng text: Solid‐state NMR spectroscopy can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here the use of two sets of experiments is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross‐polarization for heteronuclear transfers. The utility of these experiments is exemplified with application to assemblies of deuterated, fully amide‐protonated proteins from approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies from approximately 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. The resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is compared to NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly. article_processing_charge: No article_type: original author: - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga - first_name: Charles‐Adrien full_name: Arnaud, Charles‐Adrien last_name: Arnaud - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Maxime full_name: Audin, Maxime last_name: Audin - first_name: Vilius full_name: Kurauskas, Vilius last_name: Kurauskas - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Carsten full_name: Krichel, Carsten last_name: Krichel - first_name: Jia‐Ying full_name: Guan, Jia‐Ying last_name: Guan - first_name: Jerome full_name: Boisbouvier, Jerome last_name: Boisbouvier - first_name: Remco full_name: Sprangers, Remco last_name: Sprangers - first_name: Cécile full_name: Breyton, Cécile last_name: Breyton - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. ChemPhysChem. 2017;18(19):2697-2703. doi:10.1002/cphc.201700572 apa: Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., … Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201700572 chicago: Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” ChemPhysChem. Wiley, 2017. https://doi.org/10.1002/cphc.201700572. ieee: H. Fraga et al., “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins,” ChemPhysChem, vol. 18, no. 19. Wiley, pp. 2697–2703, 2017. ista: Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. ChemPhysChem. 18(19), 2697–2703. mla: Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” ChemPhysChem, vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:10.1002/cphc.201700572. short: H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel, J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18 (2017) 2697–2703. date_created: 2020-09-18T10:06:09Z date_published: 2017-08-09T00:00:00Z date_updated: 2021-01-12T08:19:19Z day: '09' doi: 10.1002/cphc.201700572 extern: '1' intvolume: ' 18' issue: '19' keyword: - Physical and Theoretical Chemistry - Atomic and Molecular Physics - and Optics language: - iso: eng month: '08' oa_version: None page: 2697-2703 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 - 1439-7641 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2017' ... --- _id: '8445' abstract: - lang: eng text: Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins. article_number: '145' article_processing_charge: No article_type: original author: - first_name: Vilius full_name: Kurauskas, Vilius last_name: Kurauskas - first_name: Sergei A. full_name: Izmailov, Sergei A. last_name: Izmailov - first_name: Olga N. full_name: Rogacheva, Olga N. last_name: Rogacheva - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Joyce full_name: Woodhouse, Joyce last_name: Woodhouse - first_name: Anastasya full_name: Shilova, Anastasya last_name: Shilova - first_name: Yi full_name: Xue, Yi last_name: Xue - first_name: Tairan full_name: Yuwen, Tairan last_name: Yuwen - first_name: Nicolas full_name: Coquelle, Nicolas last_name: Coquelle - first_name: Jacques-Philippe full_name: Colletier, Jacques-Philippe last_name: Colletier - first_name: Nikolai R. full_name: Skrynnikov, Nikolai R. last_name: Skrynnikov - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications. 2017;8. doi:10.1038/s41467-017-00165-8 apa: Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse, J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-00165-8 chicago: Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel, Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00165-8. ieee: V. Kurauskas et al., “Slow conformational exchange and overall rocking motion in ubiquitin protein crystals,” Nature Communications, vol. 8. Springer Nature, 2017. ista: Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications. 8, 145. mla: Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” Nature Communications, vol. 8, 145, Springer Nature, 2017, doi:10.1038/s41467-017-00165-8. short: V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse, A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 8 (2017). date_created: 2020-09-18T10:06:01Z date_published: 2017-07-27T00:00:00Z date_updated: 2021-01-12T08:19:19Z day: '27' doi: 10.1038/s41467-017-00165-8 extern: '1' intvolume: ' 8' language: - iso: eng month: '07' oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Slow conformational exchange and overall rocking motion in ubiquitin protein crystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '8444' abstract: - lang: eng text: Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment. article_processing_charge: No article_type: original author: - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Martin S. full_name: King, Martin S. last_name: King - first_name: Edmund R.S. full_name: Kunji, Edmund R.S. last_name: Kunji - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot citation: ama: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical Journal. 2017;113(11):2311-2315. doi:10.1016/j.bpj.2017.09.019 apa: Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., & Chipot, C. (2017). Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2017.09.019 chicago: Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2017.09.019. ieee: F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,” Biophysical Journal, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017. ista: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical Journal. 113(11), 2311–2315. mla: Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” Biophysical Journal, vol. 113, no. 11, Elsevier, 2017, pp. 2311–15, doi:10.1016/j.bpj.2017.09.019. short: F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal 113 (2017) 2311–2315. date_created: 2020-09-18T10:05:54Z date_published: 2017-12-05T00:00:00Z date_updated: 2021-01-12T08:19:18Z day: '05' doi: 10.1016/j.bpj.2017.09.019 extern: '1' intvolume: ' 113' issue: '11' keyword: - Biophysics language: - iso: eng month: '12' oa_version: None page: 2311-2315 publication: Biophysical Journal publication_identifier: issn: - 0006-3495 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2017' ... --- _id: '9065' abstract: - lang: eng text: Magnetic anisotropy in strontium iridate (Sr2IrO4) is found to be large because of the strong spin-orbit interactions. In our work, we studied the in-plane magnetic anisotropy of Sr2IrO4 and traced the anisotropic exchange interactions between the isospins in the crystal. The magnetic-field-dependent torque τ(H) showed a prominent transition from the canted antiferromagnetic state to the weak ferromagnetic (WFM) state. A comprehensive analysis was conducted to examine the isotropic and anisotropic regimes and probe the easy magnetization axis along the a b plane. The angle-dependent torque τ(θ) revealed a deviation from the sinusoidal behavior, and small differences in hysteresis were observed around 0° and 90° in the low-magnetic-field regime. This indicates that the orientation of the easy axis of the FM component is along the b axis, where the antiferromagnetic to WFM spin-flop transition occurs. We compared the coefficients of the magnetic susceptibility tensors and captured the anisotropy of the material. The in-plane τ(θ) revealed a tendency toward isotropic behavior for fields with values above the field value of the WFM transition. article_number: '155102' article_processing_charge: No article_type: original author: - first_name: Muhammad full_name: Nauman, Muhammad id: 32c21954-2022-11eb-9d5f-af9f93c24e71 last_name: Nauman orcid: 0000-0002-2111-4846 - first_name: Yunjeong full_name: Hong, Yunjeong last_name: Hong - first_name: Tayyaba full_name: Hussain, Tayyaba last_name: Hussain - first_name: M. S. full_name: Seo, M. S. last_name: Seo - first_name: S. Y. full_name: Park, S. Y. last_name: Park - first_name: N. full_name: Lee, N. last_name: Lee - first_name: Y. J. full_name: Choi, Y. J. last_name: Choi - first_name: Woun full_name: Kang, Woun last_name: Kang - first_name: Younjung full_name: Jo, Younjung last_name: Jo citation: ama: Nauman M, Hong Y, Hussain T, et al. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical Review B. 2017;96(15). doi:10.1103/physrevb.96.155102 apa: Nauman, M., Hong, Y., Hussain, T., Seo, M. S., Park, S. Y., Lee, N., … Jo, Y. (2017). In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.96.155102 chicago: Nauman, Muhammad, Yunjeong Hong, Tayyaba Hussain, M. S. Seo, S. Y. Park, N. Lee, Y. J. Choi, Woun Kang, and Younjung Jo. “In-Plane Magnetic Anisotropy in Strontium Iridate Sr2IrO4.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/physrevb.96.155102. ieee: M. Nauman et al., “In-plane magnetic anisotropy in strontium iridate Sr2IrO4,” Physical Review B, vol. 96, no. 15. American Physical Society, 2017. ista: Nauman M, Hong Y, Hussain T, Seo MS, Park SY, Lee N, Choi YJ, Kang W, Jo Y. 2017. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical Review B. 96(15), 155102. mla: Nauman, Muhammad, et al. “In-Plane Magnetic Anisotropy in Strontium Iridate Sr2IrO4.” Physical Review B, vol. 96, no. 15, 155102, American Physical Society, 2017, doi:10.1103/physrevb.96.155102. short: M. Nauman, Y. Hong, T. Hussain, M.S. Seo, S.Y. Park, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Physical Review B 96 (2017). date_created: 2021-02-02T15:49:21Z date_published: 2017-10-01T00:00:00Z date_updated: 2021-02-03T12:53:00Z day: '01' doi: 10.1103/physrevb.96.155102 extern: '1' intvolume: ' 96' issue: '15' language: - iso: eng month: '10' oa_version: None publication: Physical Review B publication_identifier: issn: - 2469-9950 - 2469-9969 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: In-plane magnetic anisotropy in strontium iridate Sr2IrO4 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ... --- _id: '9165' abstract: - lang: eng text: Advances in colloidal synthesis allow for the design of particles with controlled patches. This article reviews routes towards colloidal locomotion, where energy is consumed and converted into motion, and its implementation with active patchy particles. A special emphasis is given to phoretic swimmers, where the self-propulsion originates from an interfacial phenomenon, raising experimental challenges and opening up opportunities for particles with controlled anisotropic surface chemistry and novel behaviors. article_processing_charge: No article_type: original author: - first_name: A. full_name: Aubret, A. last_name: Aubret - first_name: S. full_name: Ramananarivo, S. last_name: Ramananarivo - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: 'Aubret A, Ramananarivo S, Palacci JA. Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science. 2017;30:81-89. doi:10.1016/j.cocis.2017.05.007' apa: 'Aubret, A., Ramananarivo, S., & Palacci, J. A. (2017). Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science. Elsevier. https://doi.org/10.1016/j.cocis.2017.05.007' chicago: 'Aubret, A., S. Ramananarivo, and Jérémie A Palacci. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.” Current Opinion in Colloid & Interface Science. Elsevier, 2017. https://doi.org/10.1016/j.cocis.2017.05.007.' ieee: 'A. Aubret, S. Ramananarivo, and J. A. Palacci, “Eppur si muove, and yet it moves: Patchy (phoretic) swimmers,” Current Opinion in Colloid & Interface Science, vol. 30. Elsevier, pp. 81–89, 2017.' ista: 'Aubret A, Ramananarivo S, Palacci JA. 2017. Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science. 30, 81–89.' mla: 'Aubret, A., et al. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.” Current Opinion in Colloid & Interface Science, vol. 30, Elsevier, 2017, pp. 81–89, doi:10.1016/j.cocis.2017.05.007.' short: A. Aubret, S. Ramananarivo, J.A. Palacci, Current Opinion in Colloid & Interface Science 30 (2017) 81–89. date_created: 2021-02-18T14:29:42Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-02-22T09:32:11Z day: '01' doi: 10.1016/j.cocis.2017.05.007 extern: '1' intvolume: ' 30' language: - iso: eng month: '07' oa_version: None page: 81-89 publication: Current Opinion in Colloid & Interface Science publication_identifier: issn: - 1359-0294 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Eppur si muove, and yet it moves: Patchy (phoretic) swimmers' type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 30 year: '2017' ... --- _id: '9190' abstract: - lang: eng text: Plant meristems carry pools of continuously active stem cells, whose activity is controlled by developmental and environmental signals. After stem cell division, daughter cells that exit the stem cell domain acquire transit amplifying cell identity before they are incorporated into organs and differentiate. In this study, we used an integrated approach to elucidate the role of HECATE (HEC) genes in regulating developmental trajectories of shoot stem cells in Arabidopsis thaliana. Our work reveals that HEC function stabilizes cell fate in distinct zones of the shoot meristem thereby controlling the spatio-temporal dynamics of stem cell differentiation. Importantly, this activity is concomitant with the local modulation of cellular responses to cytokinin and auxin, two key phytohormones regulating cell behaviour. Mechanistically, we show that HEC factors transcriptionally control and physically interact with MONOPTEROS (MP), a key regulator of auxin signalling, and modulate the autocatalytic stabilization of auxin signalling output. article_number: e30135 article_processing_charge: No article_type: original author: - first_name: Christophe full_name: Gaillochet, Christophe last_name: Gaillochet - first_name: Thomas full_name: Stiehl, Thomas last_name: Stiehl - first_name: Christian full_name: Wenzl, Christian last_name: Wenzl - first_name: Juan-José full_name: Ripoll, Juan-José last_name: Ripoll - first_name: Lindsay J full_name: Bailey-Steinitz, Lindsay J last_name: Bailey-Steinitz - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Anne full_name: Pfeiffer, Anne last_name: Pfeiffer - first_name: Andrej full_name: Miotk, Andrej last_name: Miotk - first_name: Jana P full_name: Hakenjos, Jana P last_name: Hakenjos - first_name: Joachim full_name: Forner, Joachim last_name: Forner - first_name: Martin F full_name: Yanofsky, Martin F last_name: Yanofsky - first_name: Anna full_name: Marciniak-Czochra, Anna last_name: Marciniak-Czochra - first_name: Jan U full_name: Lohmann, Jan U last_name: Lohmann citation: ama: Gaillochet C, Stiehl T, Wenzl C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. eLife. 2017;6. doi:10.7554/elife.30135 apa: Gaillochet, C., Stiehl, T., Wenzl, C., Ripoll, J.-J., Bailey-Steinitz, L. J., Li, L., … Lohmann, J. U. (2017). Control of plant cell fate transitions by transcriptional and hormonal signals. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30135 chicago: Gaillochet, Christophe, Thomas Stiehl, Christian Wenzl, Juan-José Ripoll, Lindsay J Bailey-Steinitz, Lanxin Li, Anne Pfeiffer, et al. “Control of Plant Cell Fate Transitions by Transcriptional and Hormonal Signals.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30135. ieee: C. Gaillochet et al., “Control of plant cell fate transitions by transcriptional and hormonal signals,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Gaillochet C, Stiehl T, Wenzl C, Ripoll J-J, Bailey-Steinitz LJ, Li L, Pfeiffer A, Miotk A, Hakenjos JP, Forner J, Yanofsky MF, Marciniak-Czochra A, Lohmann JU. 2017. Control of plant cell fate transitions by transcriptional and hormonal signals. eLife. 6, e30135. mla: Gaillochet, Christophe, et al. “Control of Plant Cell Fate Transitions by Transcriptional and Hormonal Signals.” ELife, vol. 6, e30135, eLife Sciences Publications, 2017, doi:10.7554/elife.30135. short: C. Gaillochet, T. Stiehl, C. Wenzl, J.-J. Ripoll, L.J. Bailey-Steinitz, L. Li, A. Pfeiffer, A. Miotk, J.P. Hakenjos, J. Forner, M.F. Yanofsky, A. Marciniak-Czochra, J.U. Lohmann, ELife 6 (2017). date_created: 2021-02-24T17:06:13Z date_published: 2017-10-23T00:00:00Z date_updated: 2021-03-02T09:33:54Z day: '23' ddc: - '580' doi: 10.7554/elife.30135 extern: '1' external_id: pmid: - '29058667' file: - access_level: open_access checksum: 51c8968a845df5077643c3e3e139d34f content_type: application/pdf creator: dernst date_created: 2021-03-02T09:29:56Z date_updated: 2021-03-02T09:29:56Z file_id: '9214' file_name: 2017_eLife_Gaillochet.pdf file_size: 11669407 relation: main_file success: 1 file_date_updated: 2021-03-02T09:29:56Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' status: public title: Control of plant cell fate transitions by transcriptional and hormonal signals 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2017' ... --- _id: '93' abstract: - lang: eng text: An electro-optomechanical device capable of microwave-to-optics conversion has recently been demonstrated, with the vision of enabling optical networks of superconducting qubits. Here we present an improved converter design that uses a three-dimensional microwave cavity for coupling between the microwave transmission line and an integrated LC resonator on the converter chip. The new design simplifies the optical assembly and decouples it from the microwave part of the setup. Experimental demonstrations show that the modular device assembly allows us to flexibly tune the microwave coupling to the converter chip while maintaining small loss. We also find that electromechanical experiments are not impacted by the additional microwave cavity. Our design is compatible with a high-finesse optical cavity and will improve optical performance. article_number: '094701' author: - first_name: Tim full_name: Menke, Tim last_name: Menke - first_name: Peter full_name: Burns, Peter last_name: Burns - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: N S full_name: Kampel, N S last_name: Kampel - first_name: Robert full_name: Peterson, Robert last_name: Peterson - first_name: Katarina full_name: Cicak, Katarina last_name: Cicak - first_name: Raymond full_name: Simmonds, Raymond last_name: Simmonds - first_name: Cindy full_name: Regal, Cindy last_name: Regal - first_name: Konrad full_name: Lehnert, Konrad last_name: Lehnert citation: ama: Menke T, Burns P, Higginbotham AP, et al. Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device. Review of Scientific Instruments. 2017;88(9). doi:10.1063/1.5000973 apa: Menke, T., Burns, P., Higginbotham, A. P., Kampel, N. S., Peterson, R., Cicak, K., … Lehnert, K. (2017). Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device. Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.5000973 chicago: Menke, Tim, Peter Burns, Andrew P Higginbotham, N S Kampel, Robert Peterson, Katarina Cicak, Raymond Simmonds, Cindy Regal, and Konrad Lehnert. “Reconfigurable Re-Entrant Cavity for Wireless Coupling to an Electro-Optomechanical Device.” Review of Scientific Instruments. American Institute of Physics, 2017. https://doi.org/10.1063/1.5000973. ieee: T. Menke et al., “Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device,” Review of Scientific Instruments, vol. 88, no. 9. American Institute of Physics, 2017. ista: Menke T, Burns P, Higginbotham AP, Kampel NS, Peterson R, Cicak K, Simmonds R, Regal C, Lehnert K. 2017. Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device. Review of Scientific Instruments. 88(9), 094701. mla: Menke, Tim, et al. “Reconfigurable Re-Entrant Cavity for Wireless Coupling to an Electro-Optomechanical Device.” Review of Scientific Instruments, vol. 88, no. 9, 094701, American Institute of Physics, 2017, doi:10.1063/1.5000973. short: T. Menke, P. Burns, A.P. Higginbotham, N.S. Kampel, R. Peterson, K. Cicak, R. Simmonds, C. Regal, K. Lehnert, Review of Scientific Instruments 88 (2017). date_created: 2018-12-11T11:44:35Z date_published: 2017-09-08T00:00:00Z date_updated: 2021-01-12T08:21:59Z day: '08' doi: 10.1063/1.5000973 extern: '1' external_id: arxiv: - '1703.06470' pmid: - '28964202' intvolume: ' 88' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.06470 month: '09' oa: 1 oa_version: Preprint pmid: 1 publication: Review of Scientific Instruments publication_status: published publisher: American Institute of Physics publist_id: '7961' quality_controlled: '1' status: public title: Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 88 year: '2017' ... --- _id: '94' abstract: - lang: eng text: We introduce a method for breaking Lorentz reciprocity based upon the noncommutation of frequency conversion and delay. The method requires no magnetic materials or resonant physics, allowing for the design of scalable and broadband nonreciprocal circuits. With this approach, two types of gyrators - universal building blocks for linear, nonreciprocal circuits - are constructed. Using one of these gyrators, we create a circulator with >15 dB of isolation across the 5-9 GHz band. Our designs may be readily extended to any platform with suitable frequency conversion elements, including semiconducting devices for telecommunication or an on-chip superconducting implementation for quantum information processing. article_number: '147703' author: - first_name: Eric full_name: Rosenthal, Eric last_name: Rosenthal - first_name: Benjamin full_name: Chapman, Benjamin last_name: Chapman - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Joseph full_name: Kerckhoff, Joseph last_name: Kerckhoff - first_name: Konrad full_name: Lehnert, Konrad last_name: Lehnert citation: ama: Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. 2017;119(14). doi:10.1103/PhysRevLett.119.147703 apa: Rosenthal, E., Chapman, B., Higginbotham, A. P., Kerckhoff, J., & Lehnert, K. (2017). Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.147703 chicago: Rosenthal, Eric, Benjamin Chapman, Andrew P Higginbotham, Joseph Kerckhoff, and Konrad Lehnert. “Breaking Lorentz Reciprocity with Frequency Conversion and Delay.” APS Physics, Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.147703. ieee: E. Rosenthal, B. Chapman, A. P. Higginbotham, J. Kerckhoff, and K. Lehnert, “Breaking Lorentz reciprocity with frequency conversion and delay,” APS Physics, Physical Review Letters, vol. 119, no. 14. American Physical Society, 2017. ista: Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. 2017. Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. 119(14), 147703. mla: Rosenthal, Eric, et al. “Breaking Lorentz Reciprocity with Frequency Conversion and Delay.” APS Physics, Physical Review Letters, vol. 119, no. 14, 147703, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.147703. short: E. Rosenthal, B. Chapman, A.P. Higginbotham, J. Kerckhoff, K. Lehnert, APS Physics, Physical Review Letters 119 (2017). date_created: 2018-12-11T11:44:35Z date_published: 2017-10-06T00:00:00Z date_updated: 2021-01-12T08:22:04Z day: '06' doi: 10.1103/PhysRevLett.119.147703 extern: '1' external_id: arxiv: - '1705.09548' intvolume: ' 119' issue: '14' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.09548 month: '10' oa: 1 oa_version: Submitted Version publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7960' quality_controlled: '1' status: public title: Breaking Lorentz reciprocity with frequency conversion and delay type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2017' ... --- _id: '9445' abstract: - lang: eng text: Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation. article_number: e30674 article_processing_charge: No article_type: original author: - first_name: David B full_name: Lyons, David B last_name: Lyons - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674 apa: Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674 chicago: Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674. ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674. mla: Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674. short: D.B. Lyons, D. Zilberman, ELife 6 (2017). date_created: 2021-06-02T14:28:58Z date_published: 2017-11-15T00:00:00Z date_updated: 2021-12-14T07:54:36Z day: '15' ddc: - '570' department: - _id: DaZi doi: 10.7554/elife.30674 extern: '1' external_id: pmid: - '29140247' file: - access_level: open_access checksum: 4cfcdd67511ae4aed3d993550e46e146 content_type: application/pdf creator: cziletti date_created: 2021-06-02T14:33:36Z date_updated: 2021-06-02T14:33:36Z file_id: '9446' file_name: 2017_eLife_Lyons.pdf file_size: 1603102 relation: main_file success: 1 file_date_updated: 2021-06-02T14:33:36Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes 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) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2017' ... --- _id: '957' abstract: - lang: eng text: Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors. alternative_title: - Methods in Molecular Biology author: - first_name: Ben full_name: Clifton, Ben last_name: Clifton - first_name: Jason full_name: Whitfield, Jason last_name: Whitfield - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Colin full_name: Jackson, Colin last_name: Jackson citation: ama: 'Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5' apa: Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5 chicago: Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5. ieee: B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87. ista: 'Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.' mla: Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5. short: B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87. date_created: 2018-12-11T11:49:24Z date_published: 2017-03-15T00:00:00Z date_updated: 2021-01-12T08:22:13Z day: '15' department: - _id: HaJa doi: 10.1007/978-1-4939-6940-1_5 editor: - first_name: Viktor full_name: Stein, Viktor last_name: Stein intvolume: ' 1596' language: - iso: eng month: '03' oa_version: None page: 71 - 87 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) publication: Synthetic Protein Switches publication_identifier: issn: - '10643745' publication_status: published publisher: Springer publist_id: '6451' quality_controlled: '1' scopus_import: 1 series_title: Synthetic Protein Switches status: public title: Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1596 year: '2017' ... --- _id: '9574' abstract: - lang: eng text: 'Consider the sum X(ξ)=∑ni=1aiξi, where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x]. In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.' article_processing_charge: No article_type: original author: - first_name: Afonso S. full_name: Bandeira, Afonso S. last_name: Bandeira - first_name: Asaf full_name: Ferber, Asaf last_name: Ferber - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 citation: ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 2017;61:93-99. doi:10.1016/j.endm.2017.06.025 apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2017.06.025 chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.endm.2017.06.025. ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood-Offord problem,” Electronic Notes in Discrete Mathematics, vol. 61. Elsevier, pp. 93–99, 2017. ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 61, 93–99. mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics, vol. 61, Elsevier, 2017, pp. 93–99, doi:10.1016/j.endm.2017.06.025. short: A.S. Bandeira, A. Ferber, M.A. Kwan, Electronic Notes in Discrete Mathematics 61 (2017) 93–99. date_created: 2021-06-21T06:31:10Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-02-23T14:01:26Z day: '01' doi: 10.1016/j.endm.2017.06.025 extern: '1' external_id: arxiv: - '1609.08136' intvolume: ' 61' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.08136 month: '08' oa: 1 oa_version: Preprint page: 93-99 publication: Electronic Notes in Discrete Mathematics publication_identifier: issn: - 1571-0653 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Resilience for the Littlewood-Offord problem type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 61 year: '2017' ... --- _id: '9590' abstract: - lang: eng text: We show that for any fixed dense graph G and bounded-degree tree T on the same number of vertices, a modest random perturbation of G will typically contain a copy of T . This combines the viewpoints of the well-studied problems of embedding trees into fixed dense graphs and into random graphs, and extends a sizeable body of existing research on randomly perturbed graphs. Specifically, we show that there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn uniformly random edges to G, the resulting graph will contain T asymptotically almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of a dense graph into super-regular pairs of comparable sizes, which may be of independent interest. article_processing_charge: No article_type: original author: - first_name: Michael full_name: Krivelevich, Michael last_name: Krivelevich - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: ama: Krivelevich M, Kwan MA, Sudakov B. Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 2017;31(1):155-171. doi:10.1137/15m1032910 apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2017). Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/15m1032910 chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” SIAM Journal on Discrete Mathematics. Society for Industrial & Applied Mathematics, 2017. https://doi.org/10.1137/15m1032910. ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Bounded-degree spanning trees in randomly perturbed graphs,” SIAM Journal on Discrete Mathematics, vol. 31, no. 1. Society for Industrial & Applied Mathematics, pp. 155–171, 2017. ista: Krivelevich M, Kwan MA, Sudakov B. 2017. Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 31(1), 155–171. mla: Krivelevich, Michael, et al. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” SIAM Journal on Discrete Mathematics, vol. 31, no. 1, Society for Industrial & Applied Mathematics, 2017, pp. 155–71, doi:10.1137/15m1032910. short: M. Krivelevich, M.A. Kwan, B. Sudakov, SIAM Journal on Discrete Mathematics 31 (2017) 155–171. date_created: 2021-06-22T12:26:25Z date_published: 2017-01-12T00:00:00Z date_updated: 2023-02-23T14:02:05Z day: '12' doi: 10.1137/15m1032910 extern: '1' external_id: arxiv: - '1507.07960' intvolume: ' 31' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.07960 month: '01' oa: 1 oa_version: Preprint page: 155-171 publication: SIAM Journal on Discrete Mathematics publication_identifier: eissn: - 1095-7146 issn: - 0895-4801 publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Bounded-degree spanning trees in randomly perturbed graphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 31 year: '2017' ... --- _id: '9588' abstract: - lang: eng text: 'Consider the sum X(ξ)=∑ni=1aiξi , where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2 ). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x] . In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.' article_processing_charge: No article_type: original author: - first_name: Afonso S. full_name: Bandeira, Afonso S. last_name: Bandeira - first_name: Asaf full_name: Ferber, Asaf last_name: Ferber - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 citation: ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood–Offord problem. Advances in Mathematics. 2017;319:292-312. doi:10.1016/j.aim.2017.08.031 apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood–Offord problem. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2017.08.031 chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood–Offord Problem.” Advances in Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.aim.2017.08.031. ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood–Offord problem,” Advances in Mathematics, vol. 319. Elsevier, pp. 292–312, 2017. ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood–Offord problem. Advances in Mathematics. 319, 292–312. mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood–Offord Problem.” Advances in Mathematics, vol. 319, Elsevier, 2017, pp. 292–312, doi:10.1016/j.aim.2017.08.031. short: A.S. Bandeira, A. Ferber, M.A. Kwan, Advances in Mathematics 319 (2017) 292–312. date_created: 2021-06-22T11:51:27Z date_published: 2017-10-15T00:00:00Z date_updated: 2023-02-23T14:01:57Z day: '15' doi: 10.1016/j.aim.2017.08.031 extern: '1' external_id: arxiv: - '1609.08136' intvolume: ' 319' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.08136 month: '10' oa: 1 oa_version: Preprint page: 292-312 publication: Advances in Mathematics publication_identifier: issn: - 0001-8708 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Resilience for the Littlewood–Offord problem type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 319 year: '2017' ... --- _id: '9589' abstract: - lang: eng text: We give an asymptotic expression for the expected number of spanning trees in a random graph with a given degree sequence , provided that the number of edges is at least , where is the maximum degree. A key part of our argument involves establishing a concentration result for a certain family of functions over random trees with given degrees, using Prüfer codes. article_processing_charge: No article_type: original author: - first_name: Catherine full_name: Greenhill, Catherine last_name: Greenhill - first_name: Mikhail full_name: Isaev, Mikhail last_name: Isaev - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Brendan D. full_name: McKay, Brendan D. last_name: McKay citation: ama: Greenhill C, Isaev M, Kwan MA, McKay BD. The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. 2017;63:6-25. doi:10.1016/j.ejc.2017.02.003 apa: Greenhill, C., Isaev, M., Kwan, M. A., & McKay, B. D. (2017). The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. Elsevier. https://doi.org/10.1016/j.ejc.2017.02.003 chicago: Greenhill, Catherine, Mikhail Isaev, Matthew Alan Kwan, and Brendan D. McKay. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” European Journal of Combinatorics. Elsevier, 2017. https://doi.org/10.1016/j.ejc.2017.02.003. ieee: C. Greenhill, M. Isaev, M. A. Kwan, and B. D. McKay, “The average number of spanning trees in sparse graphs with given degrees,” European Journal of Combinatorics, vol. 63. Elsevier, pp. 6–25, 2017. ista: Greenhill C, Isaev M, Kwan MA, McKay BD. 2017. The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. 63, 6–25. mla: Greenhill, Catherine, et al. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” European Journal of Combinatorics, vol. 63, Elsevier, 2017, pp. 6–25, doi:10.1016/j.ejc.2017.02.003. short: C. Greenhill, M. Isaev, M.A. Kwan, B.D. McKay, European Journal of Combinatorics 63 (2017) 6–25. date_created: 2021-06-22T12:18:59Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-23T14:02:00Z day: '01' doi: 10.1016/j.ejc.2017.02.003 extern: '1' external_id: arxiv: - '1606.01586' intvolume: ' 63' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.ejc.2017.02.003 month: '06' oa: 1 oa_version: Published Version page: 6-25 publication: European Journal of Combinatorics publication_identifier: issn: - 0195-6698 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The average number of spanning trees in sparse graphs with given degrees type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 63 year: '2017' ... --- _id: '963' abstract: - lang: eng text: 'Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ' alternative_title: - LIPIcs article_number: '37' author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Shibashis full_name: Guha, Shibashis last_name: Guha - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37' apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37' chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37. ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.' ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.' mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37. short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:49:26Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-23T12:35:50Z day: '01' ddc: - '004' department: - _id: ToHe doi: 10.4230/LIPIcs.MFCS.2017.37 file: - access_level: open_access checksum: f55eaf7f3c36ea07801112acfedd17d5 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:10Z date_updated: 2020-07-14T12:48:18Z file_id: '5059' file_name: IST-2017-829-v1+1_mfcs-cr.pdf file_size: 369730 relation: main_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6438' pubrep_id: '829' quality_controlled: '1' related_material: record: - id: '6005' relation: later_version status: public scopus_import: 1 status: public title: Timed network games with clocks 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) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '9709' abstract: - lang: eng text: Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina. article_processing_charge: No author: - first_name: Jason full_name: Prentice, Jason last_name: Prentice - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Mark full_name: Ioffe, Mark last_name: Ioffe - first_name: Adrianna full_name: Loback, Adrianna last_name: Loback - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc' apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc' chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.' ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.' ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.' mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.' short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017). date_created: 2021-07-23T11:34:34Z date_published: 2017-10-18T00:00:00Z date_updated: 2023-02-21T16:34:41Z day: '18' department: - _id: GaTk doi: 10.5061/dryad.1f1rc main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.1f1rc month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1197' relation: used_in_publication status: public status: public title: 'Data from: Error-robust modes of the retinal population code' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '541' abstract: - lang: eng text: 'While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed.' article_number: e1007122 author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122. ieee: N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122. mla: Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017). date_created: 2018-12-11T11:47:04Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T14:10:34Z day: '18' ddc: - '576' - '579' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122 ec_funded: 1 file: - access_level: open_access checksum: 22426d9382f21554bad5fa5967afcfd0 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:35Z date_updated: 2020-07-14T12:46:46Z file_id: '5088' file_name: IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf file_size: 1308475 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' intvolume: ' 13' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS Genetics publication_identifier: issn: - '15537390' publication_status: published publisher: Public Library of Science publist_id: '7275' pubrep_id: '959' quality_controlled: '1' related_material: record: - id: '9844' relation: research_data status: public - id: '9845' relation: research_data status: public - id: '9846' relation: research_data status: public scopus_import: 1 status: public title: Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '9847' abstract: - lang: eng text: information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data article_processing_charge: No author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Pleska M, Guet CC. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. 2017. doi:10.6084/m9.figshare.5633917.v1 apa: Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1 chicago: Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1. ieee: M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification.” The Royal Society, 2017. ista: Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification, The Royal Society, 10.6084/m9.figshare.5633917.v1. mla: Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1. short: M. Pleska, C.C. Guet, (2017). date_created: 2021-08-09T13:54:38Z date_published: 2017-11-27T00:00:00Z date_updated: 2023-02-23T12:29:44Z day: '27' department: - _id: CaGu doi: 10.6084/m9.figshare.5633917.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.5633917.v1 month: '11' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '561' relation: used_in_publication status: public status: public title: Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9845' abstract: - lang: eng text: "Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells" article_processing_charge: No author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017. ieee: N. Nikolic et al., “Mathematical model.” Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017. mla: Nikolic, Nela, et al. Mathematical Model. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s017. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017). date_created: 2021-08-09T13:31:51Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T12:25:04Z day: '18' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122.s017 month: '12' oa_version: None publisher: Public Library of Science related_material: record: - id: '541' relation: used_in_publication status: public status: public title: Mathematical model type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9849' abstract: - lang: eng text: This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:10.1371/journal.pcbi.1005609.s001 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, 10.1371/journal.pcbi.1005609.s001. mla: Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:02:34Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: NiBa - _id: CaGu doi: 10.1371/journal.pcbi.1005609.s001 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Modelling and simulation details type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9850' abstract: - lang: eng text: In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, 10.1371/journal.pcbi.1005609.s002. mla: Lukacisinova, Marta, et al. Extensions of the Model. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:05:24Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: CaGu - _id: NiBa doi: 10.1371/journal.pcbi.1005609.s002 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Extensions of the model type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9846' article_processing_charge: No author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:10.1371/journal.pgen.1007122.s016 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s016 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s016. ieee: N. Nikolic et al., “Supplementary methods.” Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Supplementary methods, Public Library of Science, 10.1371/journal.pgen.1007122.s016. mla: Nikolic, Nela, et al. Supplementary Methods. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s016. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017). date_created: 2021-08-09T13:35:17Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T12:25:04Z day: '18' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122.s016 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '541' relation: used_in_publication status: public status: public title: Supplementary methods type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '680' abstract: - lang: eng text: In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics. article_number: e1005582 author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Paul full_name: Masset, Paul last_name: Masset - first_name: Boris full_name: Gutkin, Boris last_name: Gutkin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582 apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582 chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582. ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” PLoS Computational Biology, vol. 13, no. 6. Public Library of Science, 2017. ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582. mla: Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582. short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017). date_created: 2018-12-11T11:47:53Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-23T14:10:54Z day: '01' ddc: - '571' department: - _id: GaTk doi: 10.1371/journal.pcbi.1005582 file: - access_level: open_access checksum: 796a1026076af6f4405a47d985bc7b68 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:47Z date_updated: 2020-07-14T12:47:40Z file_id: '4645' file_name: IST-2017-898-v1+1_journal.pcbi.1005582.pdf file_size: 14555676 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 13' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_identifier: issn: - 1553734X publication_status: published publisher: Public Library of Science publist_id: '7035' pubrep_id: '898' quality_controlled: '1' related_material: record: - id: '9855' relation: research_data status: public scopus_import: 1 status: public title: Sensory noise predicts divisive reshaping of receptive fields 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '9851' abstract: - lang: eng text: Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003. mla: Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:08:14Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: CaGu - _id: NiBa doi: 10.1371/journal.pcbi.1005609.s003 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Heuristic prediction for multiple stresses type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9852' abstract: - lang: eng text: We show how different combination strategies affect the fraction of individuals that are multi-resistant. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004. mla: Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:11:40Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: CaGu - _id: NiBa doi: 10.1371/journal.pcbi.1005609.s004 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Resistance frequencies for different combination strategies type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9855' abstract: - lang: eng text: Includes derivation of optimal estimation algorithm, generalisation to non-poisson noise statistics, correlated input noise, and implementation of in a multi-layer neural network. article_processing_charge: No author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Paul full_name: Masset, Paul last_name: Masset - first_name: Boris full_name: Gutkin, Boris last_name: Gutkin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001 apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001 chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001. ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017. ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public Library of Science, 10.1371/journal.pcbi.1005582.s001. mla: Chalk, Matthew J., et al. Supplementary Appendix. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582.s001. short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017). date_created: 2021-08-10T07:05:10Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-23T12:52:17Z day: '01' department: - _id: GaTk doi: 10.1371/journal.pcbi.1005582.s001 month: '06' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '680' relation: used_in_publication status: public status: public title: Supplementary appendix type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '8423' abstract: - lang: eng text: In this paper we show that for a generic strictly convex domain, one can recover the eigendata corresponding to Aubry–Mather periodic orbits of the induced billiard map from the (maximal) marked length spectrum of the domain. article_processing_charge: No article_type: original author: - first_name: Guan full_name: Huang, Guan last_name: Huang - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Alfonso full_name: Sorrentino, Alfonso last_name: Sorrentino citation: ama: Huang G, Kaloshin V, Sorrentino A. On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. 2017;167(1):175-209. doi:10.1215/00127094-2017-0038 apa: Huang, G., Kaloshin, V., & Sorrentino, A. (2017). On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2017-0038 chicago: Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” Duke Mathematical Journal. Duke University Press, 2017. https://doi.org/10.1215/00127094-2017-0038. ieee: G. Huang, V. Kaloshin, and A. Sorrentino, “On the marked length spectrum of generic strictly convex billiard tables,” Duke Mathematical Journal, vol. 167, no. 1. Duke University Press, pp. 175–209, 2017. ista: Huang G, Kaloshin V, Sorrentino A. 2017. On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. 