[{"publist_id":"8036","date_updated":"2023-10-17T11:51:06Z","date_created":"2018-12-11T11:44:11Z","volume":35,"author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","first_name":"Remy P","full_name":"Chait, Remy P"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Oxford University Press","year":"2018","pmid":1,"month":"08","publication_identifier":{"issn":["0737-4038"]},"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy163","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"abstract":[{"text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","intvolume":" 35","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"19","day":"28","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-28T00:00:00Z","article_type":"original","page":"2669 - 2684","publication":"Molecular Biology and Evolution","citation":{"ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163","apa":"Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy163","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163."}},{"title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","status":"public","publication_status":"published","intvolume":" 141","publisher":"MyJove Corporation","department":[{"_id":"MaJö"}],"_id":"6","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T11:49:25Z","date_created":"2018-12-11T11:44:07Z","volume":141,"oa_version":"None","author":[{"last_name":"Masís","first_name":"Javier","full_name":"Masís, Javier"},{"full_name":"Mankus, David","first_name":"David","last_name":"Mankus"},{"first_name":"Steffen","last_name":"Wolff","full_name":"Wolff, Steffen"},{"last_name":"Guitchounts","first_name":"Grigori","full_name":"Guitchounts, Grigori"},{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A"},{"full_name":"Cox, David","first_name":"David","last_name":"Cox"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies."}],"publist_id":"8050","isi":1,"quality_controlled":"1","publication":"Journal of visualized experiments","citation":{"ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 2018;141. doi:10.3791/58585","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of Visualized Experiments. MyJove Corporation. https://doi.org/10.3791/58585","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for characterising lesions and locating electrodes in small animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation, 2018.","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 141.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal of Visualized Experiments 141 (2018).","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments, vol. 141, MyJove Corporation, 2018, doi:10.3791/58585.","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments. MyJove Corporation, 2018. https://doi.org/10.3791/58585."},"external_id":{"isi":["000456469400103"]},"language":[{"iso":"eng"}],"date_published":"2018-11-08T00:00:00Z","doi":"10.3791/58585","scopus_import":"1","day":"08","month":"11","article_processing_charge":"No"},{"doi":"10.5281/ZENODO.1322669","date_published":"2018-10-23T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.1480665"}],"oa":1,"citation":{"chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669.","mla":"Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, 10.5281/ZENODO.1322669.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669"},"month":"10","day":"23","article_processing_charge":"No","author":[{"last_name":"Stroeymeyt","first_name":"Nathalie","full_name":"Stroeymeyt, Nathalie"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"last_name":"Crespi","first_name":"Alessandro","full_name":"Crespi, Alessandro"},{"last_name":"Mersch","first_name":"Danielle","full_name":"Mersch, Danielle"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"},{"last_name":"Keller","first_name":"Laurent","full_name":"Keller, Laurent"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7"}]},"date_updated":"2023-10-17T11:50:04Z","date_created":"2023-05-23T13:24:51Z","oa_version":"Published Version","year":"2018","_id":"13055","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Social network plasticity decreases disease transmission in a eusocial insect","department":[{"_id":"SyCr"}],"publisher":"Zenodo","abstract":[{"text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n - correction of URLs within README.txt file\r\n","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","type":"research_data_reference"},{"month":"10","publication_identifier":{"issn":["23342536"]},"main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"external_id":{"isi":["000447853100007"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1364/OPTICA.5.001210","language":[{"iso":"eng"}],"publist_id":"8033","year":"2018","publication_status":"published","department":[{"_id":"JoFi"}],"author":[{"last_name":"Botello","first_name":"Gabriel","full_name":"Botello, Gabriel"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"first_name":"Kerlos","last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos"},{"last_name":"Brown","first_name":"Elliott","full_name":"Brown, Elliott"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Sascha","last_name":"Preu","full_name":"Preu, Sascha"},{"full_name":"Segovia Vargas, Daniel","first_name":"Daniel","last_name":"Segovia Vargas"},{"first_name":"Dmitry","last_name":"Strekalov","full_name":"Strekalov, Dmitry"},{"last_name":"Munoz","first_name":"Luis","full_name":"Munoz, Luis"},{"full_name":"Schwefel, Harald","last_name":"Schwefel","first_name":"Harald"}],"date_updated":"2023-10-17T12:12:40Z","date_created":"2018-12-11T11:44:12Z","volume":5,"scopus_import":"1","day":"20","article_processing_charge":"No","publication":"Optica","citation":{"ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210","apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210","ieee":"G. Botello et al., “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” Optica, vol. 5, no. 10. pp. 1210–1219, 2018.","ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219.","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219.","mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10, 2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210.","chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, 2018. https://doi.org/10.1364/OPTICA.5.001210."},"article_type":"original","page":"1210 - 1219","date_published":"2018-10-20T00:00:00Z","type":"journal_article","abstract":[{"text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems.","lang":"eng"}],"issue":"10","_id":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","status":"public","intvolume":" 5","oa_version":"Published Version"},{"publication_identifier":{"issn":["1551-3939"]},"month":"05","quality_controlled":"1","main_file_link":[{"url":"https://hal.inria.fr/hal-00757488/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1561/1000000053","department":[{"_id":"ToHe"}],"publisher":"Now Publishers","publication_status":"published","year":"2018","volume":12,"date_created":"2018-12-16T22:59:19Z","date_updated":"2023-10-17T11:53:09Z","author":[{"first_name":"Albert","last_name":"Benveniste","full_name":"Benveniste, Albert"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"},{"first_name":"Benoît","last_name":"Caillaud","full_name":"Caillaud, Benoît"},{"last_name":"Passerone","first_name":"Roberto","full_name":"Passerone, Roberto"},{"last_name":"Raclet","first_name":"Jean Baptiste","full_name":"Raclet, Jean Baptiste"},{"full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier","first_name":"Philipp"},{"full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni-Vincentelli","first_name":"Alberto"},{"last_name":"Damm","first_name":"Werner","full_name":"Damm, Werner"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Kim G.","last_name":"Larsen","full_name":"Larsen, Kim G."}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"124-400","article_type":"original","citation":{"ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053","ieee":"A. Benveniste et al., “Contracts for system design,” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053","chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053.","mla":"Benveniste, Albert, et al. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:10.1561/1000000053.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400."