[{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions."}],"month":"06","intvolume":" 95","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/pdf/1703.00853.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["24700045"]},"publication_status":"published","volume":95,"issue":"6","ec_funded":1,"_id":"959","status":"public","type":"journal_article","date_updated":"2023-09-22T09:59:01Z","department":[{"_id":"GaTk"}],"publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"day":"28","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","isi":1,"year":"2017","doi":"10.1103/PhysRevE.95.062419","date_published":"2017-06-28T00:00:00Z","date_created":"2018-12-11T11:49:25Z","page":"062419","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419.","ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419","short":"D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 062419.","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p. 062419, 2017.","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.","ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419."},"title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","publist_id":"6446","author":[{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000404546400004"]}},{"publication_status":"published","publication_identifier":{"issn":["00221236"]},"language":[{"iso":"eng"}],"volume":273,"issue":"5","abstract":[{"lang":"eng","text":"We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1609.01254","open_access":"1"}],"scopus_import":"1","intvolume":" 273","month":"09","date_updated":"2023-09-22T10:00:18Z","department":[{"_id":"JaMa"}],"_id":"956","type":"journal_article","status":"public","year":"2017","isi":1,"publication":"Journal of Functional Analysis","day":"01","page":"1810 - 1869","date_created":"2018-12-11T11:49:24Z","doi":"10.1016/j.jfa.2017.05.003","date_published":"2017-09-01T00:00:00Z","oa":1,"publisher":"Academic Press","quality_controlled":"1","citation":{"chicago":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis. Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.","ista":"Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869.","mla":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.","ama":"Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869. doi:10.1016/j.jfa.2017.05.003","apa":"Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003","short":"E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.","ieee":"E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” Journal of Functional Analysis, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000406082300005"]},"article_processing_charge":"No","author":[{"first_name":"Eric","full_name":"Carlen, Eric","last_name":"Carlen"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publist_id":"6452","title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.","apa":"Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003","ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003."},"title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","article_processing_charge":"No","external_id":{"pmid":["28411063"]},"publist_id":"6463","author":[{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publication":"Theoretical Population Biology","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:49:22Z","doi":"10.1016/j.tpb.2017.03.003","date_published":"2017-06-01T00:00:00Z","page":"45 - 60","oa":1,"publisher":"Elsevier","quality_controlled":"1","ddc":["576"],"date_updated":"2023-09-22T10:02:21Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","_id":"952","pubrep_id":"972","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2019-04-17T06:39:45Z","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","date_updated":"2020-07-14T12:48:16Z","file_size":2073856,"creator":"dernst","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","file_id":"6327","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["00405809"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":115,"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area.","lang":"eng"}],"intvolume":" 115","month":"06","scopus_import":"1"},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS Biology","day":"30","year":"2017","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:49:22Z","doi":"10.1371/journal.pbio.2001894","date_published":"2017-05-30T00:00:00Z","article_number":"e2001894","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894","ieee":"T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017).","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894."},"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","external_id":{"isi":["000402520000012"]},"article_processing_charge":"No","author":[{"first_name":"Tom","full_name":"Schmidt, Tom","last_name":"Schmidt"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rasic","full_name":"Rasic, Gordana","first_name":"Gordana"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"first_name":"Brian","full_name":"Montgomery, Brian","last_name":"Montgomery"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"full_name":"Hoffmann, Ary","last_name":"Hoffmann","first_name":"Ary"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"publist_id":"6464","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo"}],"intvolume":" 15","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:48:16Z","file_size":5541206,"date_created":"2018-12-12T10:08:30Z","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4691","checksum":"107d290bd1159ec77b734eb2824b01c8"}],"publication_status":"published","publication_identifier":{"issn":["15449173"]},"related_material":{"record":[{"relation":"research_data","id":"9856","status":"public"},{"id":"9857","status":"public","relation":"research_data"},{"status":"public","id":"9858","relation":"research_data"}]},"volume":15,"issue":"5","_id":"951","pubrep_id":"843","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["576"],"date_updated":"2023-09-22T10:02:52Z","file_date_updated":"2020-07-14T12:48:16Z","department":[{"_id":"NiBa"}]},{"ec_funded":1,"issue":"1","volume":96,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24700045"]},"intvolume":" 96","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00219"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.","lang":"eng"}],"department":[{"_id":"GaTk"}],"date_updated":"2023-09-22T10:03:50Z","status":"public","type":"journal_article","_id":"947","date_created":"2018-12-11T11:49:21Z","doi":"10.1103/PhysRevE.96.010401","date_published":"2017-07-10T00:00:00Z","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","day":"10","year":"2017","isi":1,"oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","title":"Quantifying the entropic cost of cellular growth control","external_id":{"isi":["000405194200002"]},"article_processing_charge":"No","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"full_name":"Capuani, Fabrizio","last_name":"Capuani","first_name":"Fabrizio"},{"first_name":"Andrea","full_name":"De Martino, Andrea","last_name":"De Martino"}],"publist_id":"6470","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401.","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401.","mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.010401","apa":"De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401"},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"010401"},{"day":"30","year":"2017","date_created":"2021-08-10T07:47:07Z","doi":"10.1371/journal.pbio.2001894.s016","related_material":{"record":[{"id":"951","status":"public","relation":"used_in_publication"}]},"date_published":"2017-05-30T00:00:00Z","oa_version":"Published Version","month":"05","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016","ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016","mla":"Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016."},"date_updated":"2023-09-22T10:02:51Z","title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Rasic","full_name":"Rasic, Gordana","first_name":"Gordana"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"first_name":"Peter","full_name":"Ryan, Peter","last_name":"Ryan"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"_id":"9858","status":"public","type":"research_data_reference"},{"month":"05","publisher":"Public Library of Science ","oa_version":"Published Version","date_created":"2021-08-10T07:41:52Z","date_published":"2017-05-30T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"951","status":"public"}]},"doi":"10.1371/journal.pbio.2001894.s015","day":"30","year":"2017","status":"public","type":"research_data_reference","_id":"9857","department":[{"_id":"NiBa"}],"title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","article_processing_charge":"No","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"first_name":"Ary","full_name":"Hoffmann, Ary","last_name":"Hoffmann"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"last_name":"Turelli","full_name":"Turelli, Michael","first_name":"Michael"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T10:02:51Z","citation":{"chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015.","mla":"Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015.","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015","ieee":"T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017)."}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T10:02:51Z","citation":{"ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting Information concerning additional likelihood analyses and results, Public Library of Science, 10.1371/journal.pbio.2001894.s014.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting Information concerning additional likelihood analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","ieee":"T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017.","mla":"Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014."},"department":[{"_id":"NiBa"}],"title":"Supporting Information concerning additional likelihood analyses and results","article_processing_charge":"No","author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Rasic","full_name":"Rasic, Gordana","first_name":"Gordana"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"first_name":"Inaki","last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki"},{"last_name":"Cook","full_name":"Cook, Peter","first_name":"Peter"},{"last_name":"Ryan","full_name":"Ryan, Peter","first_name":"Peter"},{"first_name":"Scott","last_name":"Ritchie","full_name":"Ritchie, Scott"},{"full_name":"Hoffmann, Ary","last_name":"Hoffmann","first_name":"Ary"},{"last_name":"O’Neill","full_name":"O’Neill, Scott","first_name":"Scott"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"_id":"9856","status":"public","type":"research_data_reference","day":"30","year":"2017","date_created":"2021-08-10T07:36:04Z","doi":"10.1371/journal.pbio.2001894.s014","date_published":"2017-05-30T00:00:00Z","related_material":{"record":[{"status":"public","id":"951","relation":"used_in_publication"}]},"oa_version":"Published Version","month":"05","publisher":"Public Library of Science"},{"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","page":"2637 - 2649","date_created":"2018-12-11T11:49:20Z","date_published":"2017-07-06T00:00:00Z","doi":"10.1093/molbev/msx190","year":"2017","has_accepted_license":"1","isi":1,"publication":"Molecular Biology and Evolution","day":"06","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"external_id":{"isi":["000411814800016"]},"article_processing_charge":"Yes (in subscription journal)","publist_id":"6472","author":[{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","citation":{"chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2017. https://doi.org/10.1093/molbev/msx190.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190.","apa":"Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 34","month":"07","abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"oa_version":"Published Version","issue":"10","volume":34,"publication_status":"published","publication_identifier":{"issn":["07374038"]},"language":[{"iso":"eng"}],"file":[{"checksum":"009fd68043211d645ceb9d1de28274f2","file_id":"4810","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:23Z","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","date_updated":"2020-07-14T12:48:15Z","file_size":462863,"creator":"system"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"848","status":"public","_id":"945","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:48:15Z","date_updated":"2023-09-26T15:36:34Z","ddc":["570","576"]},{"title":"A moving source of matrix components is essential for De Novo basement membrane formation","external_id":{"isi":["000415815800031"]},"article_processing_charge":"No","author":[{"first_name":"Yutaka","full_name":"Matsubayashi, Yutaka","last_name":"Matsubayashi"},{"first_name":"Adam","last_name":"Louani","full_name":"Louani, Adam"},{"last_name":"Dragu","full_name":"Dragu, Anca","first_name":"Anca"},{"first_name":"Besaiz","full_name":"Sanchez Sanchez, Besaiz","last_name":"Sanchez Sanchez"},{"full_name":"Serna Morales, Eduardo","last_name":"Serna Morales","first_name":"Eduardo"},{"last_name":"Yolland","full_name":"Yolland, Lawrence","first_name":"Lawrence"},{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X"},{"last_name":"Vizcay","full_name":"Vizcay, Gema","first_name":"Gema"},{"full_name":"Fleck, Roland","last_name":"Fleck","first_name":"Roland"},{"first_name":"John","last_name":"Heddleston","full_name":"Heddleston, John"},{"first_name":"Teng","full_name":"Chew, Teng","last_name":"Chew"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"last_name":"Stramer","full_name":"Stramer, Brian","first_name":"Brian"}],"publist_id":"6905","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Matsubayashi, Yutaka, Adam Louani, Anca Dragu, Besaiz Sanchez Sanchez, Eduardo Serna Morales, Lawrence Yolland, Attila György, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.10.001.","ista":"Matsubayashi Y, Louani A, Dragu A, Sanchez Sanchez B, Serna Morales E, Yolland L, György A, Vizcay G, Fleck R, Heddleston J, Chew T, Siekhaus DE, Stramer B. 2017. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 27(22), 3526–3534e.4.","mla":"Matsubayashi, Yutaka, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology, vol. 27, no. 22, Cell Press, 2017, p. 3526–3534e.4, doi:10.1016/j.cub.2017.10.001.","short":"Y. Matsubayashi, A. Louani, A. Dragu, B. Sanchez Sanchez, E. Serna Morales, L. Yolland, A. György, G. Vizcay, R. Fleck, J. Heddleston, T. Chew, D.E. Siekhaus, B. Stramer, Current Biology 27 (2017) 3526–3534e.4.","ieee":"Y. Matsubayashi et al., “A moving source of matrix components is essential for De Novo basement membrane formation,” Current Biology, vol. 27, no. 22. Cell Press, p. 3526–3534e.4, 2017.","apa":"Matsubayashi, Y., Louani, A., Dragu, A., Sanchez Sanchez, B., Serna Morales, E., Yolland, L., … Stramer, B. (2017). A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.10.001","ama":"Matsubayashi Y, Louani A, Dragu A, et al. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 2017;27(22):3526-3534e.4. doi:10.1016/j.cub.2017.10.001"},"oa":1,"quality_controlled":"1","publisher":"Cell Press","date_created":"2018-12-11T11:48:18Z","doi":"10.1016/j.cub.2017.10.001","date_published":"2017-11-09T00:00:00Z","page":"3526 - 3534e.4","publication":"Current Biology","day":"09","year":"2017","isi":1,"has_accepted_license":"1","pubrep_id":"875","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"751","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"DaSi"}],"ddc":["570","576"],"date_updated":"2023-09-27T12:25:31Z","intvolume":" 27","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components.","lang":"eng"}],"issue":"22","volume":27,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"264cf6c6c3551486ba5ea786850e000a","file_id":"4770","file_size":4770657,"date_updated":"2020-07-14T12:47:59Z","creator":"system","file_name":"IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf","date_created":"2018-12-12T10:09:45Z"}],"publication_status":"published","publication_identifier":{"issn":["09609822"]}},{"external_id":{"isi":["000412999700021"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"first_name":"Mahmoud","full_name":"Kalaee, Mahmoud","last_name":"Kalaee"},{"full_name":"Dieterle, Paul","last_name":"Dieterle","first_name":"Paul"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6855","title":"Mechanical on chip microwave circulator","citation":{"chicago":"Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01304-x.","ista":"Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304.","mla":"Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” Nature Communications, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01304-x.","short":"S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017).","ieee":"S. Barzanjeh et al., “Mechanical on chip microwave circulator,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","apa":"Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., & Fink, J. M. (2017). Mechanical on chip microwave circulator. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01304-x","ama":"Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01304-x"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"article_number":"1304","date_created":"2018-12-11T11:48:33Z","doi":"10.1038/s41467-017-01304-x","date_published":"2017-10-16T00:00:00Z","year":"2017","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"16","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"JoFi"}],"date_updated":"2023-09-27T12:11:28Z","ddc":["539"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"867","status":"public","_id":"798","ec_funded":1,"issue":"1","volume":8,"publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-867-v1+1_s41467-017-01304-x.pdf","date_created":"2018-12-12T10:15:25Z","file_size":1467696,"date_updated":"2020-07-14T12:48:06Z","creator":"system","file_id":"5145","checksum":"b68dafa71d1834c23b742cd9987a3d5f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":"1","intvolume":" 8","month":"10","abstract":[{"lang":"eng","text":"Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout."}],"oa_version":"Published Version"},{"volume":"Part F129314","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-145034992-5"]},"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04178"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between "heavily loaded" balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance."}],"department":[{"_id":"DaAl"}],"date_updated":"2023-09-27T12:17:59Z","status":"public","conference":{"start_date":"2017-07-25","end_date":"2017-07-27","location":"Washington, WA, USA","name":"PODC: Principles of Distributed Computing"},"type":"conference","_id":"791","date_created":"2018-12-11T11:48:31Z","date_published":"2017-07-26T00:00:00Z","doi":"10.1145/3087801.3087810","page":"283 - 292","publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","day":"26","year":"2017","isi":1,"oa":1,"publisher":"ACM","quality_controlled":"1","title":"The power of choice in priority scheduling","article_processing_charge":"No","external_id":{"isi":["000462995000035"]},"publist_id":"6864","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Justin","last_name":"Kopinsky","full_name":"Kopinsky, Justin"},{"first_name":"Jerry","last_name":"Li","full_name":"Li, Jerry"},{"full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze. “The Power of Choice in Priority Scheduling.” In Proceedings of the ACM Symposium on Principles of Distributed Computing, Part F129314:283–92. ACM, 2017. https://doi.org/10.1145/3087801.3087810.","ista":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292.","mla":"Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.” Proceedings of the ACM Symposium on Principles of Distributed Computing, vol. Part F129314, ACM, 2017, pp. 283–92, doi:10.1145/3087801.3087810.","short":"D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292.","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice in priority scheduling,” in Proceedings of the ACM Symposium on Principles of Distributed Computing, Washington, WA, USA, 2017, vol. Part F129314, pp. 283–292.","ama":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority scheduling. In: Proceedings of the ACM Symposium on Principles of Distributed Computing. Vol Part F129314. ACM; 2017:283-292. doi:10.1145/3087801.3087810","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., & Nadiradze, G. (2017). The power of choice in priority scheduling. In Proceedings of the ACM Symposium on Principles of Distributed Computing (Vol. Part F129314, pp. 283–292). Washington, WA, USA: ACM. https://doi.org/10.1145/3087801.3087810"}},{"oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","date_created":"2018-12-11T11:48:32Z","date_published":"2017-12-25T00:00:00Z","doi":"10.1017/jfm.2017.699","page":"274 - 301","publication":"Journal of Fluid Mechanics","day":"25","year":"2017","isi":1,"project":[{"name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425"}],"title":"Relative periodic orbits form the backbone of turbulent pipe flow","article_processing_charge":"No","external_id":{"isi":["000414641700001"]},"author":[{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur"},{"last_name":"Short","full_name":"Short, Kimberly","first_name":"Kimberly"},{"full_name":"Farazmand, Mohammad","last_name":"Farazmand","first_name":"Mohammad"},{"full_name":"Willis, Ashley","last_name":"Willis","first_name":"Ashley"},{"first_name":"Predrag","last_name":"Cvitanović","full_name":"Cvitanović, Predrag"}],"publist_id":"6862","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833, 274–301.","chicago":"Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.699.","ieee":"N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative periodic orbits form the backbone of turbulent pipe flow,” Journal of Fluid Mechanics, vol. 833. Cambridge University Press, pp. 274–301, 2017.","short":"N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of Fluid Mechanics 833 (2017) 274–301.","ama":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 2017;833:274-301. doi:10.1017/jfm.2017.699","apa":"Budanur, N. B., Short, K., Farazmand, M., Willis, A., & Cvitanović, P. (2017). Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.699","mla":"Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” Journal of Fluid Mechanics, vol. 833, Cambridge University Press, 2017, pp. 274–301, doi:10.1017/jfm.2017.699."},"intvolume":" 833","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1705.03720","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics.","lang":"eng"}],"volume":833,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00221120"]},"status":"public","type":"journal_article","_id":"792","department":[{"_id":"BjHo"}],"date_updated":"2023-09-27T12:17:35Z"},{"article_number":"042603","citation":{"chicago":"Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” Applied Physics Letters. American Institute of Physics, 2017. https://doi.org/10.1063/1.4994661.","ista":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 111(4), 042603.","mla":"Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” Applied Physics Letters, vol. 111, no. 4, 042603, American Institute of Physics, 2017, doi:10.1063/1.4994661.","apa":"Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., & Painter, O. (2017). Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.4994661","ama":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 2017;111(4). doi:10.1063/1.4994661","ieee":"A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter, “Al transmon qubits on silicon on insulator for quantum device integration,” Applied Physics Letters, vol. 111, no. 4. American Institute of Physics, 2017.","short":"A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied Physics Letters 111 (2017)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000406779700031"]},"article_processing_charge":"No","author":[{"first_name":"Andrew J","full_name":"Keller, Andrew J","last_name":"Keller"},{"first_name":"Paul","full_name":"Dieterle, Paul","last_name":"Dieterle"},{"full_name":"Fang, Michael","last_name":"Fang","first_name":"Michael"},{"last_name":"Berger","full_name":"Berger, Brett","first_name":"Brett"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"last_name":"Painter","full_name":"Painter, Oskar","first_name":"Oskar"}],"publist_id":"6857","title":"Al transmon qubits on silicon on insulator for quantum device integration","acknowledgement":"This work was supported by the AFOSR MURI Quantum Photonic Matter (Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers (Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.J.K. acknowledges the IQIM Postdoctoral Fellowship.","oa":1,"quality_controlled":"1","publisher":"American Institute of Physics","year":"2017","isi":1,"publication":"Applied Physics Letters","day":"01","date_created":"2018-12-11T11:48:33Z","date_published":"2017-07-01T00:00:00Z","doi":"10.1063/1.4994661","_id":"796","type":"journal_article","status":"public","date_updated":"2023-09-27T12:13:36Z","department":[{"_id":"JoFi"}],"abstract":[{"text":"We present the fabrication and characterization of an aluminum transmon qubit on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This process in principle permits the co-fabrication of silicon photonic and mechanical elements, providing a route towards chip-scale integration of electro-opto-mechanical transducers for quantum networking of superconducting microwave quantum circuits. The additional processing steps are compatible with established fabrication techniques for aluminum transmon qubits on silicon.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.10195"}],"scopus_import":"1","intvolume":" 111","month":"07","publication_status":"published","publication_identifier":{"issn":["00036951"]},"language":[{"iso":"eng"}],"volume":111,"issue":"4"},{"title":"On the existence of ordinary triangles","publist_id":"6861","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek"},{"first_name":"Hossein","full_name":"Mojarrad, Hossein","last_name":"Mojarrad"},{"first_name":"Márton","full_name":"Naszódi, Márton","last_name":"Naszódi"},{"first_name":"József","full_name":"Solymosi, József","last_name":"Solymosi"},{"first_name":"Sebastian","full_name":"Stich, Sebastian","last_name":"Stich"},{"last_name":"Szedlák","full_name":"Szedlák, May","first_name":"May"}],"article_processing_charge":"No","external_id":{"isi":["000412039700003"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.","chicago":"Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” Computational Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.07.002.","apa":"Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., & Szedlák, M. (2017). On the existence of ordinary triangles. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.07.002","ama":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 2017;66:28-31. doi:10.1016/j.comgeo.2017.07.002","short":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31.","ieee":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” Computational Geometry: Theory and Applications, vol. 66. Elsevier, pp. 28–31, 2017.","mla":"Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” Computational Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 28–31, doi:10.1016/j.comgeo.2017.07.002."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.comgeo.2017.07.002","date_created":"2018-12-11T11:48:32Z","page":"28 - 31","day":"01","publication":"Computational Geometry: Theory and Applications","isi":1,"year":"2017","quality_controlled":"1","publisher":"Elsevier","oa":1,"department":[{"_id":"UlWa"}],"date_updated":"2023-09-27T12:15:16Z","status":"public","type":"journal_article","_id":"793","volume":66,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09257721"]},"publication_status":"published","month":"01","intvolume":" 66","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.08183"}],"oa_version":"Submitted Version","abstract":[{"text":"Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c > 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). ","lang":"eng"}]},{"_id":"794","type":"journal_article","status":"public","date_updated":"2023-09-27T12:14:49Z","department":[{"_id":"UlWa"}],"abstract":[{"text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1602.01346","open_access":"1"}],"month":"12","intvolume":" 66","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"1165","status":"public"}]},"volume":66,"citation":{"mla":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 1–13, doi:10.1016/j.comgeo.2017.06.016.","apa":"Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.016","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 2017;66:1-13. doi:10.1016/j.comgeo.2017.06.016","short":"R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13.","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” Computational Geometry: Theory and Applications, vol. 66. Elsevier, pp. 1–13, 2017.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.06.016.","ista":"Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 66, 1–13."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6860","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek"}],"external_id":{"isi":["000412039700001"]},"article_processing_charge":"No","title":"C-planarity of embedded cyclic c-graphs","acknowledgement":"I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous referees for many comments and suggestions that helped to improve the presentation of the result.","publisher":"Elsevier","quality_controlled":"1","oa":1,"isi":1,"year":"2017","day":"01","publication":"Computational Geometry: Theory and Applications","page":"1 - 13","doi":"10.1016/j.comgeo.2017.06.016","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:48:32Z"},{"external_id":{"isi":["000414761700002"]},"article_processing_charge":"No","author":[{"first_name":"María","full_name":"Rubio, María","last_name":"Rubio"},{"first_name":"Ko","full_name":"Matsui, Ko","last_name":"Matsui"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"first_name":"Naomi","full_name":"Kamasawa, Naomi","last_name":"Kamasawa"},{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","last_name":"Harada","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Itakura, Makoto","last_name":"Itakura","first_name":"Makoto"},{"full_name":"Molnár, Elek","last_name":"Molnár","first_name":"Elek"},{"last_name":"Abe","full_name":"Abe, Manabu","first_name":"Manabu"},{"full_name":"Sakimura, Kenji","last_name":"Sakimura","first_name":"Kenji"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"publist_id":"6932","title":"The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells","citation":{"chicago":"Rubio, María, Ko Matsui, Yugo Fukazawa, Naomi Kamasawa, Harumi Harada, Makoto Itakura, Elek Molnár, Manabu Abe, Kenji Sakimura, and Ryuichi Shigemoto. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” Brain Structure and Function. Springer, 2017. https://doi.org/10.1007/s00429-017-1408-0.","ista":"Rubio M, Matsui K, Fukazawa Y, Kamasawa N, Harada H, Itakura M, Molnár E, Abe M, Sakimura K, Shigemoto R. 2017. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. 222(8), 3375–3393.","mla":"Rubio, María, et al. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” Brain Structure and Function, vol. 222, no. 8, Springer, 2017, pp. 3375–93, doi:10.1007/s00429-017-1408-0.","ama":"Rubio M, Matsui K, Fukazawa Y, et al. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. 2017;222(8):3375-3393. doi:10.1007/s00429-017-1408-0","apa":"Rubio, M., Matsui, K., Fukazawa, Y., Kamasawa, N., Harada, H., Itakura, M., … Shigemoto, R. (2017). The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1408-0","ieee":"M. Rubio et al., “The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells,” Brain Structure and Function, vol. 222, no. 8. Springer, pp. 3375–3393, 2017.","short":"M. Rubio, K. Matsui, Y. Fukazawa, N. Kamasawa, H. Harada, M. Itakura, E. Molnár, M. Abe, K. Sakimura, R. Shigemoto, Brain Structure and Function 222 (2017) 3375–3393."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"3375 - 3393","date_created":"2018-12-11T11:48:14Z","doi":"10.1007/s00429-017-1408-0","date_published":"2017-11-01T00:00:00Z","year":"2017","has_accepted_license":"1","isi":1,"publication":"Brain Structure and Function","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:56Z","date_updated":"2023-09-27T14:14:51Z","ddc":["571"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"881","status":"public","_id":"736","issue":"8","volume":222,"publication_status":"published","publication_identifier":{"issn":["18632653"]},"language":[{"iso":"eng"}],"file":[{"checksum":"73787a22507de8fb585bb598e1418ca7","file_id":"4806","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:20Z","file_name":"IST-2017-881-v1+1_s00429-017-1408-0.pdf","date_updated":"2020-07-14T12:47:56Z","file_size":4011126,"creator":"system"}],"scopus_import":"1","intvolume":" 222","month":"11","abstract":[{"text":"The neurotransmitter receptor subtype, number, density, and distribution relative to the location of transmitter release sites are key determinants of signal transmission. AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits are prominently expressed in subsets of neurons capable of firing action potentials at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics; thus, we investigated whether the number, density, and localization of GluA3 and GluA4 subunits in these synapses are differentially organized using quantitative freeze-fracture replica immunogold labeling. We identify a positive correlation between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller. A higher number and density of GluA3 subunits are observed at AN-BC synapses, whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses. The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits, particularly GluA3, are concentrated at the center of the AN-BC synapses. The central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles are evenly distributed along the postsynaptic density. GluA4 gold labeling was homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits are distributed at AN synapses in a target-cell-dependent manner.","lang":"eng"}],"oa_version":"Published Version"},{"file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"RySh"},{"_id":"MaJö"}],"ddc":["570"],"date_updated":"2023-09-27T12:51:41Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"740","volume":6,"issue":"6","license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"file_name":"2017_WIREs_Shigemoto.pdf","date_created":"2019-11-19T07:36:18Z","creator":"dernst","file_size":1647787,"date_updated":"2020-07-14T12:47:57Z","file_id":"7045","checksum":"a9370f27b1591773b7a0de299bc81c8c","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["17597684"]},"publication_status":"published","month":"08","intvolume":" 6","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits. Together, the gains from these advances can decrease the time required for the analysis of targeted circuit motifs by over two orders of magnitude. These genetic encoded tags for electron microscopy promise to simplify the analysis of circuit motifs and become a central tool for structure‐function studies of synaptic connections in the brain. We review the current state‐of‐the‐art with an emphasis on connectomics, the quantitative analysis of neuronal structures and motifs.","lang":"eng"}],"title":"The genetic encoded toolbox for electron microscopy and connectomics","author":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"publist_id":"6927","article_processing_charge":"No","external_id":{"isi":["000412827400005"],"pmid":["28800674"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Shigemoto R, Jösch MA. 2017. The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. 6(6), e288.","chicago":"Shigemoto, Ryuichi, and Maximilian A Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” WIREs Developmental Biology. Wiley-Blackwell, 2017. https://doi.org/10.1002/wdev.288.","ieee":"R. Shigemoto and M. A. Jösch, “The genetic encoded toolbox for electron microscopy and connectomics,” WIREs Developmental Biology, vol. 6, no. 6. Wiley-Blackwell, 2017.","short":"R. Shigemoto, M.A. Jösch, WIREs Developmental Biology 6 (2017).","ama":"Shigemoto R, Jösch MA. The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. 2017;6(6). doi:10.1002/wdev.288","apa":"Shigemoto, R., & Jösch, M. A. (2017). The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. Wiley-Blackwell. https://doi.org/10.1002/wdev.288","mla":"Shigemoto, Ryuichi, and Maximilian A. Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” WIREs Developmental Biology, vol. 6, no. 6, e288, Wiley-Blackwell, 2017, doi:10.1002/wdev.288."},"article_number":"e288","doi":"10.1002/wdev.288","date_published":"2017-08-11T00:00:00Z","date_created":"2018-12-11T11:48:15Z","day":"11","publication":"WIREs Developmental Biology","isi":1,"has_accepted_license":"1","year":"2017","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1},{"oa":1,"quality_controlled":"1","publisher":"Springer","year":"2017","has_accepted_license":"1","isi":1,"publication":"Communications in Mathematical Physics","day":"01","page":"329 - 355","date_created":"2018-12-11T11:48:15Z","doi":"10.1007/s00220-017-2980-0","date_published":"2017-11-01T00:00:00Z","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Moser T, Seiringer R. Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. 2017;356(1):329-355. doi:10.1007/s00220-017-2980-0","apa":"Moser, T., & Seiringer, R. (2017). Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-2980-0","ieee":"T. Moser and R. Seiringer, “Stability of a fermionic N+1 particle system with point interactions,” Communications in Mathematical Physics, vol. 356, no. 1. Springer, pp. 329–355, 2017.","short":"T. Moser, R. Seiringer, Communications in Mathematical Physics 356 (2017) 329–355.","mla":"Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle System with Point Interactions.” Communications in Mathematical Physics, vol. 356, no. 1, Springer, 2017, pp. 329–55, doi:10.1007/s00220-017-2980-0.","ista":"Moser T, Seiringer R. 2017. Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. 356(1), 329–355.","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle System with Point Interactions.” Communications in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s00220-017-2980-0."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000409821300010"]},"article_processing_charge":"No","publist_id":"6926","author":[{"full_name":"Moser, Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"Stability of a fermionic N+1 particle system with point interactions","abstract":[{"text":"We prove that a system of N fermions interacting with an additional particle via point interactions is stable if the ratio of the mass of the additional particle to the one of the fermions is larger than some critical m*. The value of m* is independent of N and turns out to be less than 1. This fact has important implications for the stability of the unitary Fermi gas. We also characterize the domain of the Hamiltonian of this model, and establish the validity of the Tan relations for all wave functions in the domain.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 356","month":"11","publication_status":"published","publication_identifier":{"issn":["00103616"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-880-v1+1_s00220-017-2980-0.pdf","date_created":"2018-12-12T10:10:50Z","creator":"system","file_size":952639,"date_updated":"2020-07-14T12:47:57Z","checksum":"0fd9435400f91e9b3c5346319a2d24e3","file_id":"4841","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"volume":356,"issue":"1","related_material":{"record":[{"status":"public","id":"52","relation":"dissertation_contains"}]},"_id":"741","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"880","status":"public","date_updated":"2023-09-27T12:34:15Z","ddc":["539"],"file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"RoSe"}]},{"publication_status":"published","publication_identifier":{"issn":["00217824"]},"language":[{"iso":"eng"}],"volume":108,"issue":"5","abstract":[{"lang":"eng","text":"We study the norm approximation to the Schrödinger dynamics of N bosons in with an interaction potential of the form . Assuming that in the initial state the particles outside of the condensate form a quasi-free state with finite kinetic energy, we show that in the large N limit, the fluctuations around the condensate can be effectively described using Bogoliubov approximation for all . The range of β is expected to be optimal for this large class of initial states."