167(1), 175–209. mla: Huang, Guan, et al. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” Duke Mathematical Journal, vol. 167, no. 1, Duke University Press, 2017, pp. 175–209, doi:10.1215/00127094-2017-0038. short: G. Huang, V. Kaloshin, A. Sorrentino, Duke Mathematical Journal 167 (2017) 175–209. date_created: 2020-09-17T10:42:42Z date_published: 2017-12-08T00:00:00Z date_updated: 2021-01-12T08:19:11Z day: '08' doi: 10.1215/00127094-2017-0038 extern: '1' external_id: arxiv: - '1603.08838' intvolume: ' 167' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1603.08838 month: '12' oa: 1 oa_version: Preprint page: 175-209 publication: Duke Mathematical Journal publication_identifier: issn: - 0012-7094 publication_status: published publisher: Duke University Press quality_controlled: '1' status: public title: On the marked length spectrum of generic strictly convex billiard tables type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 167 year: '2017' ... --- _id: '8427' abstract: - lang: eng text: We show that any sufficiently (finitely) smooth ℤ₂-symmetric strictly convex domain sufficiently close to a circle is dynamically spectrally rigid; i.e., all deformations among domains in the same class that preserve the length of all periodic orbits of the associated billiard flow must necessarily be isometric deformations. This gives a partial answer to a question of P. Sarnak. article_processing_charge: No article_type: original author: - first_name: Jacopo full_name: De Simoi, Jacopo last_name: De Simoi - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Qiaoling full_name: Wei, Qiaoling last_name: Wei citation: ama: De Simoi J, Kaloshin V, Wei Q. Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics. 2017;186(1):277-314. doi:10.4007/annals.2017.186.1.7 apa: De Simoi, J., Kaloshin, V., & Wei, Q. (2017). Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics. Annals of Mathematics. https://doi.org/10.4007/annals.2017.186.1.7 chicago: De Simoi, Jacopo, Vadim Kaloshin, and Qiaoling Wei. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” Annals of Mathematics. Annals of Mathematics, 2017. https://doi.org/10.4007/annals.2017.186.1.7. ieee: J. De Simoi, V. Kaloshin, and Q. Wei, “Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle,” Annals of Mathematics, vol. 186, no. 1. Annals of Mathematics, pp. 277–314, 2017. ista: De Simoi J, Kaloshin V, Wei Q. 2017. Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics. 186(1), 277–314. mla: De Simoi, Jacopo, et al. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” Annals of Mathematics, vol. 186, no. 1, Annals of Mathematics, 2017, pp. 277–314, doi:10.4007/annals.2017.186.1.7. short: J. De Simoi, V. Kaloshin, Q. Wei, Annals of Mathematics 186 (2017) 277–314. date_created: 2020-09-17T10:46:42Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:19:12Z day: '01' doi: 10.4007/annals.2017.186.1.7 extern: '1' external_id: arxiv: - '1606.00230' intvolume: ' 186' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.00230 month: '07' oa: 1 oa_version: Preprint page: 277-314 publication: Annals of Mathematics publication_identifier: issn: - 0003-486X publication_status: published publisher: Annals of Mathematics quality_controlled: '1' status: public title: Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 186 year: '2017' ... --- _id: '8449' abstract: - lang: eng text: Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein. article_processing_charge: No article_type: original author: - first_name: Enrico full_name: Rennella, Enrico last_name: Rennella - first_name: Tomáš full_name: Sára, Tomáš last_name: Sára - first_name: Michael full_name: Juen, Michael last_name: Juen - first_name: Christoph full_name: Wunderlich, Christoph last_name: Wunderlich - first_name: Lionel full_name: Imbert, Lionel last_name: Imbert - first_name: Zsofia full_name: Solyom, Zsofia last_name: Solyom - first_name: Adrien full_name: Favier, Adrien last_name: Favier - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Robert full_name: Konrat, Robert last_name: Konrat - first_name: Christoph full_name: Kreutz, Christoph last_name: Kreutz - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research. 2017;45(7):4255-4268. doi:10.1093/nar/gkx044 apa: Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., … Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkx044 chicago: Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” Nucleic Acids Research. Oxford University Press, 2017. https://doi.org/10.1093/nar/gkx044. ieee: E. Rennella et al., “RNA binding and chaperone activity of the E.coli cold-shock protein CspA,” Nucleic Acids Research, vol. 45, no. 7. Oxford University Press, pp. 4255–4268, 2017. ista: Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research. 45(7), 4255–4268. mla: Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” Nucleic Acids Research, vol. 45, no. 7, Oxford University Press, 2017, pp. 4255–68, doi:10.1093/nar/gkx044. short: E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier, I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic Acids Research 45 (2017) 4255–4268. date_created: 2020-09-18T10:06:34Z date_published: 2017-04-20T00:00:00Z date_updated: 2021-01-12T08:19:20Z day: '20' doi: 10.1093/nar/gkx044 extern: '1' intvolume: ' 45' issue: '7' language: - iso: eng month: '04' oa_version: None page: 4255-4268 publication: Nucleic Acids Research publication_identifier: issn: - 0305-1048 - 1362-4962 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: RNA binding and chaperone activity of the E.coli cold-shock protein CspA type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2017' ... --- _id: '8447' abstract: - lang: eng text: 'Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility.' article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Petra full_name: Rovó, Petra last_name: Rovó - first_name: Vilius full_name: Kurauskas, Vilius last_name: Kurauskas - first_name: Rasmus full_name: Linser, Rasmus last_name: Linser - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 2017;87(10):86-95. doi:10.1016/j.ssnmr.2017.04.002' apa: 'Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., & Schanda, P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.ssnmr.2017.04.002' chicago: 'Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser, and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” Solid State Nuclear Magnetic Resonance. Elsevier, 2017. https://doi.org/10.1016/j.ssnmr.2017.04.002.' ieee: 'D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda, “Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals,” Solid State Nuclear Magnetic Resonance, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.' ista: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 87(10), 86–95.' mla: 'Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” Solid State Nuclear Magnetic Resonance, vol. 87, no. 10, Elsevier, 2017, pp. 86–95, doi:10.1016/j.ssnmr.2017.04.002.' short: D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid State Nuclear Magnetic Resonance 87 (2017) 86–95. date_created: 2020-09-18T10:06:18Z date_published: 2017-10-01T00:00:00Z date_updated: 2021-01-12T08:19:20Z day: '01' doi: 10.1016/j.ssnmr.2017.04.002 extern: '1' intvolume: ' 87' issue: '10' keyword: - Nuclear and High Energy Physics - Instrumentation - General Chemistry - Radiation language: - iso: eng month: '10' oa_version: None page: 86-95 publication: Solid State Nuclear Magnetic Resonance publication_identifier: issn: - 0926-2040 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2017' ... --- _id: '8448' abstract: - lang: eng text: We present an improved fast mixing device based on the rapid mixing of two solutions inside the NMR probe, as originally proposed by Hore and coworkers (J. Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium studies of molecular kinetics by multidimensional real-time NMR spectrsocopy. The novelty of this device is that it allows removing the injector from the NMR detection volume after mixing, and thus provides good magnetic field homogeneity independently of the initial sample volume placed in the NMR probe. The apparatus is simple to build, inexpensive, and can be used without any hardware modification on any type of liquid-state NMR spectrometer. We demonstrate the performance of our fast mixing device in terms of improved magnetic field homogeneity, and show an application to the study of protein folding and the structural characterization of transiently populated folding intermediates. article_processing_charge: No article_type: original author: - first_name: Rémi full_name: Franco, Rémi last_name: Franco - first_name: Adrien full_name: Favier, Adrien last_name: Favier - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for real-time NMR applications. Journal of Magnetic Resonance. 2017;281(8):125-129. doi:10.1016/j.jmr.2017.05.016 apa: Franco, R., Favier, A., Schanda, P., & Brutscher, B. (2017). Optimized fast mixing device for real-time NMR applications. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2017.05.016 chicago: Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized Fast Mixing Device for Real-Time NMR Applications.” Journal of Magnetic Resonance. Elsevier, 2017. https://doi.org/10.1016/j.jmr.2017.05.016. ieee: R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing device for real-time NMR applications,” Journal of Magnetic Resonance, vol. 281, no. 8. Elsevier, pp. 125–129, 2017. ista: Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129. mla: Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.” Journal of Magnetic Resonance, vol. 281, no. 8, Elsevier, 2017, pp. 125–29, doi:10.1016/j.jmr.2017.05.016. short: R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 281 (2017) 125–129. date_created: 2020-09-18T10:06:27Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:19:20Z day: '01' doi: 10.1016/j.jmr.2017.05.016 extern: '1' intvolume: ' 281' issue: '8' keyword: - Nuclear and High Energy Physics - Biophysics - Biochemistry - Condensed Matter Physics language: - iso: eng month: '08' oa_version: None page: 125-129 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Optimized fast mixing device for real-time NMR applications type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 281 year: '2017' ... --- _id: '8451' abstract: - lang: eng text: The structure, dynamics, and function of membrane proteins are intimately linked to the properties of the membrane environment in which the proteins are embedded. For structural and biophysical characterization, membrane proteins generally need to be extracted from the membrane and reconstituted in a suitable membrane‐mimicking environment. Ensuring functional and structural integrity in these environments is often a major concern. The styrene/maleic acid co‐polymer has recently been shown to be able to extract lipid/membrane protein patches directly from native membranes to form nanosize discoidal proteolipid particles, also referred to as native nanodiscs. In this work, we show that high‐resolution solid‐state NMR spectra can be obtained from an integral membrane protein in native nanodiscs, as exemplified by the 2×34 kDa bacterial cation diffusion facilitator CzcD. article_processing_charge: No article_type: original author: - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Jonas M. full_name: Dörr, Jonas M. last_name: Dörr - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: J. Antoinette full_name: Killian, J. Antoinette last_name: Killian - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. Angewandte Chemie International Edition. 2017;56(9):2508-2512. doi:10.1002/anie.201610441 apa: Bersch, B., Dörr, J. M., Hessel, A., Killian, J. A., & Schanda, P. (2017). Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201610441 chicago: Bersch, Beate, Jonas M. Dörr, Audrey Hessel, J. Antoinette Killian, and Paul Schanda. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International Edition. Wiley, 2017. https://doi.org/10.1002/anie.201610441. ieee: B. Bersch, J. M. Dörr, A. Hessel, J. A. Killian, and P. Schanda, “Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs,” Angewandte Chemie International Edition, vol. 56, no. 9. Wiley, pp. 2508–2512, 2017. ista: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. 