},"publication":"Foundations and Trends in Electronic Design Automation","date_published":"2018-05-01T00:00:00Z","type":"journal_article","issue":"2-3","abstract":[{"text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector.","lang":"eng"}],"intvolume":" 12","status":"public","title":"Contracts for system design","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5677","oa_version":"Submitted Version"},{"scopus_import":"1","day":"01","article_processing_charge":"No","page":"607 - 610","publication":"Optics Letters","citation":{"mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607.","short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing Group, 2018. https://doi.org/10.1364/OL.43.000607.","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607","ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610.","ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018.","apa":"Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.43.000607"},"date_published":"2018-02-01T00:00:00Z","type":"journal_article","abstract":[{"text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum.","lang":"eng"}],"issue":"3","title":"Coherent-perfect-absorber and laser for bound states in a continuum","status":"public","intvolume":" 43","_id":"435","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"02","quality_controlled":"1","isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"external_id":{"arxiv":["1711.01986"],"isi":["000423776600066"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.01986"}],"language":[{"iso":"eng"}],"doi":"10.1364/OL.43.000607","publist_id":"7388","ec_funded":1,"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"Optica Publishing Group","year":"2018","acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","date_updated":"2023-10-17T12:15:06Z","date_created":"2018-12-11T11:46:27Z","volume":43,"author":[{"full_name":"Midya, Bikashkali","first_name":"Bikashkali","last_name":"Midya","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konotop, Vladimir","last_name":"Konotop","first_name":"Vladimir"}]},{"abstract":[{"text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1480792,"creator":"dernst","file_name":"2018_PeerJ_Fraisse.pdf","access_level":"open_access","date_created":"2018-12-18T09:42:11Z","date_updated":"2020-07-14T12:44:48Z","checksum":"7d55ae22598a1c70759cd671600cff53","relation":"main_file","file_id":"5739"}],"status":"public","ddc":["576"],"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","intvolume":" 2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"139","day":"30","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-30T00:00:00Z","publication":"PeerJ","citation":{"chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198"},"file_date_updated":"2020-07-14T12:44:48Z","publist_id":"7784","article_number":"30083438","date_created":"2018-12-11T11:44:50Z","date_updated":"2023-10-17T12:25:28Z","volume":2018,"author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"last_name":"Gagnaire","first_name":"Pierre","full_name":"Gagnaire, Pierre"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"full_name":"Welch, John","last_name":"Welch","first_name":"John"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"publication_status":"published","publisher":"PeerJ","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2018","month":"07","language":[{"iso":"eng"}],"doi":"10.7717/peerj.5198","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000440484800002"]}},{"publication":"PeerJ","citation":{"ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325."},"date_published":"2018-10-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"33","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["576"],"title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","intvolume":" 2018","file":[{"file_name":"2018_PeerJ_Bertl.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1328344,"creator":"dernst","relation":"main_file","file_id":"5692","date_created":"2018-12-17T10:46:06Z","date_updated":"2020-07-14T12:46:06Z","checksum":"3334886c4b39678db4c4b74299ca14ba"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.","lang":"eng"}],"issue":"10","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"quality_controlled":"1","isi":1,"doi":"10.7717/peerj.5325","language":[{"iso":"eng"}],"month":"10","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","year":"2018","pmid":1,"publication_status":"published","publisher":"PeerJ","department":[{"_id":"NiBa"}],"author":[{"last_name":"Bertl","first_name":"Johanna","full_name":"Bertl, Johanna"},{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald"},{"last_name":"Blum","first_name":"Michaël","full_name":"Blum, Michaël"}],"date_created":"2018-12-11T11:44:16Z","date_updated":"2023-10-17T12:24:43Z","volume":2018,"article_number":"e5325","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"8022"},{"ec_funded":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Research","year":"2018","pmid":1,"date_updated":"2023-10-17T12:19:28Z","date_created":"2018-12-16T22:59:18Z","volume":4,"author":[{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"month":"12","publication_identifier":{"issn":["2055-0278"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833","open_access":"1"}],"external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0318-3","type":"journal_article","abstract":[{"lang":"eng","text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment."}],"issue":"12","title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","status":"public","intvolume":" 4","_id":"5673","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","day":"03","article_processing_charge":"No","page":"1082-1088","publication":"Nature Plants","citation":{"mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018."},"date_published":"2018-12-03T00:00:00Z"},{"date_updated":"2023-10-18T06:36:00Z","date_created":"2018-12-11T11:45:09Z","volume":15,"author":[{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"related_material":{"record":[{"id":"9814","relation":"research_data","status":"public"}],"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971","relation":"supplementary_material"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"The Royal Society","year":"2018","pmid":1,"file_date_updated":"2020-07-14T12:45:22Z","ec_funded":1,"publist_id":"7715","article_number":"20180073","language":[{"iso":"eng"}],"doi":"10.1098/rsif.2018.0073","isi":1,"quality_controlled":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"oa":1,"month":"03","publication_identifier":{"eissn":["1742-5662"]},"file":[{"date_updated":"2020-07-14T12:45:22Z","date_created":"2019-02-12T07:54:37Z","checksum":"444e1a9d98eb0e780671be82b13025f3","file_id":"5955","relation":"main_file","creator":"dernst","file_size":219837,"content_type":"application/pdf","file_name":"2018_RS_IbsenJensen.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","title":"Language acquisition with communication between learners","status":"public","ddc":["000"],"intvolume":" 15","_id":"198","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students."}],"issue":"140","type":"journal_article","date_published":"2018-03-01T00:00:00Z","article_type":"original","publication":"Journal of the Royal Society Interface","citation":{"ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. Journal of the Royal Society Interface. 2018;15(140). doi:10.1098/rsif.2018.0073","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language acquisition with communication between learners. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” Journal of the Royal Society Interface, vol. 15, no. 140. The Royal Society, 2018.","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:10.1098/rsif.2018.0073.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"month":"12","publication_identifier":{"issn":["2054-5703"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30662738"],"isi":["000456566500027"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1098/rsos.181286","language":[{"iso":"eng"}],"article_number":"181286","file_date_updated":"2020-07-14T12:47:13Z","year":"2018","acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"The Royal Society","author":[{"last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat"},{"last_name":"Fibla","first_name":"Martí Sànchez","full_name":"Fibla, Martí Sànchez"},{"full_name":"Valverde, Sergi","last_name":"Valverde","first_name":"Sergi"},{"last_name":"Solé","first_name":"Ricard","full_name":"Solé, Ricard"}],"date_updated":"2023-10-18T06:41:12Z","date_created":"2019-01-20T22:59:18Z","volume":5,"scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1","publication":"Royal Society Open Science","citation":{"ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286."