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05240"}],"scopus_import":"1","intvolume":" 108","month":"11","date_updated":"2023-09-27T12:52:07Z","department":[{"_id":"RoSe"}],"_id":"739","type":"journal_article","status":"public","year":"2017","isi":1,"publication":"Journal de Mathématiques Pures et Appliquées","day":"01","page":"662 - 688","date_created":"2018-12-11T11:48:15Z","date_published":"2017-11-01T00:00:00Z","doi":"10.1016/j.matpur.2017.05.013","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"mla":"Nam, Phan, and Marcin M. Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées, vol. 108, no. 5, Elsevier, 2017, pp. 662–88, doi:10.1016/j.matpur.2017.05.013.","apa":"Nam, P., & Napiórkowski, M. M. (2017). A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2017.05.013","ama":"Nam P, Napiórkowski MM. A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 2017;108(5):662-688. doi:10.1016/j.matpur.2017.05.013","ieee":"P. Nam and M. M. Napiórkowski, “A note on the validity of Bogoliubov correction to mean field dynamics,” Journal de Mathématiques Pures et Appliquées, vol. 108, no. 5. Elsevier, pp. 662–688, 2017.","short":"P. Nam, M.M. Napiórkowski, Journal de Mathématiques Pures et Appliquées 108 (2017) 662–688.","chicago":"Nam, Phan, and Marcin M Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2017. https://doi.org/10.1016/j.matpur.2017.05.013.","ista":"Nam P, Napiórkowski MM. 2017. A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 108(5), 662–688."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000414113600003"]},"publist_id":"6928","author":[{"full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"}],"title":"A note on the validity of Bogoliubov correction to mean field dynamics","project":[{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"type":"journal_article","status":"public","_id":"737","department":[{"_id":"HeEd"}],"date_updated":"2023-09-27T12:53:01Z","scopus_import":"1","month":"11","intvolume":" 231","abstract":[{"text":"We generalize Brazas’ topology on the fundamental group to the whole universal path space X˜ i.e., to the set of homotopy classes of all based paths. We develop basic properties of the new notion and provide a complete comparison of the obtained topology with the established topologies, in particular with the Lasso topology and the CO topology, i.e., the topology that is induced by the compact-open topology. It turns out that the new topology is the finest topology contained in the CO topology, for which the action of the fundamental group on the universal path space is a continuous group action.","lang":"eng"}],"oa_version":"None","volume":231,"publication_identifier":{"issn":["01668641"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Virk","full_name":"Virk, Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","first_name":"Ziga"},{"first_name":"Andreas","last_name":"Zastrow","full_name":"Zastrow, Andreas"}],"publist_id":"6930","article_processing_charge":"No","external_id":{"isi":["000413889100012"]},"title":"A new topology on the universal path space","citation":{"ista":"Virk Z, Zastrow A. 2017. A new topology on the universal path space. Topology and its Applications. 231, 186–196.","chicago":"Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path Space.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2017.09.015.","apa":"Virk, Z., & Zastrow, A. (2017). A new topology on the universal path space. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2017.09.015","ama":"Virk Z, Zastrow A. A new topology on the universal path space. Topology and its Applications. 2017;231:186-196. doi:10.1016/j.topol.2017.09.015","short":"Z. Virk, A. Zastrow, Topology and Its Applications 231 (2017) 186–196.","ieee":"Z. Virk and A. Zastrow, “A new topology on the universal path space,” Topology and its Applications, vol. 231. Elsevier, pp. 186–196, 2017.","mla":"Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path Space.” Topology and Its Applications, vol. 231, Elsevier, 2017, pp. 186–96, doi:10.1016/j.topol.2017.09.015."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","quality_controlled":"1","page":"186 - 196","date_published":"2017-11-01T00:00:00Z","doi":"10.1016/j.topol.2017.09.015","date_created":"2018-12-11T11:48:14Z","isi":1,"year":"2017","day":"01","publication":"Topology and its Applications"},{"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Bao, Zhigang, et al. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” Advances in Mathematics, vol. 319, Academic Press, 2017, pp. 251–91, doi:10.1016/j.aim.2017.08.028.","short":"Z. Bao, L. Erdös, K. Schnelli, Advances in Mathematics 319 (2017) 251–291.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Convergence rate for spectral distribution of addition of random matrices,” Advances in Mathematics, vol. 319. Academic Press, pp. 251–291, 2017.","ama":"Bao Z, Erdös L, Schnelli K. Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. 2017;319:251-291. doi:10.1016/j.aim.2017.08.028","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2017). Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2017.08.028","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2017.08.028.","ista":"Bao Z, Erdös L, Schnelli K. 2017. Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. 319, 251–291."},"title":"Convergence rate for spectral distribution of addition of random matrices","author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","last_name":"Schnelli"}],"publist_id":"6935","external_id":{"isi":["000412150400010"]},"article_processing_charge":"No","acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804, Hong Kong RGC grant ECS 26301517, and the Göran Gustafsson Foundation","publisher":"Academic Press","quality_controlled":"1","oa":1,"day":"15","publication":"Advances in Mathematics","isi":1,"year":"2017","date_published":"2017-10-15T00:00:00Z","doi":"10.1016/j.aim.2017.08.028","date_created":"2018-12-11T11:48:13Z","page":"251 - 291","_id":"733","status":"public","type":"journal_article","date_updated":"2023-09-28T11:30:42Z","department":[{"_id":"LaEr"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Let A and B be two N by N deterministic Hermitian matrices and let U be an N by N Haar distributed unitary matrix. It is well known that the spectral distribution of the sum H = A + UBU∗ converges weakly to the free additive convolution of the spectral distributions of A and B, as N tends to infinity. We establish the optimal convergence rate in the bulk of the spectrum."}],"month":"10","intvolume":" 319","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1606.03076","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":319,"ec_funded":1},{"project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” Nano Letters, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.","ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710."},"title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","external_id":{"isi":["000411043500078"]},"article_processing_charge":"No","author":[{"first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukusic","full_name":"Vukusic, Lada","orcid":"0000-0003-2424-8636"},{"full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6808","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","publication":"Nano Letters","day":"10","year":"2017","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:48:47Z","date_published":"2017-08-10T00:00:00Z","doi":"10.1021/acs.nanolett.7b02627","page":"5706 - 5710","_id":"840","pubrep_id":"865","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["539"],"date_updated":"2023-09-26T15:50:22Z","file_date_updated":"2020-07-14T12:48:13Z","department":[{"_id":"GeKa"}],"oa_version":"Published Version","abstract":[{"text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"intvolume":" 17","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:33Z","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","creator":"system","date_updated":"2020-07-14T12:48:13Z","file_size":2449546,"file_id":"4951","checksum":"761371a0129b2aa442424b9561450ece","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["15306984"]},"ec_funded":1,"volume":17,"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","id":"69","relation":"dissertation_contains"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"issue":"9"},{"article_number":"170547","article_processing_charge":"No","external_id":{"isi":["000406670000025"]},"publist_id":"6527","author":[{"first_name":"Julia","last_name":"Giehr","full_name":"Giehr, Julia"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"}],"title":"Ant queens increase their reproductive efforts after pathogen infection","citation":{"mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:10.1098/rsos.170547.","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017).","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” Royal Society Open Science, vol. 4, no. 7. Royal Society, The, 2017.","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 2017;4(7). doi:10.1098/rsos.170547","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.170547","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science. Royal Society, The, 2017. https://doi.org/10.1098/rsos.170547.","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Royal Society, The","quality_controlled":"1","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","date_created":"2018-12-11T11:49:10Z","doi":"10.1098/rsos.170547","date_published":"2017-07-05T00:00:00Z","year":"2017","isi":1,"has_accepted_license":"1","publication":"Royal Society Open Science","day":"05","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"849","status":"public","_id":"914","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:48:15Z","date_updated":"2023-09-26T15:45:47Z","ddc":["576","592"],"scopus_import":"1","intvolume":" 4","month":"07","abstract":[{"lang":"eng","text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect."}],"oa_version":"Published Version","related_material":{"record":[{"id":"9853","status":"public","relation":"research_data"}]},"issue":"7","volume":4,"publication_status":"published","publication_identifier":{"issn":["20545703"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:08:24Z","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","date_updated":"2020-07-14T12:48:15Z","file_size":530412,"creator":"system","checksum":"351ae5e7a37e6e7d9295cd41146c4190","file_id":"4684","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}]},{"project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"article_processing_charge":"No","external_id":{"isi":["000412232600019"]},"publist_id":"6533","author":[{"orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"title":"When does frequency-independent selection maintain genetic variation?","citation":{"ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129","apa":"Novak, S., & Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.117.300129."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","page":"653 - 668","date_created":"2018-12-11T11:49:09Z","date_published":"2017-10-01T00:00:00Z","doi":"10.1534/genetics.117.300129","year":"2017","isi":1,"has_accepted_license":"1","publication":"Genetics","day":"01","type":"journal_article","pubrep_id":"974","status":"public","_id":"910","file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"NiBa"}],"date_updated":"2023-09-26T15:49:15Z","ddc":["576"],"scopus_import":"1","intvolume":" 207","month":"10","abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"oa_version":"Submitted Version","ec_funded":1,"issue":"2","volume":207,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f7c32dabf52e6d9e709d9203761e39fd","file_id":"5264","creator":"system","date_updated":"2020-07-14T12:48:15Z","file_size":494268,"date_created":"2018-12-12T10:17:12Z","file_name":"IST-2018-974-v1+1_manuscript.pdf"}]},{"_id":"835","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"859","status":"public","date_updated":"2023-09-26T15:51:28Z","ddc":["570","576","616"],"extern":"1","file_date_updated":"2020-07-14T12:48:12Z","abstract":[{"lang":"eng","text":"An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined."}],"oa_version":"Published Version","intvolume":" 8","month":"07","publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"checksum":"99a3d63308d4250eda0a35341171f80e","file_id":"5153","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-859-v1+1_ncomms15990.pdf","date_created":"2018-12-12T10:15:32Z","file_size":3027104,"date_updated":"2020-07-14T12:48:12Z","creator":"system"}],"volume":8,"article_number":"15990","citation":{"ista":"Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I, Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 8, 15990.","chicago":"Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15990.","short":"K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I. Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications 8 (2017).","ieee":"K. Makhijani et al., “Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K., … Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15990","ama":"Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 2017;8. doi:10.1038/ncomms15990","mla":"Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications, vol. 8, 15990, Nature Publishing Group, 2017, doi:10.1038/ncomms15990."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000406360100001"]},"author":[{"last_name":"Makhijani","full_name":"Makhijani, Kalpana","first_name":"Kalpana"},{"first_name":"Brandy","last_name":"Alexander","full_name":"Alexander, Brandy"},{"first_name":"Deepti","last_name":"Rao","full_name":"Rao, Deepti"},{"last_name":"Petraki","full_name":"Petraki, Sophia","first_name":"Sophia"},{"first_name":"Leire","full_name":"Herboso, Leire","last_name":"Herboso"},{"full_name":"Kukar, Katelyn","last_name":"Kukar","first_name":"Katelyn"},{"full_name":"Batool, Itrat","last_name":"Batool","first_name":"Itrat"},{"id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","full_name":"Wachner, Stephanie","last_name":"Wachner"},{"first_name":"Katrina","full_name":"Gold, Katrina","last_name":"Gold"},{"last_name":"Wong","full_name":"Wong, Corinna","first_name":"Corinna"},{"first_name":"Michael","full_name":"O'Connor, Michael","last_name":"O'Connor"},{"first_name":"Katja","last_name":"Brückner","full_name":"Brückner, Katja"}],"publist_id":"6813","title":"Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2017","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"27","date_created":"2018-12-11T11:48:45Z","doi":"10.1038/ncomms15990","date_published":"2017-07-27T00:00:00Z"},{"date_updated":"2023-09-26T15:50:52Z","department":[{"_id":"HeEd"}],"_id":"836","status":"public","type":"conference","conference":{"name":"ACA: Applications of Computer Algebra","start_date":"2015-07-20","end_date":"2015-07-23","location":"Kalamata, Greece"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331956930-7"]},"publication_status":"published","volume":198,"ec_funded":1,"oa_version":"None","abstract":[{"text":"Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces.","lang":"eng"}],"month":"07","intvolume":" 198","alternative_title":["PROMS"],"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the Kronecker canonical form. In: Special Sessions in Applications of Computer Algebra. Vol 198. Springer; 2017:119-136. doi:10.1007/978-3-319-56932-1_8","apa":"Ethier, M., Jablonski, G., & Mrozek, M. (2017). Finding eigenvalues of self-maps with the Kronecker canonical form. In Special Sessions in Applications of Computer Algebra (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. https://doi.org/10.1007/978-3-319-56932-1_8","ieee":"M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps with the Kronecker canonical form,” in Special Sessions in Applications of Computer Algebra, Kalamata, Greece, 2017, vol. 198, pp. 119–136.","short":"M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications of Computer Algebra, Springer, 2017, pp. 119–136.","mla":"Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” Special Sessions in Applications of Computer Algebra, vol. 198, Springer, 2017, pp. 119–36, doi:10.1007/978-3-319-56932-1_8.","ista":"Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with the Kronecker canonical form. Special Sessions in Applications of Computer Algebra. ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.","chicago":"Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” In Special Sessions in Applications of Computer Algebra, 198:119–36. Springer, 2017. https://doi.org/10.1007/978-3-319-56932-1_8."},"title":"Finding eigenvalues of self-maps with the Kronecker canonical form","author":[{"last_name":"Ethier","full_name":"Ethier, Marc","first_name":"Marc"},{"id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz","last_name":"Jablonski","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz"},{"first_name":"Marian","last_name":"Mrozek","full_name":"Mrozek, Marian"}],"publist_id":"6812","article_processing_charge":"No","external_id":{"isi":["000434088200008"]},"project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"day":"27","publication":"Special Sessions in Applications of Computer Algebra","isi":1,"year":"2017","date_published":"2017-07-27T00:00:00Z","doi":"10.1007/978-3-319-56932-1_8","date_created":"2018-12-11T11:48:46Z","page":"119 - 136","quality_controlled":"1","publisher":"Springer"},{"publist_id":"6525","author":[{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"last_name":"Abu Alhaija","full_name":"Abu Alhaija, Carsten","first_name":"Carsten"},{"first_name":"Dagmar","last_name":"Kainmueller","full_name":"Kainmueller, Dagmar"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"external_id":{"isi":["000418371407018"]},"article_processing_charge":"No","title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","citation":{"chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747.","ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.","mla":"Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.","ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"page":"7062-7071","date_published":"2017-01-01T00:00:00Z","doi":"10.1109/CVPR.2017.747","date_created":"2018-12-11T11:49:11Z","isi":1,"has_accepted_license":"1","year":"2017","day":"01","quality_controlled":"1","publisher":"IEEE","oa":1,"file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"VlKo"}],"date_updated":"2023-09-26T15:41:40Z","ddc":["000"],"type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2017-07-21","end_date":"2017-07-26","location":"Honolulu, HA, United States"},"status":"public","_id":"916","volume":2017,"ec_funded":1,"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","file":[{"date_created":"2019-01-18T12:49:38Z","file_name":"2017_CVPR_Swoboda2.pdf","date_updated":"2020-07-14T12:48:15Z","file_size":944332,"creator":"dernst","checksum":"e38a2740daad1ea178465843b5072906","file_id":"5848","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 2017","abstract":[{"lang":"eng","text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each."}],"oa_version":"Submitted Version"},{"page":"4990-4999","date_created":"2018-12-11T11:49:11Z","doi":"10.1109/CVPR.2017.530","date_published":"2017-07-01T00:00:00Z","year":"2017","isi":1,"has_accepted_license":"1","day":"01","oa":1,"quality_controlled":"1","publisher":"IEEE","article_processing_charge":"No","external_id":{"isi":["000418371405009"]},"publist_id":"6526","author":[{"last_name":"Swoboda","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"},{"first_name":"Bjoern","full_name":"Andres, Bjoern","last_name":"Andres"}],"title":"A message passing algorithm for the minimum cost multicut problem","citation":{"chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.","mla":"Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530.","ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530","apa":"Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530","short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"volume":2017,"publication_status":"published","publication_identifier":{"isbn":["978-153860457-1"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5849","checksum":"7e51dacefa693574581a32da3eff63dc","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-01-18T12:52:46Z","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf","date_updated":"2020-07-14T12:48:15Z","file_size":883264,"creator":"dernst"}],"scopus_import":"1","intvolume":" 2017","month":"07","abstract":[{"text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.","lang":"eng"}],"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"VlKo"}],"date_updated":"2023-09-26T15:43:27Z","ddc":["000"],"conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26","location":"Honolulu, HA, United States","start_date":"2017-07-21"},"type":"conference","status":"public","_id":"915"},{"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"citation":{"mla":"Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526.","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","ieee":"P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.","ama":"Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526","apa":"Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.526","chicago":"Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.526.","ista":"Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000418371405005"]},"author":[{"full_name":"Swoboda, Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"},{"full_name":"Kuske, Jan","last_name":"Kuske","first_name":"Jan"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"publist_id":"6524","title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","oa":1,"quality_controlled":"1","publisher":"IEEE","year":"2017","isi":1,"has_accepted_license":"1","day":"01","page":"4950-4960","date_created":"2018-12-11T11:49:11Z","doi":"10.1109/CVPR.2017.526","date_published":"2017-07-01T00:00:00Z","_id":"917","conference":{"start_date":"2017-07-21","location":"Honolulu, HA, United States","end_date":"2017-07-26","name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","status":"public","date_updated":"2023-09-26T15:41:11Z","ddc":["000"],"department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:48:15Z","abstract":[{"text":"We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 2017","month":"07","publication_status":"published","publication_identifier":{"isbn":["978-153860457-1"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5847","checksum":"72fd291046bd8e5717961bd68f6b6f03","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_CVPR_Swoboda.pdf","date_created":"2019-01-18T12:45:55Z","creator":"dernst","file_size":898652,"date_updated":"2020-07-14T12:48:15Z"}],"ec_funded":1,"volume":2017},{"publication_identifier":{"issn":["00368075"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":356,"issue":"6345","ec_funded":1,"abstract":[{"lang":"eng","text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation."}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/"}],"month":"06","intvolume":" 356","date_updated":"2023-09-26T15:38:05Z","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"_id":"943","type":"journal_article","status":"public","isi":1,"year":"2017","day":"30","publication":"Science","page":"1379 - 1383","doi":"10.1126/science.aam5887","date_published":"2017-06-30T00:00:00Z","date_created":"2018-12-11T11:49:20Z","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"citation":{"ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887.","ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887","apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","ieee":"M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6474","author":[{"last_name":"Zagórski","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"first_name":"Yoji","last_name":"Tabata","full_name":"Tabata, Yoji"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"last_name":"Lutolf","full_name":"Lutolf, Matthias","first_name":"Matthias"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","first_name":"Tobias"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"article_processing_charge":"No","external_id":{"isi":["000404351500036"],"pmid":["28663499"]},"title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"},{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"201439","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["08966273"]},"ec_funded":1,"issue":"3","volume":94,"oa_version":"None","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms."}],"intvolume":" 94","month":"05","scopus_import":"1","date_updated":"2023-09-26T15:37:02Z","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"_id":"944","status":"public","type":"journal_article","publication":"Neuron","day":"03","year":"2017","isi":1,"date_created":"2018-12-11T11:49:20Z","date_published":"2017-05-03T00:00:00Z","doi":"10.1016/j.neuron.2017.04.012","page":"517 - 533.e3","publisher":"Cell Press","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:10.1016/j.neuron.2017.04.012.","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2017.04.012","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 2017;94(3):517-533.e3. doi:10.1016/j.neuron.2017.04.012","ieee":"R. J. Beattie et al., “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” Neuron, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017.","short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron. Cell Press, 2017. https://doi.org/10.1016/j.neuron.2017.04.012.","ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3."