[{"type":"journal_article","status":"public","_id":"959","department":[{"_id":"GaTk"}],"date_updated":"2023-09-22T09:59:01Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1703.00853.pdf"}],"scopus_import":"1","intvolume":" 95","month":"06","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."}],"oa_version":"Submitted Version","ec_funded":1,"volume":95,"issue":"6","publication_status":"published","publication_identifier":{"issn":["24700045"]},"language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"external_id":{"isi":["000404546400004"]},"article_processing_charge":"No","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"}],"publist_id":"6446","title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","citation":{"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.","short":"D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","page":"062419","date_created":"2018-12-11T11:49:25Z","date_published":"2017-06-28T00:00:00Z","doi":"10.1103/PhysRevE.95.062419","year":"2017","isi":1,"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","day":"28"},{"date_updated":"2023-09-22T10:00:18Z","department":[{"_id":"JaMa"}],"_id":"956","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00221236"]},"publication_status":"published","volume":273,"issue":"5","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"09","intvolume":" 273","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.01254"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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."},"title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance","publist_id":"6452","author":[{"last_name":"Carlen","full_name":"Carlen, Eric","first_name":"Eric"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"external_id":{"isi":["000406082300005"]},"article_processing_charge":"No","day":"01","publication":"Journal of Functional Analysis","isi":1,"year":"2017","doi":"10.1016/j.jfa.2017.05.003","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:49:24Z","page":"1810 - 1869","quality_controlled":"1","publisher":"Academic Press","oa":1},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","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","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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."},"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"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"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","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:16Z","file_size":2073856,"date_created":"2019-04-17T06:39:45Z","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6327","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01"}],"publication_status":"published","publication_identifier":{"issn":["00405809"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":115,"_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","ddc":["576"],"date_updated":"2023-09-22T10:02:21Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z"},{"isi":1,"has_accepted_license":"1","year":"2017","day":"30","publication":"PLoS Biology","date_published":"2017-05-30T00:00:00Z","doi":"10.1371/journal.pbio.2001894","date_created":"2018-12-11T11:49:22Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"citation":{"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).","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6464","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Gordana","last_name":"Rasic","full_name":"Rasic, Gordana"},{"last_name":"Turley","full_name":"Turley, Andrew","first_name":"Andrew"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"last_name":"Cook","full_name":"Cook, Peter","first_name":"Peter"},{"first_name":"Peter","full_name":"Ryan, Peter","last_name":"Ryan"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"article_processing_charge":"No","external_id":{"isi":["000402520000012"]},"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","article_number":"e2001894","publication_identifier":{"issn":["15449173"]},"publication_status":"published","file":[{"checksum":"107d290bd1159ec77b734eb2824b01c8","file_id":"4691","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:08:30Z","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","creator":"system","date_updated":"2020-07-14T12:48:16Z","file_size":5541206}],"language":[{"iso":"eng"}],"issue":"5","volume":15,"related_material":{"record":[{"relation":"research_data","id":"9856","status":"public"},{"id":"9857","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9858"}]},"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"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","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 15","date_updated":"2023-09-22T10:02:52Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","_id":"951","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)"},"status":"public","pubrep_id":"843"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["24700045"]},"publication_status":"published","volume":96,"issue":"1","ec_funded":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"}],"month":"07","intvolume":" 96","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00219"}],"date_updated":"2023-09-22T10:03:50Z","department":[{"_id":"GaTk"}],"_id":"947","status":"public","type":"journal_article","day":"10","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","isi":1,"year":"2017","date_published":"2017-07-10T00:00:00Z","doi":"10.1103/PhysRevE.96.010401","date_created":"2018-12-11T11:49:21Z","quality_controlled":"1","publisher":"American Institute of Physics","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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","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.","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.","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.","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."