},"article_type":"original","date_published":"2018-12-12T00:00:00Z","type":"journal_article","abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"issue":"12","_id":"5859","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Chromatic transitions in the emergence of syntax networks","status":"public","intvolume":" 5","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T14:38:09Z","checksum":"9664d4417f6b792242e31eea77ce9501","relation":"main_file","file_id":"5924","file_size":646732,"content_type":"application/pdf","creator":"dernst","file_name":"2018_RoyalSocOS_Corominas.pdf","access_level":"open_access"}]},{"publication":"arXiv","external_id":{"arxiv":["1804.07752"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07752"}],"citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. .","apa":"Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752."},"date_published":"2018-04-20T00:00:00Z","language":[{"iso":"eng"}],"day":"20","month":"04","article_processing_charge":"No","_id":"6183","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","status":"public","title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","department":[{"_id":"LaEr"}],"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger","full_name":"Krüger, Torben H"}],"related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"later_version","id":"14694"}]},"date_updated":"2023-12-18T10:46:08Z","date_created":"2019-03-28T09:20:06Z","oa_version":"Preprint","article_number":"1804.07752","type":"preprint","abstract":[{"lang":"eng","text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases."}]},{"doi":"10.48550/arXiv.1804.03057","date_published":"2018-09-13T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"ista":"Akopyan A, Avvakumov S, Karasev R. 2018. Convex fair partitions into arbitrary number of pieces. 1804.03057.","apa":"Akopyan, A., Avvakumov, S., & Karasev, R. (2018). Convex fair partitions into arbitrary number of pieces. arXiv. https://doi.org/10.48550/arXiv.1804.03057","ieee":"A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary number of pieces.” arXiv, 2018.","ama":"Akopyan A, Avvakumov S, Karasev R. Convex fair partitions into arbitrary number of pieces. 2018. doi:10.48550/arXiv.1804.03057","chicago":"Akopyan, Arseniy, Sergey Avvakumov, and Roman Karasev. “Convex Fair Partitions into Arbitrary Number of Pieces.” arXiv, 2018. https://doi.org/10.48550/arXiv.1804.03057.","mla":"Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.","short":"A. Akopyan, S. Avvakumov, R. Karasev, (2018)."},"main_file_link":[{"url":"https://arxiv.org/abs/1804.03057","open_access":"1"}],"external_id":{"arxiv":["1804.03057"]},"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","day":"13","month":"09","related_material":{"record":[{"id":"8156","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Avvakumov, Sergey","first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roman","last_name":"Karasev","full_name":"Karasev, Roman"}],"oa_version":"Preprint","date_created":"2018-12-11T11:44:30Z","date_updated":"2023-12-18T10:51:02Z","_id":"75","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"arXiv","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"publication_status":"published","status":"public","title":"Convex fair partitions into arbitrary number of pieces","ec_funded":1,"abstract":[{"text":"We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higher-dimensional generalization.","lang":"eng"}],"type":"preprint","article_number":"1804.03057"},{"day":"13","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2018-11-13T00:00:00Z","publication":"Annales Henri Poincare","citation":{"apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary Schur process and applications I. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-018-0723-1","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1."},"article_type":"original","page":"3663-3742","abstract":[{"text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions.","lang":"eng"}],"issue":"12","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2018_Annales_Betea.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3084674,"creator":"dernst","relation":"main_file","file_id":"5866","date_created":"2019-01-21T15:18:55Z","date_updated":"2020-07-14T12:47:03Z","checksum":"0c38abe73569b7166b7487ad5d23cc68"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"556","ddc":["500"],"title":"The free boundary Schur process and applications I","status":"public","intvolume":" 19","month":"11","publication_identifier":{"issn":["1424-0637"]},"doi":"10.1007/s00023-018-0723-1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1704.05809"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"file_date_updated":"2020-07-14T12:47:03Z","ec_funded":1,"publist_id":"7258","author":[{"last_name":"Betea","first_name":"Dan","full_name":"Betea, Dan"},{"full_name":"Bouttier, Jeremie","last_name":"Bouttier","first_name":"Jeremie"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"},{"first_name":"Mirjana","last_name":"Vuletic","full_name":"Vuletic, Mirjana"}],"date_updated":"2024-02-20T10:48:17Z","date_created":"2018-12-11T11:47:09Z","volume":19,"year":"2018","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LaEr"},{"_id":"JaMa"}]},{"date_created":"2018-12-12T12:31:36Z","date_updated":"2024-02-21T13:41:17Z","file":[{"file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","access_level":"open_access","file_size":1737958,"content_type":"application/zip","creator":"system","relation":"main_file","file_id":"5600","date_created":"2018-12-12T13:02:34Z","date_updated":"2020-07-14T12:47:05Z","checksum":"53c17082848e12f3c2e1b4185b578208"}],"oa_version":"Published Version","author":[{"full_name":"Alhaija, Hassan","first_name":"Hassan","last_name":"Alhaija"},{"full_name":"Sellent, Anita","last_name":"Sellent","first_name":"Anita"},{"full_name":"Kondermann, Daniel","last_name":"Kondermann","first_name":"Daniel"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"}],"contributor":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","contributor_type":"researcher","last_name":"Swoboda"}],"related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-319-24947-6_23","relation":"research_paper"}]},"title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","status":"public","ddc":["001"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"VlKo"}],"year":"2018","_id":"5573","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","text":"Graph matching problems for large displacement optical flow of RGB-D images."}],"file_date_updated":"2020-07-14T12:47:05Z","datarep_id":"82","type":"research_data","date_published":"2018-01-04T00:00:00Z","doi":"10.15479/AT:ISTA:82","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","mla":"Alhaija, Hassan, et al. Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:82.","chicago":"Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother. “Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:82.","ama":"Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. 2018. doi:10.15479/AT:ISTA:82","ieee":"H. Alhaija, A. Sellent, D. Kondermann, and C. Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018.","apa":"Alhaija, H., Sellent, A., Kondermann, D., & Rother, C. (2018). Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:82","ista":"Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology Austria, 10.15479/AT:ISTA:82."},"month":"01","day":"04","article_processing_charge":"No","has_accepted_license":"1","keyword":["graph matching","quadratic assignment problem<"]},{"file_date_updated":"2020-07-14T12:47:06Z","abstract":[{"text":"Data on Austrian open access publication output at Emerald from 2013-2017 including data analysis.","lang":"ger"}],"type":"research_data","datarep_id":"89","file":[{"file_size":222011,"content_type":"application/zip","creator":"system","access_level":"open_access","file_name":"IST-2018-89-v1+1_Emerald_Austrian_Publications_2013-2017.zip","checksum":"786b599abfae6c355dee87835f414549","date_updated":"2020-07-14T12:47:06Z","date_created":"2018-12-12T13:02:39Z","relation":"main_file","file_id":"5604"}],"oa_version":"Submitted Version","date_updated":"2024-02-21T13:41:32Z","date_created":"2018-12-12T12:31:37Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"278"}]},"author":[{"first_name":"Márton","last_name":"Villányi","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"E-Lib"}],"status":"public","title":"Emerald Austrian Publications 2013-2017","ddc":["020"],"_id":"5577","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","article_processing_charge":"No","has_accepted_license":"1","day":"16","month":"01","keyword":["Publication analysis","Bibliography","Open Access"],"doi":"10.15479/AT:ISTA:89","date_published":"2018-01-16T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ama":"Villányi M. 