[{"month":"08","publication_identifier":{"issn":["0737-4038"]},"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"oa":1,"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy163","publist_id":"8036","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2018","pmid":1,"date_created":"2018-12-11T11:44:11Z","date_updated":"2023-10-17T11:51:06Z","volume":35,"author":[{"full_name":"Palmer, Adam","last_name":"Palmer","first_name":"Adam"},{"first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"scopus_import":"1","day":"28","article_processing_charge":"No","article_type":"original","page":"2669 - 2684","publication":"Molecular Biology and Evolution","citation":{"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.","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.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","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.","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.","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"},"date_published":"2018-08-28T00:00:00Z","type":"journal_article","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","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","status":"public","intvolume":" 35","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"19","oa_version":"Submitted Version"},{"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","status":"public","publication_status":"published","title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","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"},{"last_name":"Wolff","first_name":"Steffen","full_name":"Wolff, Steffen"},{"full_name":"Guitchounts, Grigori","last_name":"Guitchounts","first_name":"Grigori"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A"},{"last_name":"Cox","first_name":"David","full_name":"Cox, David"}],"scopus_import":"1","day":"08","month":"11","article_processing_charge":"No","quality_controlled":"1","isi":1,"publication":"Journal of visualized experiments","external_id":{"isi":["000456469400103"]},"citation":{"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.","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","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.","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."},"language":[{"iso":"eng"}],"date_published":"2018-11-08T00:00:00Z","doi":"10.3791/58585"},{"article_processing_charge":"No","day":"23","month":"10","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"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,"citation":{"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","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","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).","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."},"date_published":"2018-10-23T00:00:00Z","doi":"10.5281/ZENODO.1322669","type":"research_data_reference","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"}],"_id":"13055","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","department":[{"_id":"SyCr"}],"ddc":["570"],"status":"public","title":"Social network plasticity decreases disease transmission in a eusocial insect","related_material":{"record":[{"id":"7","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie","last_name":"Stroeymeyt"},{"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"},{"first_name":"Danielle","last_name":"Mersch","full_name":"Mersch, Danielle"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"last_name":"Keller","first_name":"Laurent","full_name":"Keller, Laurent"}],"oa_version":"Published Version","date_updated":"2023-10-17T11:50:04Z","date_created":"2023-05-23T13:24:51Z"},{"publication":"Optica","citation":{"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.","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.","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.","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","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.","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."},"article_type":"original","page":"1210 - 1219","date_published":"2018-10-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22","status":"public","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","intvolume":" 5","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"10","oa":1,"main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"external_id":{"isi":["000447853100007"]},"isi":1,"quality_controlled":"1","doi":"10.1364/OPTICA.5.001210","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["23342536"]},"year":"2018","publication_status":"published","department":[{"_id":"JoFi"}],"author":[{"full_name":"Botello, Gabriel","last_name":"Botello","first_name":"Gabriel"},{"last_name":"Sedlmeir","first_name":"Florian","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"},{"full_name":"Brown, Elliott","first_name":"Elliott","last_name":"Brown"},{"full_name":"Leuchs, Gerd","first_name":"Gerd","last_name":"Leuchs"},{"last_name":"Preu","first_name":"Sascha","full_name":"Preu, Sascha"},{"first_name":"Daniel","last_name":"Segovia Vargas","full_name":"Segovia Vargas, Daniel"},{"full_name":"Strekalov, Dmitry","last_name":"Strekalov","first_name":"Dmitry"},{"full_name":"Munoz, Luis","last_name":"Munoz","first_name":"Luis"},{"full_name":"Schwefel, Harald","last_name":"Schwefel","first_name":"Harald"}],"date_created":"2018-12-11T11:44:12Z","date_updated":"2023-10-17T12:12:40Z","volume":5,"publist_id":"8033"},{"language":[{"iso":"eng"}],"doi":"10.1561/1000000053","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00757488/"}],"oa":1,"publication_identifier":{"issn":["1551-3939"]},"month":"05","volume":12,"date_created":"2018-12-16T22:59:19Z","date_updated":"2023-10-17T11:53:09Z","author":[{"last_name":"Benveniste","first_name":"Albert","full_name":"Benveniste, Albert"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"full_name":"Caillaud, Benoît","last_name":"Caillaud","first_name":"Benoît"},{"full_name":"Passerone, Roberto","last_name":"Passerone","first_name":"Roberto"},{"full_name":"Raclet, Jean Baptiste","first_name":"Jean Baptiste","last_name":"Raclet"},{"full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier","first_name":"Philipp"},{"first_name":"Alberto","last_name":"Sangiovanni-Vincentelli","full_name":"Sangiovanni-Vincentelli, Alberto"},{"full_name":"Damm, Werner","first_name":"Werner","last_name":"Damm"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Kim G.","last_name":"Larsen","full_name":"Larsen, Kim G."}],"publisher":"Now Publishers","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2018","date_published":"2018-05-01T00:00:00Z","page":"124-400","article_type":"original","citation":{"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.","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.","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.","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","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.","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","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."},"publication":"Foundations and Trends in Electronic Design Automation","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 12","status":"public","title":"Contracts for system design","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5677","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"}],"type":"journal_article"}]