2017. Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. Angewandte Chemie International Edition. 56(9), 2508–2512. mla: Bersch, Beate, et al. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International Edition, vol. 56, no. 9, Wiley, 2017, pp. 2508–12, doi:10.1002/anie.201610441. short: B. Bersch, J.M. Dörr, A. Hessel, J.A. Killian, P. Schanda, Angewandte Chemie International Edition 56 (2017) 2508–2512. date_created: 2020-09-18T10:06:50Z date_published: 2017-01-27T00:00:00Z date_updated: 2021-01-12T08:19:22Z day: '27' doi: 10.1002/anie.201610441 extern: '1' intvolume: ' 56' issue: '9' language: - iso: eng month: '01' oa_version: None page: 2508-2512 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 56 year: '2017' ... --- _id: '8450' abstract: - lang: eng text: Methyl groups are very useful probes of structure, dynamics, and interactions in protein NMR spectroscopy. In particular, methyl-directed experiments provide high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking environment. In this chapter, we discuss the approach for labeling methyl groups in E. coli-based protein expression, as exemplified with the mitochondrial carrier GGC. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Vilius full_name: Kurauskas, Vilius last_name: Kurauskas - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Remy full_name: Sounier, Remy last_name: Sounier citation: ama: 'Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: Membrane Protein Structure and Function Characterization. Vol 1635. Springer Nature; 2017:109-123. doi:10.1007/978-1-4939-7151-0_6' apa: Kurauskas, V., Schanda, P., & Sounier, R. (2017). Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In Membrane protein structure and function characterization (Vol. 1635, pp. 109–123). Springer Nature. https://doi.org/10.1007/978-1-4939-7151-0_6 chicago: Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” In Membrane Protein Structure and Function Characterization, 1635:109–23. Springer Nature, 2017. https://doi.org/10.1007/978-1-4939-7151-0_6. ieee: V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling strategies for NMR studies of membrane proteins,” in Membrane protein structure and function characterization, vol. 1635, Springer Nature, 2017, pp. 109–123. ista: 'Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: Membrane protein structure and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.' mla: Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” Membrane Protein Structure and Function Characterization, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:10.1007/978-1-4939-7151-0_6. short: V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and Function Characterization, Springer Nature, 2017, pp. 109–123. date_created: 2020-09-18T10:06:44Z date_published: 2017-07-29T00:00:00Z date_updated: 2022-08-26T09:14:20Z day: '29' doi: 10.1007/978-1-4939-7151-0_6 extern: '1' intvolume: ' 1635' language: - iso: eng month: '07' oa_version: None page: 109-123 publication: Membrane protein structure and function characterization publication_identifier: isbn: - '9781493971497' - '9781493971510' issn: - 1064-3745 - 1940-6029 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Methyl-specific isotope labeling strategies for NMR studies of membrane proteins type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1635 year: '2017' ... --- _id: '9137' abstract: - lang: eng text: Pools of air cooled by partial rain evaporation span up to several hundreds of kilometers in nature and typically last less than 1 day, ultimately losing their identity to the large-scale flow. These fundamentally differ in character from the radiatively-driven dry pools defining convective aggregation. Advancement in remote sensing and in computer capabilities has promoted exploration of how precipitation-induced cold pool processes modify the convective spectrum and life cycle. This contribution surveys current understanding of such cold pools over the tropical and subtropical oceans. In shallow convection with low rain rates, the cold pools moisten, preserving the near-surface equivalent potential temperature or increasing it if the surface moisture fluxes cannot ventilate beyond the new surface layer; both conditions indicate downdraft origin air from within the boundary layer. When rain rates exceed ∼ 2 mm h−1, convective-scale downdrafts can bring down drier air of lower equivalent potential temperature from above the boundary layer. The resulting density currents facilitate the lifting of locally thermodynamically favorable air and can impose an arc-shaped mesoscale cloud organization. This organization allows clouds capable of reaching 4–5 km within otherwise dry environments. These are more commonly observed in the northern hemisphere trade wind regime, where the flow to the intertropical convergence zone is unimpeded by the equator. Their near-surface air properties share much with those shown from cold pools sampled in the equatorial Indian Ocean. Cold pools are most effective at influencing the mesoscale organization when the atmosphere is moist in the lower free troposphere and dry above, suggesting an optimal range of water vapor paths. Outstanding questions on the relationship between cold pools, their accompanying moisture distribution and cloud cover are detailed further. Near-surface water vapor rings are documented in one model inside but near the cold pool edge; these are not consistent with observations, but do improve with smaller horizontal grid spacings. article_processing_charge: No article_type: original author: - first_name: Paquita full_name: Zuidema, Paquita last_name: Zuidema - first_name: Giuseppe full_name: Torri, Giuseppe last_name: Torri - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Arunchandra full_name: Chandra, Arunchandra last_name: Chandra citation: ama: Zuidema P, Torri G, Muller CJ, Chandra A. A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. Surveys in Geophysics. 2017;38(6):1283-1305. doi:10.1007/s10712-017-9447-x apa: Zuidema, P., Torri, G., Muller, C. J., & Chandra, A. (2017). A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. Surveys in Geophysics. Springer Nature. https://doi.org/10.1007/s10712-017-9447-x chicago: Zuidema, Paquita, Giuseppe Torri, Caroline J Muller, and Arunchandra Chandra. “A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their Interactions with the Larger-Scale Environment.” Surveys in Geophysics. Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9447-x. ieee: P. Zuidema, G. Torri, C. J. Muller, and A. Chandra, “A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment,” Surveys in Geophysics, vol. 38, no. 6. Springer Nature, pp. 1283–1305, 2017. ista: Zuidema P, Torri G, Muller CJ, Chandra A. 2017. A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. Surveys in Geophysics. 38(6), 1283–1305. mla: Zuidema, Paquita, et al. “A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their Interactions with the Larger-Scale Environment.” Surveys in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1283–305, doi:10.1007/s10712-017-9447-x. short: P. Zuidema, G. Torri, C.J. Muller, A. Chandra, Surveys in Geophysics 38 (2017) 1283–1305. date_created: 2021-02-15T14:20:07Z date_published: 2017-11-14T00:00:00Z date_updated: 2022-01-24T12:41:45Z day: '14' doi: 10.1007/s10712-017-9447-x extern: '1' intvolume: ' 38' issue: '6' keyword: - Geochemistry and Petrology - Geophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10712-017-9447-x month: '11' oa: 1 oa_version: Published Version page: 1283-1305 publication: Surveys in Geophysics publication_identifier: issn: - 0169-3298 - 1573-0956 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 38 year: '2017' ... --- _id: '9138' abstract: - lang: eng text: Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network. article_processing_charge: No article_type: original author: - first_name: Christopher E. full_name: Holloway, Christopher E. last_name: Holloway - first_name: Allison A. full_name: Wing, Allison A. last_name: Wing - first_name: Sandrine full_name: Bony, Sandrine last_name: Bony - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Hirohiko full_name: Masunaga, Hirohiko last_name: Masunaga - first_name: Tristan S. full_name: L’Ecuyer, Tristan S. last_name: L’Ecuyer - first_name: David D. full_name: Turner, David D. last_name: Turner - first_name: Paquita full_name: Zuidema, Paquita last_name: Zuidema citation: ama: Holloway CE, Wing AA, Bony S, et al. Observing convective aggregation. Surveys in Geophysics. 2017;38(6):1199-1236. doi:10.1007/s10712-017-9419-1 apa: Holloway, C. E., Wing, A. A., Bony, S., Muller, C. J., Masunaga, H., L’Ecuyer, T. S., … Zuidema, P. (2017). Observing convective aggregation. Surveys in Geophysics. Springer Nature. https://doi.org/10.1007/s10712-017-9419-1 chicago: Holloway, Christopher E., Allison A. Wing, Sandrine Bony, Caroline J Muller, Hirohiko Masunaga, Tristan S. L’Ecuyer, David D. Turner, and Paquita Zuidema. “Observing Convective Aggregation.” Surveys in Geophysics. Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9419-1. ieee: C. E. Holloway et al., “Observing convective aggregation,” Surveys in Geophysics, vol. 38, no. 6. Springer Nature, pp. 1199–1236, 2017. ista: Holloway CE, Wing AA, Bony S, Muller CJ, Masunaga H, L’Ecuyer TS, Turner DD, Zuidema P. 2017. Observing convective aggregation. Surveys in Geophysics. 38(6), 1199–1236. mla: Holloway, Christopher E., et al. “Observing Convective Aggregation.” Surveys in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1199–236, doi:10.1007/s10712-017-9419-1. short: C.E. Holloway, A.A. Wing, S. Bony, C.J. Muller, H. Masunaga, T.S. L’Ecuyer, D.D. Turner, P. Zuidema, Surveys in Geophysics 38 (2017) 1199–1236. date_created: 2021-02-15T14:20:38Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-01-24T12:43:13Z day: '01' doi: 10.1007/s10712-017-9419-1 extern: '1' intvolume: ' 38' issue: '6' keyword: - Geochemistry and Petrology - Geophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10712-017-9419-1 month: '11' oa: 1 oa_version: Published Version page: 1199-1236 publication: Surveys in Geophysics publication_identifier: issn: - 0169-3298 - 1573-0956 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Observing convective aggregation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 38 year: '2017' ... --- _id: '9139' abstract: - lang: eng text: Organized convection in the tropics occurs across a range of spatial and temporal scales and strongly influences cloud cover and humidity. One mode of organization found is “self-aggregation,” in which moist convection spontaneously organizes into one or several isolated clusters despite spatially homogeneous boundary conditions and forcing. Self-aggregation is driven by interactions between clouds, moisture, radiation, surface fluxes, and circulation, and occurs in a wide variety of idealized simulations of radiative–convective equilibrium. Here we provide a review of convective self-aggregation in numerical simulations, including its character, causes, and effects. We describe the evolution of self-aggregation including its time and length scales and the physical mechanisms leading to its triggering and maintenance, and we also discuss possible links to climate and climate change. article_processing_charge: No article_type: original author: - first_name: Allison A. full_name: Wing, Allison A. last_name: Wing - first_name: Kerry full_name: Emanuel, Kerry last_name: Emanuel - first_name: Christopher E. full_name: Holloway, Christopher E. last_name: Holloway - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: ama: 'Wing AA, Emanuel K, Holloway CE, Muller CJ. Convective self-aggregation in numerical simulations: A review. Surveys in Geophysics. 2017;38(6):1173-1197. doi:10.1007/s10712-017-9408-4' apa: 'Wing, A. A., Emanuel, K., Holloway, C. E., & Muller, C. J. (2017). Convective self-aggregation in numerical simulations: A review. Surveys in Geophysics. Springer Nature. https://doi.org/10.1007/s10712-017-9408-4' chicago: 'Wing, Allison A., Kerry Emanuel, Christopher E. Holloway, and Caroline J Muller. “Convective Self-Aggregation in Numerical Simulations: A Review.” Surveys in Geophysics. Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9408-4.' ieee: 'A. A. Wing, K. Emanuel, C. E. Holloway, and C. J. Muller, “Convective self-aggregation in numerical simulations: A review,” Surveys in Geophysics, vol. 38, no. 6. Springer Nature, pp. 1173–1197, 2017.' ista: 'Wing AA, Emanuel K, Holloway CE, Muller CJ. 2017. Convective self-aggregation in numerical simulations: A review. Surveys in Geophysics. 38(6), 1173–1197.' mla: 'Wing, Allison A., et al. “Convective Self-Aggregation in Numerical Simulations: A Review.” Surveys in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1173–97, doi:10.1007/s10712-017-9408-4.' short: A.A. Wing, K. Emanuel, C.E. Holloway, C.J. Muller, Surveys in Geophysics 38 (2017) 1173–1197. date_created: 2021-02-15T14:20:56Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-01-24T12:42:36Z day: '01' doi: 10.1007/s10712-017-9408-4 extern: '1' intvolume: ' 38' issue: '6' keyword: - Geochemistry and Petrology - Geophysics language: - iso: eng month: '11' oa_version: None page: 1173-1197 publication: Surveys in Geophysics publication_identifier: issn: - 0169-3298 - 1573-0956 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Convective self-aggregation in numerical simulations: A review' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 38 year: '2017' ... --- _id: '9152' abstract: - lang: eng text: Previous numerical studies of the dissipation of internal tides in idealized settings suggest the existence of a critical latitude (~29°) where dissipation is enhanced. But observations only indicate a modest enhancement at this latitude. To resolve this difference between observational and numerical results, the authors study the latitudinal dependence of internal tides’ dissipation in more realistic conditions. In particular, the ocean is not a quiescent medium; the presence of large-scale currents or mesoscale eddies can impact the propagation and dissipation of internal tides. This paper investigates the impact of a weak background mean current in numerical simulations. The authors focus on the local dissipation of high spatial mode internal waves near their generation site. The vertical profile of dissipation and its variation with latitude without the mean current are consistent with earlier studies. But adding a weak mean current has a major impact on the latitudinal distribution of dissipation. The peak at the critical latitude disappears, and the dissipation is closer to a constant, albeit with two weak peaks at ~25° and ~35° latitude. This disappearance results from the Doppler shift of the internal tides’ frequency, which hinders the nonlinear transfer of energy to small-scale secondary waves via the parametric subharmonic instability (PSI). The new two weak peaks correspond to the Doppler-shifted critical latitudes of the left- and right-propagating waves. The results are confirmed in simulations with simple sinusoidal topography. Thus, although nonlinear transfers via PSI are efficient at dissipating internal tides, the exact location of the dissipation is sensitive to large-scale oceanic conditions. article_processing_charge: No article_type: original author: - first_name: O. full_name: Richet, O. last_name: Richet - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: J.-M. full_name: Chomaz, J.-M. last_name: Chomaz citation: ama: Richet O, Muller CJ, Chomaz J-M. Impact of a mean current on the internal tide energy dissipation at the critical latitude. Journal of Physical Oceanography. 2017;47(6):1457-1472. doi:10.1175/jpo-d-16-0197.1 apa: Richet, O., Muller, C. J., & Chomaz, J.-M. (2017). Impact of a mean current on the internal tide energy dissipation at the critical latitude. Journal of Physical Oceanography. American Meteorological Society. https://doi.org/10.1175/jpo-d-16-0197.1 chicago: Richet, O., Caroline J Muller, and J.-M. Chomaz. “Impact of a Mean Current on the Internal Tide Energy Dissipation at the Critical Latitude.” Journal of Physical Oceanography. American Meteorological Society, 2017. https://doi.org/10.1175/jpo-d-16-0197.1. ieee: O. Richet, C. J. Muller, and J.-M. Chomaz, “Impact of a mean current on the internal tide energy dissipation at the critical latitude,” Journal of Physical Oceanography, vol. 47, no. 6. American Meteorological Society, pp. 1457–1472, 2017. ista: Richet O, Muller CJ, Chomaz J-M. 2017. Impact of a mean current on the internal tide energy dissipation at the critical latitude. Journal of Physical Oceanography. 47(6), 1457–1472. mla: Richet, O., et al. “Impact of a Mean Current on the Internal Tide Energy Dissipation at the Critical Latitude.” Journal of Physical Oceanography, vol. 47, no. 6, American Meteorological Society, 2017, pp. 1457–72, doi:10.1175/jpo-d-16-0197.1. short: O. Richet, C.J. Muller, J.-M. Chomaz, Journal of Physical Oceanography 47 (2017) 1457–1472. date_created: 2021-02-15T15:11:04Z date_published: 2017-06-01T00:00:00Z date_updated: 2022-01-24T13:36:31Z day: '01' doi: 10.1175/jpo-d-16-0197.1 extern: '1' intvolume: ' 47' issue: '6' keyword: - Oceanography language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1175/JPO-D-16-0197.1 month: '06' oa: 1 oa_version: Published Version page: 1457-1472 publication: Journal of Physical Oceanography publication_identifier: issn: - 0022-3670 - 1520-0485 publication_status: published publisher: American Meteorological Society quality_controlled: '1' status: public title: Impact of a mean current on the internal tide energy dissipation at the critical latitude type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 47 year: '2017' ... --- _id: '934' abstract: - lang: eng text: During puberty, the mouse mammary gland develops into a highly branched epithelial network. Owing to the absence of exclusive stem cell markers, the location, multiplicity, dynamics and fate of mammary stem cells (MaSCs), which drive branching morphogenesis, are unknown. Here we show that morphogenesis is driven by proliferative terminal end buds that terminate or bifurcate with near equal probability, in a stochastic and time-invariant manner, leading to a heterogeneous epithelial network. We show that the majority of terminal end bud cells function as highly proliferative, lineage-committed MaSCs that are heterogeneous in their expression profile and short-term contribution to ductal extension. Yet, through cell rearrangements during terminal end bud bifurcation, each MaSC is able to contribute actively to long-term growth. Our study shows that the behaviour of MaSCs is not directly linked to a single expression profile. Instead, morphogenesis relies upon lineage-restricted heterogeneous MaSC populations that function as single equipotent pools in the long term. author: - first_name: Colinda full_name: Scheele, Colinda last_name: Scheele - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Mauro full_name: Muraro, Mauro last_name: Muraro - first_name: Anoek full_name: Zomer, Anoek last_name: Zomer - first_name: Nathalia full_name: Langedijk, Nathalia last_name: Langedijk - first_name: Alexander full_name: Van Oudenaarden, Alexander last_name: Van Oudenaarden - first_name: Benjamin full_name: Simons, Benjamin last_name: Simons - first_name: Jacco full_name: Van Rheenen, Jacco last_name: Van Rheenen citation: ama: Scheele C, Hannezo EB, Muraro M, et al. Identity and dynamics of mammary stem cells during branching morphogenesis. Nature. 2017;542(7641):313-317. doi:10.1038/nature21046 apa: Scheele, C., Hannezo, E. B., Muraro, M., Zomer, A., Langedijk, N., Van Oudenaarden, A., … Van Rheenen, J. (2017). Identity and dynamics of mammary stem cells during branching morphogenesis. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21046 chicago: Scheele, Colinda, Edouard B Hannezo, Mauro Muraro, Anoek Zomer, Nathalia Langedijk, Alexander Van Oudenaarden, Benjamin Simons, and Jacco Van Rheenen. “Identity and Dynamics of Mammary Stem Cells during Branching Morphogenesis.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21046. ieee: C. Scheele et al., “Identity and dynamics of mammary stem cells during branching morphogenesis,” Nature, vol. 542, no. 7641. Nature Publishing Group, pp. 313–317, 2017. ista: Scheele C, Hannezo EB, Muraro M, Zomer A, Langedijk N, Van Oudenaarden A, Simons B, Van Rheenen J. 2017. Identity and dynamics of mammary stem cells during branching morphogenesis. Nature. 542(7641), 313–317. mla: Scheele, Colinda, et al. “Identity and Dynamics of Mammary Stem Cells during Branching Morphogenesis.” Nature, vol. 542, no. 7641, Nature Publishing Group, 2017, pp. 313–17, doi:10.1038/nature21046. short: C. Scheele, E.B. Hannezo, M. Muraro, A. Zomer, N. Langedijk, A. Van Oudenaarden, B. Simons, J. Van Rheenen, Nature 542 (2017) 313–317. date_created: 2018-12-11T11:49:17Z date_published: 2017-02-16T00:00:00Z date_updated: 2021-01-12T08:22:01Z day: '16' doi: 10.1038/nature21046 extern: '1' intvolume: ' 542' issue: '7641' language: - iso: eng month: '02' oa_version: None page: 313 - 317 publication: Nature publication_identifier: issn: - '00280836' publication_status: published publisher: Nature Publishing Group publist_id: '6505' quality_controlled: '1' status: public title: Identity and dynamics of mammary stem cells during branching morphogenesis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 542 year: '2017' ... --- _id: '936' abstract: - lang: eng text: Homeostatic replacement of epithelial cells from basal precursors is a multistep process involving progenitor cell specification, radial intercalation and, finally, apical surface emergence. Recent data demonstrate that actin-based pushing under the control of the formin protein Fmn1 drives apical emergence in nascent multiciliated epithelial cells (MCCs), but little else is known about this actin network or the control of Fmn1. Here, we explore the role of the small GTPase RhoA in MCC apical emergence. Disruption of RhoA function reduced the rate of apical surface expansion and decreased the final size of the apical domain. Analysis of cell shapes suggests that RhoA alters the balance of forces exerted on the MCC apical surface. Finally, quantitative time-lapse imaging and fluorescence recovery after photobleaching studies argue that RhoA works in concert with Fmn1 to control assembly of the specialized apical actin network in MCCs. These data provide new molecular insights into epithelial apical surface assembly and could also shed light on mechanisms of apical lumen formation author: - first_name: Jakub full_name: Sedzinski, Jakub last_name: Sedzinski - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Fan full_name: Tu, Fan last_name: Tu - first_name: Maté full_name: Biro, Maté last_name: Biro - first_name: John full_name: Wallingford, John last_name: Wallingford citation: ama: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. 2017;130(5). doi:10.1242/jcs.202234 apa: Sedzinski, J., Hannezo, E. B., Tu, F., Biro, M., & Wallingford, J. (2017). RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.202234 chicago: Sedzinski, Jakub, Edouard B Hannezo, Fan Tu, Maté Biro, and John Wallingford. “RhoA Regulates Actin Network Dynamics during Apical Surface Emergence in Multiciliated Epithelial Cells .” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.202234. ieee: J. Sedzinski, E. B. Hannezo, F. Tu, M. Biro, and J. Wallingford, “RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells ,” Journal of Cell Science, vol. 130, no. 5. Company of Biologists, 2017. ista: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. 2017. RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. 