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Villányi, (2018).","chicago":"Villányi, Márton. “Emerald Austrian Publications 2013-2017.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:89."}},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Villányi, Márton. “IOP Austrian Publications 2012-2015.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:90.","mla":"Villányi, Márton. IOP Austrian Publications 2012-2015. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:90.","short":"M. Villányi, (2018).","ista":"Villányi M. 2018. IOP Austrian Publications 2012-2015, Institute of Science and Technology Austria, 10.15479/AT:ISTA:90.","ieee":"M. Villányi, “IOP Austrian Publications 2012-2015.” Institute of Science and Technology Austria, 2018.","apa":"Villányi, M. (2018). 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Data Check IOP Scopus vs. Publisher. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:86.","short":"M. Villányi, (2018).","ista":"Villányi M. 2018. Data Check IOP Scopus vs. Publisher, Institute of Science and Technology Austria, 10.15479/AT:ISTA:86.","apa":"Villányi, M. (2018). Data Check IOP Scopus vs. Publisher. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:86","ieee":"M. Villányi, “Data Check IOP Scopus vs. Publisher.” Institute of Science and Technology Austria, 2018.","ama":"Villányi M. Data Check IOP Scopus vs. Publisher. 2018. doi:10.15479/AT:ISTA:86"},"oa":1,"abstract":[{"text":"Comparison of Scopus' and publisher's data on Austrian publication output at IOP. ","lang":"ger"}],"file_date_updated":"2020-07-14T12:47:05Z","datarep_id":"86","type":"research_data","date_updated":"2024-02-21T13:42:21Z","date_created":"2018-12-12T12:31:37Z","oa_version":"Submitted Version","file":[{"file_id":"5642","relation":"main_file","checksum":"c7a61147bd15cb4ae45878d270628c06","date_updated":"2020-07-14T12:47:05Z","date_created":"2018-12-12T13:05:14Z","access_level":"open_access","file_name":"IST-2018-86-v1+1_Data_Check_IOP_Scopus_vs._Publisher.zip","creator":"system","content_type":"application/zip","file_size":12283857}],"author":[{"full_name":"Villányi, Márton","first_name":"Márton","last_name":"Villányi","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426"}],"related_material":{"record":[{"id":"278","status":"public","relation":"part_of_dissertation"}]},"status":"public","ddc":["020"],"title":"Data Check IOP Scopus vs. Publisher","publisher":"Institute of Science and Technology Austria","department":[{"_id":"E-Lib"}],"year":"2018","_id":"5574","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"278","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken","publisher":"Universität Wien","department":[{"_id":"E-Lib"}],"author":[{"full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","last_name":"Villányi","first_name":"Márton"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"5577"},{"relation":"dissertation_contains","status":"public","id":"5574"},{"status":"public","relation":"dissertation_contains","id":"5578"},{"id":"5579","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"5576"},{"id":"5575","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"5582"},{"id":"5581","relation":"dissertation_contains","status":"public"},{"id":"5580","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:45:34Z","date_updated":"2024-02-21T13:44:07Z","oa_version":"Published Version","type":"dissertation","abstract":[{"text":"Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance.","lang":"eng"}],"publist_id":"7624","citation":{"ista":"Villányi M. 2018. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","apa":"Villányi, M. (2018). Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","ieee":"M. Villányi, “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken,” Universität Wien, 2018.","ama":"Villányi M. 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Oxford University Press. https://doi.org/10.1093/nar/gky079","ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079","chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.","short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931.","mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079."},"publication":"Nucleic Acids Research","issue":"6","abstract":[{"lang":"eng","text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress."}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"3ff4f545c27e11a4cd20ccb30778793e","date_updated":"2020-07-14T12:46:27Z","date_created":"2018-12-12T10:15:30Z","file_id":"5151","relation":"main_file","creator":"system","file_size":5027978,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf"}],"pubrep_id":"971","intvolume":" 46","title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","status":"public","ddc":["576"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"438","month":"04","language":[{"iso":"eng"}],"doi":"10.1093/nar/gky079","project":[{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000429009500021"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:46:27Z","volume":46,"date_created":"2018-12-11T11:46:29Z","date_updated":"2024-02-21T13:44:45Z","related_material":{"record":[{"id":"5569","status":"public","relation":"popular_science"}]},"author":[{"full_name":"Nikolic, Nela","last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Vandervelde","first_name":"Alexandra","full_name":"Vandervelde, Alexandra"},{"first_name":"Tanino","last_name":"Albanese","full_name":"Albanese, Tanino"},{"last_name":"Gelens","first_name":"Lendert","full_name":"Gelens, Lendert"},{"full_name":"Moll, Isabella","first_name":"Isabella","last_name":"Moll"}],"department":[{"_id":"CaGu"}],"publisher":"Oxford University Press","publication_status":"published","year":"2018"},{"doi":"10.7554/eLife.35684","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000441388200001"]},"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"isi":1,"quality_controlled":"1","month":"08","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5586"}]},"author":[{"full_name":"Picard, Marion A","first_name":"Marion A","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"full_name":"Cosseau, Celine","first_name":"Celine","last_name":"Cosseau"},{"last_name":"Ferré","first_name":"Sabrina","full_name":"Ferré, Sabrina"},{"full_name":"Quack, Thomas","last_name":"Quack","first_name":"Thomas"},{"last_name":"Grevelding","first_name":"Christoph","full_name":"Grevelding, Christoph"},{"last_name":"Couté","first_name":"Yohann","full_name":"Couté, Yohann"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"volume":7,"date_created":"2018-12-11T11:44:47Z","date_updated":"2024-02-21T13:45:12Z","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","year":"2018","department":[{"_id":"BeVi"}],"publisher":"eLife Sciences Publications","publication_status":"published","publist_id":"7792","file_date_updated":"2020-07-14T12:44:43Z","article_number":"e35684","date_published":"2018-08-13T00:00:00Z","citation":{"mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684.","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","ieee":"M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684"},"publication":"eLife","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"13","scopus_import":"1","file":[{"relation":"main_file","file_id":"5695","checksum":"d6331d4385b1fffd6b47b45d5949d841","date_updated":"2020-07-14T12:44:43Z","date_created":"2018-12-17T11:55:05Z","access_level":"open_access","file_name":"2018_eLife_Picard.pdf","file_size":3158125,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"131","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 7","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","ddc":["570"],"status":"public","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5584","year":"2018","title":"Nonlinear decoding of a complex movie from the mammalian retina","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"author":[{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"last_name":"Botella-Soler","first_name":"Vicente","full_name":"Botella-Soler, Vicente"},{"last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"292"}]},"date_created":"2018-12-12T12:31:39Z","date_updated":"2024-02-21T13:45:26Z","oa_version":"Published