},"title":"Quantifying the entropic cost of cellular growth control","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"first_name":"Fabrizio","last_name":"Capuani","full_name":"Capuani, Fabrizio"},{"first_name":"Andrea","full_name":"De Martino, Andrea","last_name":"De Martino"}],"publist_id":"6470","article_processing_charge":"No","external_id":{"isi":["000405194200002"]},"article_number":"010401","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"day":"30","year":"2017","date_created":"2021-08-10T07:47:07Z","doi":"10.1371/journal.pbio.2001894.s016","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"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"},{"full_name":"Rasic, Gordana","last_name":"Rasic","first_name":"Gordana"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"first_name":"Brian","full_name":"Montgomery, Brian","last_name":"Montgomery"},{"first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"last_name":"Ryan","full_name":"Ryan, Peter","first_name":"Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"full_name":"Hoffmann, Ary","last_name":"Hoffmann","first_name":"Ary"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"last_name":"Turelli","full_name":"Turelli, Michael","first_name":"Michael"}],"_id":"9858","status":"public","type":"research_data_reference"},{"department":[{"_id":"NiBa"}],"title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gordana","last_name":"Rasic","full_name":"Rasic, Gordana"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"first_name":"Brian","full_name":"Montgomery, Brian","last_name":"Montgomery"},{"first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe"},{"first_name":"Peter","full_name":"Cook, Peter","last_name":"Cook"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","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"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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).","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","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","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.","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.","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."},"date_updated":"2023-09-22T10:02:51Z","status":"public","type":"research_data_reference","_id":"9857","related_material":{"record":[{"status":"public","id":"951","relation":"used_in_publication"}]},"date_published":"2017-05-30T00:00:00Z","doi":"10.1371/journal.pbio.2001894.s015","date_created":"2021-08-10T07:41:52Z","day":"30","year":"2017","month":"05","publisher":"Public Library of Science ","oa_version":"Published Version"},{"publisher":"Public Library of Science","month":"05","oa_version":"Published Version","date_created":"2021-08-10T07:36:04Z","doi":"10.1371/journal.pbio.2001894.s014","date_published":"2017-05-30T00:00:00Z","related_material":{"record":[{"id":"951","status":"public","relation":"used_in_publication"}]},"year":"2017","day":"30","type":"research_data_reference","status":"public","_id":"9856","article_processing_charge":"No","author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"first_name":"Peter","full_name":"Cook, Peter","last_name":"Cook"},{"last_name":"Ryan","full_name":"Ryan, Peter","first_name":"Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"last_name":"Hoffmann","full_name":"Hoffmann, Ary","first_name":"Ary"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"title":"Supporting Information concerning additional likelihood analyses and results","department":[{"_id":"NiBa"}],"date_updated":"2023-09-22T10:02:51Z","citation":{"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.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"publisher":"Oxford University Press","quality_controlled":"1","oa":1,"date_published":"2017-07-06T00:00:00Z","doi":"10.1093/molbev/msx190","date_created":"2018-12-11T11:49:20Z","page":"2637 - 2649","day":"06","publication":"Molecular Biology and Evolution","has_accepted_license":"1","isi":1,"year":"2017","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","publist_id":"6472","author":[{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans"},{"last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000411814800016"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","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.","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"},"month":"07","intvolume":" 34","scopus_import":"1","oa_version":"Published Version","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."}],"issue":"10","volume":34,"file":[{"creator":"system","file_size":462863,"date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","date_created":"2018-12-12T10:10:23Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"009fd68043211d645ceb9d1de28274f2","file_id":"4810"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07374038"]},"publication_status":"published","status":"public","pubrep_id":"848","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":"945","file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"BeVi"}],"ddc":["570","576"],"date_updated":"2023-09-26T15:36:34Z"},{"quality_controlled":"1","publisher":"Cell Press","oa":1,"has_accepted_license":"1","isi":1,"year":"2017","day":"09","publication":"Current Biology","page":"3526 - 3534e.4","doi":"10.1016/j.cub.2017.10.001","date_published":"2017-11-09T00:00:00Z","date_created":"2018-12-11T11:48:18Z","citation":{"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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Yutaka","full_name":"Matsubayashi, Yutaka","last_name":"Matsubayashi"},{"last_name":"Louani","full_name":"Louani, Adam","first_name":"Adam"},{"first_name":"Anca","full_name":"Dragu, Anca","last_name":"Dragu"},{"first_name":"Besaiz","last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz"},{"full_name":"Serna Morales, Eduardo","last_name":"Serna Morales","first_name":"Eduardo"},{"first_name":"Lawrence","last_name":"Yolland","full_name":"Yolland, Lawrence"},{"full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vizcay","full_name":"Vizcay, Gema","first_name":"Gema"},{"first_name":"Roland","full_name":"Fleck, Roland","last_name":"Fleck"},{"last_name":"Heddleston","full_name":"Heddleston, John","first_name":"John"},{"full_name":"Chew, Teng","last_name":"Chew","first_name":"Teng"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stramer, Brian","last_name":"Stramer","first_name":"Brian"}],"publist_id":"6905","external_id":{"isi":["000415815800031"]},"article_processing_charge":"No","title":"A moving source of matrix components is essential for De Novo basement membrane formation","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"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 27","publication_identifier":{"issn":["09609822"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:59Z","file_size":4770657,"creator":"system","date_created":"2018-12-12T10:09:45Z","file_name":"IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4770","checksum":"264cf6c6c3551486ba5ea786850e000a"}],"language":[{"iso":"eng"}],"volume":27,"issue":"22","_id":"751","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)"},"status":"public","pubrep_id":"875","date_updated":"2023-09-27T12:25:31Z","ddc":["570","576"],"department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:47:59Z"}]