130(5). mla: Sedzinski, Jakub, et al. “RhoA Regulates Actin Network Dynamics during Apical Surface Emergence in Multiciliated Epithelial Cells .” Journal of Cell Science, vol. 130, no. 5, Company of Biologists, 2017, doi:10.1242/jcs.202234. short: J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Journal of Cell Science 130 (2017). date_created: 2018-12-11T11:49:17Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:22:02Z day: '01' doi: 10.1242/jcs.202234 extern: '1' intvolume: ' 130' issue: '5' language: - iso: eng month: '01' oa_version: None publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6507' quality_controlled: '1' status: public title: 'RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells ' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2017' ... --- _id: '937' abstract: - lang: eng text: During epithelial cytokinesis, the remodelling of adhesive cell-cell contacts between the dividing cell and its neighbours has profound implications for the integrity, arrangement and morphogenesis of proliferative tissues. In both vertebrates and invertebrates, this remodelling requires the activity of non-muscle myosin II (MyoII) in the interphasic cells neighbouring the dividing cell. However, the mechanisms that coordinate cytokinesis and MyoII activity in the neighbours are unknown. Here we show that in the Drosophila notum epithelium, each cell division is associated with a mechanosensing and transmission event that controls MyoII dynamics in neighbouring cells. We find that the ring pulling forces promote local junction elongation, which results in local E-cadherin dilution at the ingressing adherens junction. In turn, the reduction in E-cadherin concentration and the contractility of the neighbouring cells promote self-organized actomyosin flows, ultimately leading to accumulation of MyoII at the base of the ingressing junction. Although force transduction has been extensively studied in the context of adherens junction reinforcement to stabilize adhesive cell-cell contacts, we propose an alternative mechanosensing mechanism that coordinates actomyosin dynamics between epithelial cells and sustains the remodelling of the adherens junction in response to mechanical forces. author: - first_name: Diana full_name: Pinheiro, Diana last_name: Pinheiro - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Sophie full_name: Herszterg, Sophie last_name: Herszterg - first_name: Floris full_name: Bosveld, Floris last_name: Bosveld - first_name: Isabelle full_name: Gaugué, Isabelle last_name: Gaugué - first_name: Maria full_name: Balakireva, Maria last_name: Balakireva - first_name: Zhimin full_name: Wang, Zhimin last_name: Wang - first_name: Inês full_name: Cristo, Inês last_name: Cristo - first_name: Stéphane full_name: Rigaud, Stéphane last_name: Rigaud - first_name: Olga full_name: Markova, Olga last_name: Markova - first_name: Yohanns full_name: Bellaïche, Yohanns last_name: Bellaïche citation: ama: Pinheiro D, Hannezo EB, Herszterg S, et al. Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. 2017;545(7652):103-107. doi:10.1038/nature22041 apa: Pinheiro, D., Hannezo, E. B., Herszterg, S., Bosveld, F., Gaugué, I., Balakireva, M., … Bellaïche, Y. (2017). Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. Nature Publishing Group. https://doi.org/10.1038/nature22041 chicago: Pinheiro, Diana, Edouard B Hannezo, Sophie Herszterg, Floris Bosveld, Isabelle Gaugué, Maria Balakireva, Zhimin Wang, et al. “Transmission of Cytokinesis Forces via E Cadherin Dilution and Actomyosin Flows.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature22041. ieee: D. Pinheiro et al., “Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows,” Nature, vol. 545, no. 7652. Nature Publishing Group, pp. 103–107, 2017. ista: Pinheiro D, Hannezo EB, Herszterg S, Bosveld F, Gaugué I, Balakireva M, Wang Z, Cristo I, Rigaud S, Markova O, Bellaïche Y. 2017. Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. 545(7652), 103–107. mla: Pinheiro, Diana, et al. “Transmission of Cytokinesis Forces via E Cadherin Dilution and Actomyosin Flows.” Nature, vol. 545, no. 7652, Nature Publishing Group, 2017, pp. 103–07, doi:10.1038/nature22041. short: D. Pinheiro, E.B. Hannezo, S. Herszterg, F. Bosveld, I. Gaugué, M. Balakireva, Z. Wang, I. Cristo, S. Rigaud, O. Markova, Y. Bellaïche, Nature 545 (2017) 103–107. date_created: 2018-12-11T11:49:18Z date_published: 2017-05-04T00:00:00Z date_updated: 2021-01-12T08:22:02Z day: '04' doi: 10.1038/nature22041 extern: '1' intvolume: ' 545' issue: '7652' language: - iso: eng month: '05' oa_version: None page: 103 - 107 publication: Nature publication_identifier: issn: - '00280836' publication_status: published publisher: Nature Publishing Group publist_id: '6504' quality_controlled: '1' status: public title: Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 545 year: '2017' ... --- _id: '941' abstract: - lang: eng text: 'Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ ' author: - first_name: Xuan full_name: Le, Xuan last_name: Le - first_name: Duc Hiep full_name: Chu, Duc Hiep id: 3598E630-F248-11E8-B48F-1D18A9856A87 last_name: Chu - first_name: David full_name: Lo, David last_name: Lo - first_name: Claire full_name: Le Goues, Claire last_name: Le Goues - first_name: Willem full_name: Visser, Willem last_name: Visser citation: ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225' apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225' chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic  PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.' ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic  PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379.' ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.' mla: 'Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic  PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.' short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379. conference: end_date: 2017-07-14 location: Santa Barbara, CA, United States name: 'ISSTA: International Symposium on Software Testing and Analysis' start_date: 2017-07-10 date_created: 2018-12-11T11:49:19Z date_published: 2017-07-10T00:00:00Z date_updated: 2021-01-12T08:22:05Z day: '10' department: - _id: ToHe doi: 10.1145/3092703.3098225 language: - iso: eng month: '07' oa_version: None page: '376 - 379 ' project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis publication_status: published publisher: ACM publist_id: '6478' quality_controlled: '1' scopus_import: 1 status: public title: 'JFIX: Semantics-based repair of Java programs via symbolic PathFinder' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '9506' abstract: - lang: eng text: Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation. article_number: '87' article_processing_charge: No author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2 apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2 chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2. ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017. ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87. mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature, 2017, doi:10.1186/s13059-017-1230-2. short: D. Zilberman, Genome Biology 18 (2017). date_created: 2021-06-07T12:27:39Z date_published: 2017-05-09T00:00:00Z date_updated: 2021-12-14T07:55:02Z day: '09' ddc: - '570' department: - _id: DaZi doi: 10.1186/s13059-017-1230-2 extern: '1' external_id: pmid: - '28486944' file: - access_level: open_access checksum: 5a455ad914e7d225b1baa4ab07fd925e content_type: application/pdf creator: asandaue date_created: 2021-06-07T12:31:36Z date_updated: 2021-06-07T12:31:36Z file_id: '9507' file_name: 2017_GenomeBiology_Zilberman.pdf file_size: 278183 relation: main_file success: 1 file_date_updated: 2021-06-07T12:31:36Z has_accepted_license: '1' intvolume: ' 18' issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: eissn: - 1465-6906 issn: - 1474-760X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: An evolutionary case for functional gene body methylation in plants and animals 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) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 18 year: '2017' ... --- _id: '958' abstract: - lang: eng text: Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors. alternative_title: - Methods in Molecular Biology author: - first_name: Joshua full_name: Mitchell, Joshua last_name: Mitchell - first_name: William full_name: Zhang, William last_name: Zhang - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Megan full_name: O'Mara, Megan last_name: O'Mara - first_name: Colin full_name: Jackson, Colin last_name: Jackson citation: ama: 'Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6' apa: Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6 chicago: Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6. ieee: J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99. ista: 'Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99.' mla: Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6. short: J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99. date_created: 2018-12-11T11:49:24Z date_published: 2017-05-15T00:00:00Z date_updated: 2021-01-12T08:22:13Z day: '15' department: - _id: HaJa doi: 10.1007/978-1-4939-6940-1_6 editor: - first_name: Viktor full_name: Stein, Viktor last_name: Stein intvolume: ' 1596' language: - iso: eng month: '05' oa_version: None page: 89 - 99 publication: Synthetic Protein Switches publication_identifier: issn: - '10643745' publication_status: published publisher: Springer publist_id: '6450' quality_controlled: '1' scopus_import: 1 series_title: Synthetic Protein Switches status: public title: Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1596 year: '2017' ... --- _id: '9660' abstract: - lang: eng text: In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable. article_number: '104707' article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Gareth A. full_name: Tribello, Gareth A. last_name: Tribello - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: 'Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 2017;147(10). doi:10.1063/1.4997180' apa: 'Cheng, B., Tribello, G. A., & Ceriotti, M. (2017). The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4997180' chicago: 'Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4997180.' ieee: 'B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit,” The Journal of Chemical Physics, vol. 147, no. 10. AIP Publishing, 2017.' ista: 'Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 147(10), 104707.' mla: 'Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics, vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:10.1063/1.4997180.' short: B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147 (2017). date_created: 2021-07-15T08:13:29Z date_published: 2017-09-14T00:00:00Z date_updated: 2023-02-23T14:04:02Z day: '14' doi: 10.1063/1.4997180 extern: '1' external_id: arxiv: - '1703.06062' pmid: - '28915742' intvolume: ' 147' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html month: '09' oa: 1 oa_version: Submitted Version pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 147 year: '2017' ... --- _id: '9661' abstract: - lang: eng text: Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this paper, we introduce a thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory. article_number: '034106' article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. 2017;146(3). doi:10.1063/1.4973883 apa: Cheng, B., & Ceriotti, M. (2017). Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4973883 chicago: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4973883. ieee: B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic models of homogeneous nucleation,” The Journal of Chemical Physics, vol. 146, no. 3. AIP Publishing, 2017. ista: Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106. mla: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical Physics, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:10.1063/1.4973883. short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017). date_created: 2021-07-15T08:27:31Z date_published: 2017-01-21T00:00:00Z date_updated: 2021-08-09T12:31:57Z day: '21' doi: 10.1063/1.4973883 extern: '1' external_id: arxiv: - '1610.01322' pmid: - '28109231' intvolume: ' 146' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.01322 month: '01' oa: 1 oa_version: Preprint pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Bridging the gap between atomistic and macroscopic models of homogeneous nucleation type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 146 year: '2017' ...