Version","file":[{"checksum":"6808748837b9afbbbabc2a356ca2b88a","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:24Z","relation":"main_file","file_id":"5590","content_type":"application/octet-stream","file_size":1142543971,"creator":"system","access_level":"open_access","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat"},{"file_size":702336,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:25Z","checksum":"d6d6cd07743038fe3a12352983fcf9dd","relation":"main_file","file_id":"5591"},{"date_created":"2018-12-12T13:02:26Z","date_updated":"2020-07-14T12:47:07Z","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","file_id":"5592","relation":"main_file","creator":"system","file_size":432,"content_type":"application/octet-stream","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","access_level":"open_access"},{"access_level":"open_access","file_name":"IST-2018-98-v1+4_README.txt","creator":"system","content_type":"text/plain","file_size":986,"file_id":"5593","relation":"main_file","checksum":"2a83b011012e21e934b4596285b1a183","date_created":"2018-12-12T13:02:26Z","date_updated":"2020-07-14T12:47:07Z"}],"datarep_id":"98","type":"research_data","abstract":[{"lang":"eng","text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. "}],"file_date_updated":"2020-07-14T12:47:07Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98.","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98"},"project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"date_published":"2018-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:98","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"day":"29","month":"03","has_accepted_license":"1","article_processing_charge":"No"},{"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","acknowledgement":"ERC, Grant/Award Number: 250152","year":"2018","volume":18,"date_updated":"2024-02-21T13:45:00Z","date_created":"2018-12-11T11:45:37Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5583"}]},"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"},{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"ec_funded":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000441753000007"]},"language":[{"iso":"eng"}],"doi":"10.1111/1755-0998.12782","month":"09","intvolume":" 18","status":"public","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","_id":"286","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","type":"journal_article","issue":"5","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"page":"988 - 999","citation":{"ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999.","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999."},"publication":"Molecular Ecology Resources","date_published":"2018-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"has_accepted_license":"1","article_processing_charge":"No","day":"24","month":"07","keyword":["schistosoma","Z-chromosome","gene expression"],"date_published":"2018-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:109","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109.","short":"B. Vicoso, (2018).","mla":"Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109.","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109"},"oa":1,"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"abstract":[{"lang":"eng","text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)."}],"file_date_updated":"2020-07-14T12:47:08Z","type":"research_data","datarep_id":"109","contributor":[{"last_name":"Picard","first_name":"Marion A","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"131","relation":"research_paper","status":"public"}]},"author":[{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"file":[{"creator":"system","file_size":11918144,"content_type":"application/zip","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","access_level":"open_access","date_created":"2018-12-12T13:02:35Z","date_updated":"2020-07-14T12:47:08Z","checksum":"e60b484bd6f55c08eb66a189cb72c923","file_id":"5601","relation":"main_file"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:40Z","date_updated":"2024-02-21T13:45:12Z","_id":"5586","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"status":"public","title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)"},{"doi":"10.15479/AT:ISTA:95","date_published":"2018-02-12T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.","short":"T. Ellis, (2018).","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95"},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","day":"12","month":"02","file":[{"relation":"main_file","file_id":"5606","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:41Z","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","access_level":"open_access","file_size":122048,"content_type":"text/csv","creator":"system"},{"file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","access_level":"open_access","content_type":"text/csv","file_size":235980,"creator":"system","relation":"main_file","file_id":"5607","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:42Z","checksum":"92347586ae4f8a6eb7c04354797bf314"},{"creator":"system","content_type":"text/csv","file_size":311712,"file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","access_level":"open_access","date_created":"2018-12-12T13:02:43Z","date_updated":"2020-07-14T12:47:07Z","checksum":"3300813645a54e6c5c39f41917228354","file_id":"5608","relation":"main_file"},{"date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:44Z","checksum":"e739fc473567fd8f39438b445fc46147","relation":"main_file","file_id":"5609","file_size":342090,"content_type":"application/zip","creator":"system","file_name":"IST-2018-95-v1+4_faps_scripts.zip","access_level":"open_access"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:39Z","date_updated":"2024-02-21T13:45:01Z","related_material":{"record":[{"id":"286","relation":"research_paper","status":"public"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"status":"public","title":"Data and Python scripts supporting Python package FAPS","year":"2018","_id":"5583","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:07Z","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"type":"research_data","datarep_id":"95"},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.","mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","short":"T. Bergmiller, N. Nikolic, (2018).","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74"},"date_published":"2018-02-07T00:00:00Z","doi":"10.15479/AT:ISTA:74","keyword":["microscopy","microfluidics"],"article_processing_charge":"No","has_accepted_license":"1","day":"07","month":"02","year":"2018","_id":"5569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","title":"Time-lapse microscopy data","status":"public","ddc":["579"],"related_material":{"record":[{"id":"438","relation":"research_paper","status":"public"}]},"author":[{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela"}],"oa_version":"Published Version","file":[{"creator":"system","content_type":"application/zip","file_size":3558703796,"file_name":"IST-2018-74-v1+2_15-11-05.zip","access_level":"open_access","date_created":"2018-12-12T13:04:39Z","date_updated":"2020-07-14T12:47:04Z","checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637","relation":"main_file"},{"file_name":"IST-2018-74-v1+3_15-07-31.zip","access_level":"open_access","file_size":1830422606,"content_type":"application/zip","creator":"system","relation":"main_file","file_id":"5638","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:55Z","checksum":"bf26649af310ef6892d68576515cde6d"},{"creator":"system","file_size":2140849248,"content_type":"application/zip","access_level":"open_access","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:05:11Z","file_id":"5639","relation":"main_file"}],"date_updated":"2024-02-21T13:44:45Z","date_created":"2018-12-12T12:31:35Z","type":"research_data","datarep_id":"74","publist_id":"7385","file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}]},{"citation":{"apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9."},"publication":"Nature Communications","date_published":"2018-07-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"30","intvolume":" 9","ddc":["570"],"title":"Statistical mechanics for metabolic networks during steady state growth","status":"public","_id":"161","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"date_created":"2018-12-17T16:44:28Z","date_updated":"2020-07-14T12:45:06Z","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","file_id":"5728","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1043205,"file_name":"2018_NatureComm_DeMartino.pdf","access_level":"open_access"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000440149300021"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-05417-9","month":"07","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publisher":"Springer Nature","publication_status":"published","year":"2018","volume":9,"date_updated":"2024-02-21T13:45:39Z","date_created":"2018-12-11T11:44:57Z","related_material":{"record":[{"id":"5587","status":"public","relation":"popular_science"}]},"author":[{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino"},{"full_name":"Mc, Andersson Anna","last_name":"Mc","first_name":"Andersson Anna"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"article_number":"2988","ec_funded":1,"publist_id":"7760","file_date_updated":"2020-07-14T12:45:06Z"},{"keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"month":"09","day":"21","article_processing_charge":"No","has_accepted_license":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","apa":"De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62.","short":"D. De Martino, G. Tkačik, (2018).","mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62."