},"title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","external_id":{"isi":["000400466700011"]},"article_processing_charge":"No","author":[{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","last_name":"Postiglione","full_name":"Postiglione, Maria P"},{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","last_name":"Burnett"},{"first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010"},{"full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Xiao, Guanxi","last_name":"Xiao","first_name":"Guanxi"},{"last_name":"Klezovitch","full_name":"Klezovitch, Olga","first_name":"Olga"},{"first_name":"Valeri","last_name":"Vasioukhin","full_name":"Vasioukhin, Valeri"},{"last_name":"Ghashghaei","full_name":"Ghashghaei, Troy","first_name":"Troy"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"publist_id":"6473","project":[{"call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}]},{"oa_version":"None","abstract":[{"lang":"eng","text":"A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. "}],"month":"09","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-145035105-8"]},"volume":"F130154","_id":"942","status":"public","conference":{"start_date":"2017-09-04","location":"Paderborn, Germany","end_date":"2017-09-08","name":"FSE: Foundations of Software Engineering"},"type":"conference","date_updated":"2023-09-26T15:38:36Z","department":[{"_id":"ToHe"}],"quality_controlled":"1","publisher":"ACM","day":"01","year":"2017","isi":1,"date_created":"2018-12-11T11:49:19Z","date_published":"2017-09-01T00:00:00Z","doi":"10.1145/3106237.3106309","page":"593 - 604","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,” F130154:593–604. ACM, 2017. https://doi.org/10.1145/3106237.3106309.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604.","mla":"Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604. doi:10.1145/3106237.3106309","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). S3: Syntax- and semantic-guided repair synthesis via programming by examples (Vol. F130154, pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn, Germany: ACM. https://doi.org/10.1145/3106237.3106309","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604."},"title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","article_processing_charge":"No","external_id":{"isi":["000414279300055"]},"publist_id":"6477","author":[{"first_name":"Xuan","full_name":"Le, Xuan","last_name":"Le"},{"id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep","last_name":"Chu","full_name":"Chu, Duc Hiep"},{"full_name":"Lo, David","last_name":"Lo","first_name":"David"},{"last_name":"Le Goues","full_name":"Le Goues, Claire","first_name":"Claire"},{"full_name":"Visser, Willem","last_name":"Visser","first_name":"Willem"}]},{"publication_identifier":{"issn":["00319007"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":119,"ec_funded":1,"abstract":[{"lang":"eng","text":"We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.04085 ","open_access":"1"}],"month":"07","intvolume":" 119","date_updated":"2023-09-26T15:39:46Z","department":[{"_id":"MiLe"}],"_id":"939","type":"journal_article","status":"public","isi":1,"year":"2017","day":"18","publication":"Physical Review Letters","date_published":"2017-07-18T00:00:00Z","doi":"10.1103/PhysRevLett.119.033905","date_created":"2018-12-11T11:49:18Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"citation":{"ieee":"B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.","short":"B. Midya, V. Konotop, Physical Review Letters 119 (2017).","apa":"Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905","ama":"Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 2017;119(3). doi:10.1103/PhysRevLett.119.033905","mla":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.","ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6481","author":[{"last_name":"Midya","full_name":"Midya, Bikashkali","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vladimir","full_name":"Konotop, Vladimir","last_name":"Konotop"}],"external_id":{"isi":["000405718200012"]},"article_processing_charge":"No","title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","article_number":"033905","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"_id":"9853","type":"research_data_reference","status":"public","date_updated":"2023-09-26T15:45:47Z","citation":{"ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Raw data from ant queens increase their reproductive efforts after pathogen infection, The Royal Society, 10.6084/m9.figshare.5117788.v1.","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5117788.v1.","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Raw data from ant queens increase their reproductive efforts after pathogen infection.” The Royal Society, 2017.","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, (2017).","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Raw data from ant queens increase their reproductive efforts after pathogen infection. 2017. doi:10.6084/m9.figshare.5117788.v1","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Raw data from ant queens increase their reproductive efforts after pathogen infection. The Royal Society. https://doi.org/10.6084/m9.figshare.5117788.v1","mla":"Giehr, Julia, et al. Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection. The Royal Society, 2017, doi:10.6084/m9.figshare.5117788.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Giehr, Julia","last_name":"Giehr","first_name":"Julia"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"full_name":"Schrempf, Alexandra","last_name":"Schrempf","first_name":"Alexandra"}],"article_processing_charge":"No","title":"Raw data from ant queens increase their reproductive efforts after pathogen infection","department":[{"_id":"SyCr"}],"abstract":[{"lang":"eng","text":"Egg laying rates and infection loads of C. obscurior queens"}],"oa_version":"Published Version","publisher":"The Royal Society","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.5117788.v1"}],"month":"06","year":"2017","day":"19","doi":"10.6084/m9.figshare.5117788.v1","date_published":"2017-06-19T00:00:00Z","related_material":{"record":[{"status":"public","id":"914","relation":"used_in_publication"}]},"date_created":"2021-08-10T06:57:57Z"},{"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","date_created":"2018-12-11T11:48:41Z","date_published":"2017-10-03T00:00:00Z","doi":"10.1073/pnas.1713372114","page":"10666 - 10671","publication":"PNAS","day":"03","year":"2017","isi":1,"project":[{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics"},{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","external_id":{"pmid":["28923953"],"isi":["000412130500061"]},"article_processing_charge":"No","author":[{"first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","full_name":"De Vos, Marjon"},{"last_name":"Zagórski","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"last_name":"Mcnally","full_name":"Mcnally, Alan","first_name":"Alan"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6827","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671.","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114."},"intvolume":" 114","month":"10","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. "}],"ec_funded":1,"issue":"40","volume":114,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00278424"]},"status":"public","type":"journal_article","_id":"822","department":[{"_id":"ToBo"}],"date_updated":"2023-09-26T16:18:48Z"},{"oa":1,"publisher":"Springer","quality_controlled":"1","day":"28","year":"2017","isi":1,"date_created":"2018-12-11T11:48:45Z","doi":"10.1007/978-3-319-64689-3_32","date_published":"2017-07-28T00:00:00Z","page":"397 - 409","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32.","ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","mla":"Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32.","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409.","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.","apa":"Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32","ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:10.1007/978-3-319-64689-3_32"},"title":"Streaming algorithm for Euler characteristic curves of multidimensional images","editor":[{"first_name":"Michael","full_name":"Felsberg, Michael","last_name":"Felsberg"},{"last_name":"Heyden","full_name":"Heyden, Anders","first_name":"Anders"},{"last_name":"Krüger","full_name":"Krüger, Norbert","first_name":"Norbert"}],"external_id":{"isi":["000432085900032"]},"article_processing_charge":"No","author":[{"first_name":"Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","full_name":"Heiss, Teresa","orcid":"0000-0002-1780-2689"},{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6815","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams."}],"intvolume":" 10424","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02045"}],"alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["03029743"]},"volume":10424,"_id":"833","status":"public","conference":{"end_date":"2017-08-24","location":"Ystad, Sweden","start_date":"2017-08-22","name":"CAIP: Computer Analysis of Images and Patterns"},"type":"conference","date_updated":"2023-09-26T16:10:03Z","department":[{"_id":"HeEd"}]},{"author":[{"last_name":"Pfurr","full_name":"Pfurr, Sabrina","first_name":"Sabrina"},{"last_name":"Chu","full_name":"Chu, Yu","first_name":"Yu"},{"last_name":"Bohrer","full_name":"Bohrer, Christian","first_name":"Christian"},{"full_name":"Greulich, Franziska","last_name":"Greulich","first_name":"Franziska"},{"orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"last_name":"Mammadzada","full_name":"Mammadzada, Könül","first_name":"Könül"},{"last_name":"Hils","full_name":"Hils, Miriam","first_name":"Miriam"},{"first_name":"Sebastian","last_name":"Arnold","full_name":"Arnold, Sebastian"},{"first_name":"Verdon","last_name":"Taylor","full_name":"Taylor, Verdon"},{"first_name":"Kristina","full_name":"Schachtrup, Kristina","last_name":"Schachtrup"},{"first_name":"N Henriette","last_name":"Uhlenhaut","full_name":"Uhlenhaut, N Henriette"},{"first_name":"Christian","full_name":"Schachtrup, Christian","last_name":"Schachtrup"}],"publist_id":"6846","external_id":{"isi":["000414025600007"]},"article_processing_charge":"No","title":"The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development","department":[{"_id":"SiHi"}],"citation":{"short":"S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M. Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development 144 (2017) 3917–3931.","ieee":"S. Pfurr et al., “The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development,” Development, vol. 144. Company of Biologists, pp. 3917–3931, 2017.","ama":"Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 2017;144:3917-3931. doi:10.1242/dev.145698","apa":"Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K., … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. Company of Biologists. https://doi.org/10.1242/dev.145698","mla":"Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development, vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:10.1242/dev.145698.","ista":"Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 144, 3917–3931.","chicago":"Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.145698."},"date_updated":"2023-09-26T16:20:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","status":"public","_id":"805","page":"3917 - 3931","date_published":"2017-10-31T00:00:00Z","volume":144,"doi":"10.1242/dev.145698","date_created":"2018-12-11T11:48:36Z","isi":1,"publication_status":"published","year":"2017","day":"31","publication":"Development","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Company of Biologists","scopus_import":"1","month":"10","intvolume":" 144","abstract":[{"lang":"eng","text":"During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2)."}],"oa_version":"None"},{"article_number":"104201","title":"Thouless energy and multifractality across the many-body localization transition","external_id":{"isi":["000409429300004"]},"article_processing_charge":"No","publist_id":"6814","author":[{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zlatko","full_name":"Zlatko, Papic","first_name":"Papic"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201.","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201","apa":"Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10. American Physical Society, 2017.","short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201."},"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We acknowledge useful discussions with V. Kravtsov, T. Grover, and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","date_created":"2018-12-11T11:48:45Z","date_published":"2017-09-06T00:00:00Z","doi":"10.1103/PhysRevB.96.104201","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"06","year":"2017","isi":1,"status":"public","type":"journal_article","_id":"834","department":[{"_id":"MaSe"}],"date_updated":"2023-09-26T15:51:54Z","intvolume":" 96","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1610.02389","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"issue":"10","volume":96,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24699950"]}},{"status":"public","type":"journal_article","_id":"823","department":[{"_id":"GaTk"}],"date_updated":"2023-09-26T16:18:12Z","month":"09","intvolume":" 2017","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.06303"}],"oa_version":"Submitted Version","abstract":[{"text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.","lang":"eng"}],"issue":"9","volume":2017,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["17425468"]},"publication_status":"published","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"093404","title":"Phase transitions in integer linear problems","publist_id":"6826","author":[{"first_name":"Simona","last_name":"Colabrese","full_name":"Colabrese, Simona"},{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"last_name":"Leuzzi","full_name":"Leuzzi, Luca","first_name":"Luca"},{"first_name":"Enzo","last_name":"Marinari","full_name":"Marinari, Enzo"}],"article_processing_charge":"No","external_id":{"isi":["000411842900001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9. IOPscience, 2017.","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3","apa":"Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.","ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3."},"publisher":"IOPscience","quality_controlled":"1","oa":1,"date_published":"2017-09-26T00:00:00Z","doi":"10.1088/1742-5468/aa85c3","date_created":"2018-12-11T11:48:41Z","day":"26","publication":" Journal of Statistical Mechanics: Theory and Experiment","isi":1,"year":"2017"},{"article_number":"R1","title":"Heteroclinic path to spatially localized chaos in pipe flow","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"publist_id":"6824","article_processing_charge":"No","external_id":{"isi":["000408326300001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge University Press, 2017, doi:10.1017/jfm.2017.516.","ama":"Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516","apa":"Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.516","short":"N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).","ieee":"N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University Press, 2017.","chicago":"Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.516.","ista":"Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1."},"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"date_published":"2017-08-18T00:00:00Z","doi":"10.1017/jfm.2017.516","date_created":"2018-12-11T11:48:42Z","day":"18","publication":"Journal of Fluid Mechanics","isi":1,"year":"2017","status":"public","type":"journal_article","_id":"824","department":[{"_id":"BjHo"}],"date_updated":"2023-09-26T16:17:43Z","month":"08","intvolume":" 827","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.10484","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff.","lang":"eng"}],"volume":827,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00221120"]},"publication_status":"published"},{"type":"journal_article","pubrep_id":"1009","status":"public","_id":"799","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:48:06Z","date_updated":"2023-09-27T11:00:19Z","ddc":["581"],"scopus_import":"1","intvolume":" 58","month":"08","abstract":[{"text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","volume":58,"issue":"10","publication_status":"published","publication_identifier":{"issn":["00320781"]},"language":[{"iso":"eng"}],"file":[{"file_size":1352913,"date_updated":"2020-07-14T12:48:06Z","creator":"dernst","file_name":"2017_PlantCellPhysio_Kitakura.pdf","date_created":"2019-04-17T07:52:34Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6333","checksum":"bd3e3a94d55416739cbb19624bb977f8"}],"article_number":"1801-1811","article_processing_charge":"No","external_id":{"isi":["000413220400019"],"pmid":["29016942"]},"publist_id":"6854","author":[{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"first_name":"Yuki","full_name":"Matsuura, Yuki","last_name":"Matsuura"},{"first_name":"Luca","full_name":"Santuari, Luca","last_name":"Santuari"},{"first_name":"Hirotaka","last_name":"Kouno","full_name":"Kouno, Hirotaka"},{"first_name":"Kohei","last_name":"Arima","full_name":"Arima, Kohei"},{"first_name":"Christian","full_name":"Hardtke, Christian","last_name":"Hardtke"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Tatsuo","last_name":"Kakimoto","full_name":"Kakimoto, Tatsuo"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"}],"title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","citation":{"ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811.","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118.","short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","ieee":"S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017.","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118","mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:10.1093/pcp/pcx118."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","date_created":"2018-12-11T11:48:34Z","date_published":"2017-08-21T00:00:00Z","doi":"10.1093/pcp/pcx118","year":"2017","has_accepted_license":"1","isi":1,"publication":"Plant and Cell Physiology","day":"21"},{"volume":8,"issue":"1","ec_funded":1,"file":[{"creator":"system","file_size":4261832,"date_updated":"2020-07-14T12:48:07Z","file_name":"IST-2017-914-v1+1_s41467-017-00936-3.pdf","date_created":"2018-12-12T10:15:17Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5135","checksum":"7e2c7621afd5f802338e92e8619f024d"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","month":"10","intvolume":" 8","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"PeJo"}],"ddc":["571"],"date_updated":"2023-09-27T10:59:41Z","status":"public","pubrep_id":"914","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"800","date_published":"2017-10-02T00:00:00Z","doi":"10.1038/s41467-017-00936-3","date_created":"2018-12-11T11:48:34Z","day":"02","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2017","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"title":"Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus","publist_id":"6853","author":[{"first_name":"Michael","last_name":"Strüber","full_name":"Strüber, Michael"},{"last_name":"Sauer","full_name":"Sauer, Jonas","first_name":"Jonas"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"}],"article_processing_charge":"No","external_id":{"isi":["000412053100004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758.","chicago":"Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00936-3.","apa":"Strüber, M., Sauer, J., Jonas, P. M., & Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00936-3","ama":"Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00936-3","short":"M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).","ieee":"M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00936-3."},"project":[{"call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"}],"article_number":"758"},{"language":[{"iso":"eng"}],"file":[{"file_name":"2017_Cell_Samwer.pdf","date_created":"2019-01-18T13:45:40Z","file_size":17666637,"date_updated":"2020-07-14T12:48:08Z","creator":"dernst","file_id":"5852","checksum":"64897b0c5373f22273f598e4672c60ff","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["00928674"]},"volume":170,"issue":"5","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function."}],"intvolume":" 170","month":"08","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-27T10:59:14Z","department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:48:08Z","_id":"803","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","publication":"Cell","day":"24","year":"2017","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:48:35Z","doi":"10.1016/j.cell.2017.07.038","date_published":"2017-08-24T00:00:00Z","page":"956 - 972","oa":1,"quality_controlled":"1","publisher":"Cell Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:10.1016/j.cell.2017.07.038.","apa":"Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., & Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.07.038","ama":"Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 2017;170(5):956-972. doi:10.1016/j.cell.2017.07.038","ieee":"M. Samwer et al., “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” Cell, vol. 170, no. 5. Cell Press, pp. 956–972, 2017.","short":"M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972.","chicago":"Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.038.","ista":"Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972."},"title":"DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes","external_id":{"isi":["000408372400014"]},"article_processing_charge":"No","publist_id":"6848","author":[{"last_name":"Samwer","full_name":"Samwer, Matthias","first_name":"Matthias"},{"last_name":"Schneider","full_name":"Schneider, Maximilian","first_name":"Maximilian"},{"full_name":"Hoefler, Rudolf","last_name":"Hoefler","first_name":"Rudolf"},{"id":"309D50DA-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp S","last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133"},{"full_name":"Jude, Julian","last_name":"Jude","first_name":"Julian"},{"full_name":"Zuber, Johannes","last_name":"Zuber","first_name":"Johannes"},{"full_name":"Gerlic, Daniel","last_name":"Gerlic","first_name":"Daniel"}]},{"article_processing_charge":"No","external_id":{"isi":["000412965700036"]},"author":[{"full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133","last_name":"Schmalhorst","first_name":"Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Deluweit","full_name":"Deluweit, Felix","first_name":"Felix"},{"last_name":"Scherrers","full_name":"Scherrers, Roger","first_name":"Roger"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6847","title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","citation":{"mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:10.1021/acs.jctc.7b00374.","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017.","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053.","ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374","apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., & Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374","chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation. American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374.","ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","page":"5039 - 5053","date_created":"2018-12-11T11:48:35Z","date_published":"2017-10-10T00:00:00Z","doi":"10.1021/acs.jctc.7b00374","year":"2017","isi":1,"publication":"Journal of Chemical Theory and Computation","day":"10","type":"journal_article","status":"public","_id":"804","department":[{"_id":"CaHe"}],"date_updated":"2023-09-27T10:58:45Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.03773"}],"scopus_import":"1","intvolume":" 13","month":"10","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides."}],"oa_version":"Submitted Version","volume":13,"issue":"10","publication_status":"published","publication_identifier":{"issn":["15499618"]},"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:58Z","file_size":1841650,"creator":"system","date_created":"2018-12-12T10:17:32Z","file_name":"IST-2017-915-v1+1_s41467-017-01191-2.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5287","checksum":"99ceee57549dc0461e3adfc037ec70a9"}],"publication_status":"published","publication_identifier":{"issn":["20411723"]},"issue":"1","volume":8,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics."}],"intvolume":" 8","month":"12","scopus_import":"1","ddc":["571"],"date_updated":"2023-09-27T12:27:30Z","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:58Z","_id":"746","pubrep_id":"915","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"Nature Communications","day":"01","year":"2017","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:48:17Z","doi":"10.1038/s41467-017-01191-2","date_published":"2017-12-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"E. Aloisi, K. Le Corf, J. Dupuis, P. Zhang, M. Ginger, V. Labrousse, M. Spatuzza, M. Georg Haberl, L. Costa, R. Shigemoto, A. Tappe Theodor, F. Drago, P. Vincenzo Piazza, C. Mulle, L. Groc, L. Ciranna, M. Catania, A. Frick, Nature Communications 8 (2017).","ieee":"E. Aloisi et al., “Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","ama":"Aloisi E, Le Corf K, Dupuis J, et al. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01191-2","apa":"Aloisi, E., Le Corf, K., Dupuis, J., Zhang, P., Ginger, M., Labrousse, V., … Frick, A. (2017). Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01191-2","mla":"Aloisi, Elisabetta, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications, vol. 8, no. 1, 1103, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01191-2.","ista":"Aloisi E, Le Corf K, Dupuis J, Zhang P, Ginger M, Labrousse V, Spatuzza M, Georg Haberl M, Costa L, Shigemoto R, Tappe Theodor A, Drago F, Vincenzo Piazza P, Mulle C, Groc L, Ciranna L, Catania M, Frick A. 2017. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 8(1), 1103.","chicago":"Aloisi, Elisabetta, Katy Le Corf, Julien Dupuis, Pei Zhang, Melanie Ginger, Virginie Labrousse, Michela Spatuzza, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01191-2."},"title":"Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice","external_id":{"isi":["000413571300004"]},"article_processing_charge":"No","publist_id":"6921","author":[{"full_name":"Aloisi, Elisabetta","last_name":"Aloisi","first_name":"Elisabetta"},{"first_name":"Katy","full_name":"Le Corf, Katy","last_name":"Le Corf"},{"last_name":"Dupuis","full_name":"Dupuis, Julien","first_name":"Julien"},{"full_name":"Zhang, Pei","last_name":"Zhang","first_name":"Pei"},{"full_name":"Ginger, Melanie","last_name":"Ginger","first_name":"Melanie"},{"last_name":"Labrousse","full_name":"Labrousse, Virginie","first_name":"Virginie"},{"first_name":"Michela","last_name":"Spatuzza","full_name":"Spatuzza, Michela"},{"first_name":"Matthias","last_name":"Georg Haberl","full_name":"Georg Haberl, Matthias"},{"first_name":"Lara","last_name":"Costa","full_name":"Costa, Lara"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Anke","full_name":"Tappe Theodor, Anke","last_name":"Tappe Theodor"},{"first_name":"Fillippo","last_name":"Drago","full_name":"Drago, Fillippo"},{"first_name":"Pier","full_name":"Vincenzo Piazza, Pier","last_name":"Vincenzo Piazza"},{"last_name":"Mulle","full_name":"Mulle, Christophe","first_name":"Christophe"},{"last_name":"Groc","full_name":"Groc, Laurent","first_name":"Laurent"},{"first_name":"Lucia","full_name":"Ciranna, Lucia","last_name":"Ciranna"},{"last_name":"Catania","full_name":"Catania, Maria","first_name":"Maria"},{"first_name":"Andreas","full_name":"Frick, Andreas","last_name":"Frick"}],"article_number":"1103"},{"title":"Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses","author":[{"full_name":"Chen, Chong","last_name":"Chen","first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Satterfield, Rachel","last_name":"Satterfield","first_name":"Rachel"},{"last_name":"Young","full_name":"Young, Samuel","first_name":"Samuel"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6907","external_id":{"isi":["000416216700007"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Chen, C., Satterfield, R., Young, S., & Jonas, P. M. (2017). Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.10.122","ama":"Chen C, Satterfield R, Young S, Jonas PM. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. 2017;21(8):2082-2089. doi:10.1016/j.celrep.2017.10.122","short":"C. Chen, R. Satterfield, S. Young, P.M. Jonas, Cell Reports 21 (2017) 2082–2089.","ieee":"C. Chen, R. Satterfield, S. Young, and P. M. Jonas, “Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses,” Cell Reports, vol. 21, no. 8. Cell Press, pp. 2082–2089, 2017.","mla":"Chen, Chong, et al. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports, vol. 21, no. 8, Cell Press, 2017, pp. 2082–89, doi:10.1016/j.celrep.2017.10.122.","ista":"Chen C, Satterfield R, Young S, Jonas PM. 2017. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. 21(8), 2082–2089.","chicago":"Chen, Chong, Rachel Satterfield, Samuel Young, and Peter M Jonas. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.10.122."},"project":[{"grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"}],"doi":"10.1016/j.celrep.2017.10.122","date_published":"2017-11-21T00:00:00Z","date_created":"2018-12-11T11:48:18Z","page":"2082 - 2089","day":"21","publication":"Cell Reports","has_accepted_license":"1","isi":1,"year":"2017","quality_controlled":"1","publisher":"Cell Press","oa":1,"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"PeJo"}],"ddc":["570","571"],"date_updated":"2023-09-27T12:26:04Z","status":"public","pubrep_id":"874","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"749","volume":21,"issue":"8","related_material":{"record":[{"id":"324","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"checksum":"a6afa3764909bf6edafa07982d8e1cee","file_id":"4737","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:09:14Z","file_name":"IST-2017-874-v1+1_PIIS2211124717316029.pdf","creator":"system","date_updated":"2020-07-14T12:47:59Z","file_size":2759195}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["22111247"]},"publication_status":"published","month":"11","intvolume":" 21","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, Syt7 is strongly expressed in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. To resolve this apparent contradiction, we examined the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment, and facilitation. In combination, these three effects ensure efficient transmitter release during high-frequency activity and guarantee frequency independence of inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency of high-frequency inhibitory synaptic transmission"}]},{"citation":{"short":"T. Priklopil, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 433 (2017) 64–72.","ieee":"T. Priklopil, K. Chatterjee, and M. Nowak, “Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma,” Journal of Theoretical Biology, vol. 433. Elsevier, pp. 64–72, 2017.","apa":"Priklopil, T., Chatterjee, K., & Nowak, M. (2017). Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2017.08.025","ama":"Priklopil T, Chatterjee K, Nowak M. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. 2017;433:64-72. doi:10.1016/j.jtbi.2017.08.025","mla":"Priklopil, Tadeas, et al. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” Journal of Theoretical Biology, vol. 433, Elsevier, 2017, pp. 64–72, doi:10.1016/j.jtbi.2017.08.025.","ista":"Priklopil T, Chatterjee K, Nowak M. 2017. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. 433, 64–72.","chicago":"Priklopil, Tadeas, Krishnendu Chatterjee, and Martin Nowak. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” Journal of Theoretical Biology. Elsevier, 2017. https://doi.org/10.1016/j.jtbi.2017.08.025."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6923","author":[{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"isi":["000412039800007"],"pmid":["28867224"]},"title":"Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"isi":1,"has_accepted_license":"1","year":"2017","day":"21","publication":" Journal of Theoretical Biology","page":"64 - 72","date_published":"2017-11-21T00:00:00Z","doi":"10.1016/j.jtbi.2017.08.025","date_created":"2018-12-11T11:48:16Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_updated":"2023-09-27T12:29:02Z","ddc":["000","570"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:58Z","_id":"744","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","publication_identifier":{"issn":["00225193"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:58Z","file_size":537323,"date_created":"2019-11-19T07:57:39Z","file_name":"2017_JournTheoretBio_Priklopil.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"4b43af1615ebf1a861840cb03d8a320c","file_id":"7047"}],"language":[{"iso":"eng"}],"volume":433,"ec_funded":1,"abstract":[{"text":"In evolutionary game theory interactions between individuals are often assumed obligatory. However, in many real-life situations, individuals can decide to opt out of an interaction depending on the information they have about the opponent. We consider a simple evolutionary game theoretic model to study such a scenario, where at each encounter between two individuals the type of the opponent (cooperator/defector) is known with some probability, and where each individual either accepts or opts out of the interaction. If the type of the opponent is unknown, a trustful individual accepts the interaction, whereas a suspicious individual opts out of the interaction. If either of the two individuals opt out both individuals remain without an interaction. We show that in the prisoners dilemma optional interactions along with suspicious behaviour facilitates the emergence of trustful cooperation.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","month":"11","intvolume":" 433"},{"article_processing_charge":"No","external_id":{"isi":["000412934800005"]},"publist_id":"6922","author":[{"full_name":"Xu, Duo","last_name":"Xu","first_name":"Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Warnecke, Sascha","last_name":"Warnecke","first_name":"Sascha"},{"last_name":"Song","full_name":"Song, Baofang","first_name":"Baofang"},{"orcid":"0000-0002-0179-9737","full_name":"Ma, Xingyu","last_name":"Ma","first_name":"Xingyu","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"title":"Transition to turbulence in pulsating pipe flow","citation":{"mla":"Xu, Duo, et al. “Transition to Turbulence in Pulsating Pipe Flow.” Journal of Fluid Mechanics, vol. 831, Cambridge University Press, 2017, pp. 418–32, doi:10.1017/jfm.2017.620.","short":"D. Xu, S. Warnecke, B. Song, X. Ma, B. Hof, Journal of Fluid Mechanics 831 (2017) 418–432.","ieee":"D. Xu, S. Warnecke, B. Song, X. Ma, and B. Hof, “Transition to turbulence in pulsating pipe flow,” Journal of Fluid Mechanics, vol. 831. Cambridge University Press, pp. 418–432, 2017.","ama":"Xu D, Warnecke S, Song B, Ma X, Hof B. Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. 2017;831:418-432. doi:10.1017/jfm.2017.620","apa":"Xu, D., Warnecke, S., Song, B., Ma, X., & Hof, B. (2017). Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.620","chicago":"Xu, Duo, Sascha Warnecke, Baofang Song, Xingyu Ma, and Björn Hof. “Transition to Turbulence in Pulsating Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.620.","ista":"Xu D, Warnecke S, Song B, Ma X, Hof B. 2017. Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. 831, 418–432."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"page":"418 - 432","date_created":"2018-12-11T11:48:17Z","doi":"10.1017/jfm.2017.620","date_published":"2017-11-25T00:00:00Z","year":"2017","isi":1,"publication":"Journal of Fluid Mechanics","day":"25","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"date_updated":"2023-09-27T12:28:12Z","type":"journal_article","status":"public","_id":"745","ec_funded":1,"volume":831,"publication_status":"published","publication_identifier":{"issn":["00221120"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.03738"}],"scopus_import":"1","intvolume":" 831","month":"11","abstract":[{"lang":"eng","text":"Fluid flows in nature and applications are frequently subject to periodic velocity modulations. Surprisingly, even for the generic case of flow through a straight pipe, there is little consensus regarding the influence of pulsation on the transition threshold to turbulence: while most studies predict a monotonically increasing threshold with pulsation frequency (i.e. Womersley number, ), others observe a decreasing threshold for identical parameters and only observe an increasing threshold at low . In the present study we apply recent advances in the understanding of transition in steady shear flows to pulsating pipe flow. For moderate pulsation amplitudes we find that the first instability encountered is subcritical (i.e. requiring finite amplitude disturbances) and gives rise to localized patches of turbulence ('puffs') analogous to steady pipe flow. By monitoring the impact of pulsation on the lifetime of turbulence we map the onset of turbulence in parameter space. Transition in pulsatile flow can be separated into three regimes. At small Womersley numbers the dynamics is dominated by the decay turbulence suffers during the slower part of the cycle and hence transition is delayed significantly. As shown in this regime thresholds closely agree with estimates based on a quasi-steady flow assumption only taking puff decay rates into account. The transition point predicted in the zero limit equals to the critical point for steady pipe flow offset by the oscillation Reynolds number (i.e. the dimensionless oscillation amplitude). In the high frequency limit on the other hand, puff lifetimes are identical to those in steady pipe flow and hence the transition threshold appears to be unaffected by flow pulsation. In the intermediate frequency regime the transition threshold sharply drops (with increasing ) from the decay dominated (quasi-steady) threshold to the steady pipe flow level."}],"oa_version":"Submitted Version"},{"month":"12","intvolume":" 365","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798458"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia."}],"volume":365,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03064522"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"747","department":[{"_id":"GaNo"}],"date_updated":"2023-09-27T12:26:59Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_published":"2017-12-04T00:00:00Z","doi":"10.1016/j.neuroscience.2017.09.034","date_created":"2018-12-11T11:48:17Z","page":"23 - 32","day":"04","publication":"Neuroscience","isi":1,"year":"2017","title":"Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus","author":[{"full_name":"Brǎiloiu, Eugen","last_name":"Brǎiloiu","first_name":"Eugen"},{"first_name":"Matthew","full_name":"Mcguire, Matthew","last_name":"Mcguire"},{"first_name":"Shadaria","full_name":"Shuler, Shadaria","last_name":"Shuler"},{"id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Deliu","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena"},{"last_name":"Barr","full_name":"Barr, Jeffrey","first_name":"Jeffrey"},{"last_name":"Abood","full_name":"Abood, Mary","first_name":"Mary"},{"first_name":"Gabriela","full_name":"Brailoiu, Gabriela","last_name":"Brailoiu"}],"publist_id":"6911","article_processing_charge":"No","external_id":{"isi":["000415966200003"],"pmid":["28951324"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Brǎiloiu E, Mcguire M, Shuler S, Deliu E, Barr J, Abood M, Brailoiu G. 2017. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 365, 23–32.","chicago":"Brǎiloiu, Eugen, Matthew Mcguire, Shadaria Shuler, Elena Deliu, Jeffrey Barr, Mary Abood, and Gabriela Brailoiu. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” Neuroscience. Elsevier, 2017. https://doi.org/10.1016/j.neuroscience.2017.09.034.","short":"E. Brǎiloiu, M. Mcguire, S. Shuler, E. Deliu, J. Barr, M. Abood, G. Brailoiu, Neuroscience 365 (2017) 23–32.","ieee":"E. Brǎiloiu et al., “Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus,” Neuroscience, vol. 365. Elsevier, pp. 23–32, 2017.","ama":"Brǎiloiu E, Mcguire M, Shuler S, et al. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 2017;365:23-32. doi:10.1016/j.neuroscience.2017.09.034","apa":"Brǎiloiu, E., Mcguire, M., Shuler, S., Deliu, E., Barr, J., Abood, M., & Brailoiu, G. (2017). Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2017.09.034","mla":"Brǎiloiu, Eugen, et al. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” Neuroscience, vol. 365, Elsevier, 2017, pp. 23–32, doi:10.1016/j.neuroscience.2017.09.034."}}]