},"doi":"10.15479/AT:ISTA:62","date_published":"2018-09-21T00:00:00Z","datarep_id":"111","type":"research_data","abstract":[{"text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:08Z","ec_funded":1,"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","ddc":["530"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"year":"2018","_id":"5587","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:45:39Z","date_created":"2018-12-12T12:31:41Z","oa_version":"Published Version","file":[{"file_size":14376,"content_type":"application/zip","creator":"system","file_name":"IST-2018-111-v1+1_CODES.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T13:05:13Z","checksum":"97992e3e8cf8544ec985a48971708726","relation":"main_file","file_id":"5641"}],"author":[{"first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"161"}]}},{"author":[{"full_name":"Kelemen, Réka K","first_name":"Réka K","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"related_material":{"record":[{"id":"5571","relation":"popular_science","status":"public"},{"relation":"popular_science","status":"public","id":"5572"}]},"date_created":"2018-12-11T11:47:04Z","date_updated":"2024-02-21T13:48:27Z","volume":208,"year":"2018","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Genetics Society of America","file_date_updated":"2020-07-14T12:46:50Z","ec_funded":1,"publist_id":"7274","doi":"10.1534/genetics.117.300513","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000419356300024"]},"quality_controlled":"1","isi":1,"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"month":"01","pubrep_id":"1058","file":[{"file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1311661,"creator":"system","relation":"main_file","file_id":"5132","date_created":"2018-12-12T10:15:14Z","date_updated":"2020-07-14T12:46:50Z","checksum":"2123845e7031a0cf043905be160f9e69"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"542","status":"public","title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","ddc":["576"],"intvolume":" 208","abstract":[{"text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2018-01-01T00:00:00Z","publication":"Genetics","citation":{"mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513.","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513","ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","apa":"Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300513"},"article_type":"original","page":"365 - 375","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:10Z","article_number":"71","volume":1,"date_updated":"2024-02-21T13:48:42Z","date_created":"2018-12-18T13:22:58Z","related_material":{"record":[{"id":"7196","status":"public","relation":"part_of_dissertation"},{"id":"5559","relation":"popular_science","status":"public"}]},"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"department":[{"_id":"KrCh"}],"publisher":"Springer Nature","publication_status":"published","year":"2018","publication_identifier":{"issn":["2399-3642"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1038/s42003-018-0078-7","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000461126500071"]},"oa":1,"issue":"1","abstract":[{"text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5752","checksum":"a9db825fa3b64a51ff3de035ec973b3e","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-18T13:37:04Z","access_level":"open_access","file_name":"2018_CommBiology_Pavlogiannis.pdf","file_size":1804194,"content_type":"application/pdf","creator":"dernst"}],"pubrep_id":"1045","intvolume":" 1","title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","ddc":["004","519","576"],"status":"public","_id":"5751","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","has_accepted_license":"1","day":"14","scopus_import":"1","date_published":"2018-06-14T00:00:00Z","citation":{"apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7."},"publication":"Communications Biology"},{"date_created":"2018-12-19T14:22:35Z","date_updated":"2024-02-21T13:59:18Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"FileS1.zip","creator":"cfraisse","content_type":"application/zip","file_size":369837892,"file_id":"5758","relation":"main_file","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","date_created":"2018-12-19T14:19:52Z","date_updated":"2020-07-14T12:47:11Z"},{"file_name":"FileS2.zip","access_level":"open_access","file_size":84856909,"content_type":"application/zip","creator":"cfraisse","relation":"main_file","file_id":"5759","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","checksum":"3592e467b4d8206650860b612d6e12f3"},{"checksum":"c37ac5d5437c457338afc128c1240655","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","relation":"main_file","file_id":"5760","content_type":"text/plain","file_size":881133,"creator":"cfraisse","access_level":"open_access","file_name":"FileS3.txt"},{"file_name":"FileS4.txt","access_level":"open_access","creator":"cfraisse","content_type":"text/plain","file_size":883742,"file_id":"5761","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"943dfd14da61817441e33e3e3cb8cdb9"},{"date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","file_id":"5762","relation":"main_file","creator":"cfraisse","file_size":2495437,"content_type":"text/plain","file_name":"FileS5.txt","access_level":"open_access"},{"file_id":"5763","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_name":"FileS6.txt","access_level":"open_access","creator":"cfraisse","file_size":15913457,"content_type":"text/plain"},{"creator":"cfraisse","file_size":2584120,"content_type":"text/plain","file_name":"FileS7.txt","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764","relation":"main_file"},{"content_type":"text/plain","file_size":2446059,"creator":"cfraisse","file_name":"FileS8.txt","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","relation":"main_file","file_id":"5765"},{"relation":"main_file","file_id":"5766","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_name":"FileS9.txt","access_level":"open_access","content_type":"text/plain","file_size":100737,"creator":"cfraisse"}],"author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"6089"}]},"status":"public","ddc":["576"],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"_id":"5757","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"file_date_updated":"2020-07-14T12:47:11Z","ec_funded":1,"type":"research_data","doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"C. Fraisse, (2018).","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757."},"oa":1,"day":"19","month":"12","has_accepted_license":"1","article_processing_charge":"No","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"]},{"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:TH_1040","publication_identifier":{"issn":["2663-337X"]},"month":"07","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2018","date_updated":"2024-02-22T14:34:33Z","date_created":"2018-12-11T11:44:53Z","related_material":{"record":[{"id":"1677","relation":"part_of_dissertation","status":"public"},{"id":"550","relation":"part_of_dissertation","status":"public"},{"id":"6183","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"566"},{"id":"1010","status":"public","relation":"part_of_dissertation"},{"id":"6240","relation":"part_of_dissertation","status":"public"},{"id":"6184","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"}],"ec_funded":1,"publist_id":"7772","file_date_updated":"2020-07-14T12:44:57Z","page":"456","citation":{"ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","apa":"Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","mla":"Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.","chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040."},"date_published":"2018-07-12T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"12","ddc":["515","519"],"status":"public","title":"Dyson equation and eigenvalue statistics of random matrices","_id":"149","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","file_name":"2018_thesis_Alt.pdf","creator":"dernst","content_type":"application/pdf","file_size":5801709,"file_id":"6241","relation":"main_file","checksum":"d4dad55a7513f345706aaaba90cb1bb8","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z"},{"creator":"dernst","file_size":3802059,"content_type":"application/zip","access_level":"closed","file_name":"2018_thesis_Alt_source.zip","checksum":"d73fcf46300dce74c403f2b491148ab4","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z","file_id":"6242","relation":"source_file"}],"oa_version":"Published Version","pubrep_id":"1040","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations.","lang":"eng"}]},{"scopus_import":"1","day":"14","article_processing_charge":"No","article_type":"original","publication":"The Journal of Chemical Physics","citation":{"short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591.","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591","ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018.","apa":"Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591","ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307."},"date_published":"2018-03-14T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field."}],"issue":"10","title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","status":"public","intvolume":" 148","_id":"415","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"03","quality_controlled":"1","isi":1,"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"arxiv":["1711.09904"],"isi":["000427517200065"]},"main_file_link":[{"url":"https://arxiv.org/abs/1711.09904","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1063/1.5017591","article_number":"104307","ec_funded":1,"publist_id":"7408","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","year":"2018","date_created":"2018-12-11T11:46:21Z","date_updated":"2024-02-28T13:01:59Z","volume":148,"author":[{"full_name":"Rzadkowski, Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","first_name":"Wojciech","last_name":"Rzadkowski"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]}},{"month":"07","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["000448185000055"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"doi":"10.1145/3197517.3201336","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"article_number":"94","file_date_updated":"2020-07-14T12:44:45Z","ec_funded":1,"publist_id":"7789","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2018","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"first_name":"Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas"},{"first_name":"Matthias","last_name":"Mueller Fischer","full_name":"Mueller Fischer, Matthias"},{"full_name":"Chentanez, Nuttapong","last_name":"Chentanez","first_name":"Nuttapong"},{"full_name":"Macklin, Miles","last_name":"Macklin","first_name":"Miles"},{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/"}]},"date_created":"2018-12-11T11:44:48Z","date_updated":"2024-02-28T13:58:51Z","volume":37,"scopus_import":"1","day":"30","has_accepted_license":"1","article_processing_charge":"No","publication":"ACM Transactions on Graphics","citation":{"mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336"},"date_published":"2018-07-30T00:00:00Z","type":"journal_article","alternative_title":["SIGGRAPH"],"abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"issue":"4","_id":"134","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Water surface wavelets","ddc":["000"],"intvolume":" 37","oa_version":"Published Version","file":[{"file_id":"5744","relation":"main_file","date_created":"2018-12-18T09:59:23Z","date_updated":"2020-07-14T12:44:45Z","checksum":"db75ebabe2ec432bf41389e614d6ef62","file_name":"2018_ACM_Jeschke.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":22185016}]},{"related_material":{"link":[{"url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Timur","last_name":"Tscherbul","full_name":"Tscherbul, Timur"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"volume":121,"date_created":"2019-04-17T10:53:38Z","date_updated":"2024-02-28T13:15:09Z","year":"2018","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","article_number":"165301","doi":"10.1103/physrevlett.121.165301","language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"}],"quality_controlled":"1","isi":1,"month":"10","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6339","intvolume":" 121","status":"public","title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","issue":"16","abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"type":"journal_article","date_published":"2018-10-16T00:00:00Z","citation":{"mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301.","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301"},"publication":"Physical Review Letters","article_processing_charge":"No","day":"16","scopus_import":"1"},{"scopus_import":"1","article_processing_charge":"No","day":"16","citation":{"ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018)."},"publication":"Physical Review Letters","date_published":"2018-10-16T00:00:00Z","type":"journal_article","issue":"16","abstract":[{"text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ","lang":"eng"}],"intvolume":" 121","status":"public","title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","_id":"417","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"10","project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"oa":1,"external_id":{"arxiv":["1803.07990"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.121.165301","article_number":"165301","publist_id":"8025","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2018","volume":121,"date_created":"2018-12-11T11:46:22Z","date_updated":"2024-02-28T13:14:53Z","author":[{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin"},{"full_name":"Tscherbul, Timur","last_name":"Tscherbul","first_name":"Timur"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}]},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6269"}]},"author":[{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek","full_name":"Adamowski, Maciek"},{"full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","first_name":"Urszula","full_name":"Kania, Urszula"},{"full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"De Jaeger, Geert","first_name":"Geert","last_name":"De Jaeger"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"}],"volume":30,"date_updated":"2024-03-28T23:30:06Z","date_created":"2018-12-11T11:46:20Z","pmid":1,"acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","year":"2018","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","publication_status":"published","ec_funded":1,"publist_id":"7417","file_date_updated":"2022-05-23T09:12:38Z","doi":"10.1105/tpc.17.00785","language":[{"iso":"eng"}],"external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"month":"04","file":[{"relation":"main_file","file_id":"11406","checksum":"4e165e653b67d3f0684697f21aace5a1","success":1,"date_created":"2022-05-23T09:12:38Z","date_updated":"2022-05-23T09:12:38Z","access_level":"open_access","file_name":"2018_PlantCell_Adamowski.pdf","file_size":4407538,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"412","intvolume":" 30","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","status":"public","ddc":["580"],"issue":"3","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"type":"journal_article","date_published":"2018-04-09T00:00:00Z","citation":{"ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785."},"publication":"The Plant Cell","page":"700 - 716","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"09","scopus_import":"1"},{"date_published":"2018-07-27T00:00:00Z","citation":{"ama":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018","apa":"Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018","ieee":"D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.","ista":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087.","short":"D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).","mla":"Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.","chicago":"Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018."},"publication":"eNeuro","article_processing_charge":"No","has_accepted_license":"1","day":"27","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"f4915d45fc7ad4648b7b7a13fdecca01","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T12:48:36Z","file_id":"5921","relation":"main_file","creator":"dernst","file_size":3746884,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_ENeuro_Guerrero.pdf"}],"intvolume":" 5","ddc":["570"],"status":"public","title":"Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5914","issue":"4","abstract":[{"text":"With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1523/ENEURO.0087-18.2018","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","name":"Interneuron plasticity during spatial learning","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000443994700007"]},"month":"07","volume":5,"date_updated":"2024-03-28T23:30:10Z","date_created":"2019-02-03T22:59:16Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6849"}]},"author":[{"id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374","first_name":"Dámaris K","last_name":"Rangel Guerrero","full_name":"Rangel Guerrero, Dámaris K"},{"full_name":"Donnett, James G.","last_name":"Donnett","first_name":"James G."},{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"},{"last_name":"Kovács","first_name":"Krisztián","orcid":"0000-0001-6251-1007","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","full_name":"Kovács, Krisztián"}],"publisher":"Society of Neuroscience","department":[{"_id":"JoCs"}],"publication_status":"published","year":"2018","ec_funded":1,"file_date_updated":"2020-07-14T12:47:13Z","article_number":"e0087"},{"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"402","status":"public","title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","intvolume":" 359","abstract":[{"lang":"eng","text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined."}],"issue":"6382","type":"journal_article","date_published":"2018-03-23T00:00:00Z","publication":"Science","citation":{"ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662","ieee":"M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018.","ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662","chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.","mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662.","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411."},"article_type":"original","page":"1408 - 1411","day":"23","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Brown, Markus","first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","first_name":"Frank P","last_name":"Assen"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"first_name":"Helga","last_name":"Schachner","full_name":"Schachner, Helga"},{"full_name":"Asfour, Gabriele","first_name":"Gabriele","last_name":"Asfour"},{"full_name":"Bagó Horváth, Zsuzsanna","last_name":"Bagó Horváth","first_name":"Zsuzsanna"},{"last_name":"Stein","first_name":"Jens","full_name":"Stein, Jens"},{"full_name":"Uhrin, Pavel","last_name":"Uhrin","first_name":"Pavel"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"}],"related_material":{"record":[{"id":"6947","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-28T23:30:09Z","date_created":"2018-12-11T11:46:16Z","volume":359,"acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"American Association for the Advancement of Science","ec_funded":1,"publist_id":"7428","doi":"10.1126/science.aal3662","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000428043600047"],"pmid":["29567714"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aal3662"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"}],"month":"03"},{"page":"88","citation":{"chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.","mla":"Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992.","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","apa":"Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992"},"date_published":"2018-03-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No","title":"The branched chain amino acids in autism spectrum disorders ","ddc":["570","616"],"status":"public","_id":"395","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"source_file","file_id":"6217","checksum":"9f5231c96e0ad945040841a8630232da","date_created":"2019-04-05T09:19:17Z","date_updated":"2021-02-11T23:30:15Z","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Tarlungeanu_source.docx","file_size":43684035,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst"},{"checksum":"0c33c370aa2010df5c552db57a6d01e9","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-05T09:19:17Z","file_id":"6218","embargo":"2018-03-15","relation":"main_file","creator":"dernst","file_size":30511532,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_Thesis_Tarlungeanu.pdf"}],"oa_version":"Published Version","pubrep_id":"992","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ","lang":"eng"}],"project":[{"grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"supervisor":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_992","month":"03","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","year":"2018","date_updated":"2023-09-07T12:38:59Z","date_created":"2018-12-11T11:46:14Z","author":[{"full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","first_name":"Dora-Clara"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1183"}]},"file_date_updated":"2021-02-11T23:30:15Z","publist_id":"7434"},{"publist_id":"8003","file_date_updated":"2021-02-11T23:30:13Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"RySh"}],"publication_status":"published","year":"2018","date_created":"2018-12-11T11:44:22Z","date_updated":"2023-09-07T12:39:22Z","related_material":{"record":[{"id":"682","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Case","first_name":"Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J"}],"publication_identifier":{"issn":["2663-337X"]},"month":"06","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_1032","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism."}],"title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","ddc":["571","576"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"51","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/msword","file_size":141270528,"file_name":"2018_Thesis_Case_Source.doc","embargo_to":"open_access","access_level":"closed","date_updated":"2021-02-11T23:30:13Z","date_created":"2019-04-09T07:16:26Z","checksum":"dcc7b55619d8509dd62b8e99d6cdee44","file_id":"6251","relation":"source_file"},{"relation":"main_file","embargo":"2019-07-05","file_id":"6252","checksum":"f69fdd5c8709c4e618aa8c1a1221153d","date_created":"2019-04-09T07:16:23Z","date_updated":"2021-02-11T11:17:14Z","access_level":"open_access","file_name":"2018_Thesis_Case.pdf","content_type":"application/pdf","file_size":15193621,"creator":"dernst"}],"pubrep_id":"1032","has_accepted_license":"1","article_processing_charge":"No","day":"27","page":"186","citation":{"ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032","ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.","apa":"Case, M. J. (2018). From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1032","ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria.","short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018.","mla":"Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1032.","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1032."},"date_published":"2018-06-27T00:00:00Z"},{"day":"21","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-11-21T00:00:00Z","citation":{"chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","mla":"Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057.","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","apa":"Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057","ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:10.15479/AT:ISTA:th1057"},"page":"1 - 139","abstract":[{"lang":"eng","text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1057","file":[{"file_id":"6396","relation":"source_file","date_updated":"2019-11-23T23:30:03Z","date_created":"2019-05-10T07:47:04Z","checksum":"41fdbf5fdce312802935d88a8ad9932c","file_name":"Thesis_LaukoterSusanne_FINAL.docx","embargo_to":"open_access","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":17949175},{"date_created":"2019-05-10T07:47:04Z","date_updated":"2021-02-11T11:17:16Z","checksum":"53001a9a0c9e570e598d861bb0af28aa","file_id":"6397","embargo":"2019-11-21","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":21187245,"file_name":"Thesis_LaukoterSusanne_FINAL.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"title":"Role of genomic imprinting in cerebral cortex development","status":"public","month":"11","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th1057","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2021-02-11T11:17:16Z","publist_id":"8046","author":[{"first_name":"Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne"}],"date_created":"2018-12-11T11:44:08Z","date_updated":"2023-09-07T12:40:44Z","year":"2018","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SiHi"}]}]