[{"oa":1,"abstract":[{"text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data.","lang":"eng"}],"publisher":"Elsevier","acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n","date_created":"2018-12-11T11:47:27Z","publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","title":"Well-posedness for mean-field evolutions arising in superconductivity","arxiv":1,"date_updated":"2023-09-19T10:39:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00268"}],"quality_controlled":"1","external_id":{"arxiv":["1607.00268"],"isi":["000437975500005"]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","date_published":"2018-08-01T00:00:00Z","year":"2018","citation":{"chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319.","mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.","ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319.","ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","apa":"Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004","ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004"},"issue":"5","intvolume":" 35","author":[{"full_name":"Duerinckx, Mitia","first_name":"Mitia","last_name":"Duerinckx"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer"}],"isi":1,"scopus_import":"1","page":"1267-1319","department":[{"_id":"JuFi"}],"article_processing_charge":"No","oa_version":"Submitted Version","month":"08","type":"journal_article","day":"01","doi":"10.1016/j.anihpc.2017.11.004","volume":35,"_id":"606","publist_id":"7199"},{"oa_version":"Submitted Version","type":"journal_article","month":"08","scopus_import":"1","isi":1,"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"page":"108-120","article_processing_charge":"No","publist_id":"7198","doi":"10.1016/j.physd.2017.10.015","day":"01","_id":"607","volume":"376-377","date_created":"2018-12-11T11:47:28Z","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","publication":"Physica D: Nonlinear Phenomena","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"date_updated":"2024-10-09T20:58:45Z","arxiv":1,"oa":1,"abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"publisher":"Elsevier","author":[{"last_name":"Bodova","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","first_name":"Katarina"},{"full_name":"Haskovec, Jan","first_name":"Jan","last_name":"Haskovec"},{"first_name":"Peter","full_name":"Markowich, Peter","last_name":"Markowich"}],"quality_controlled":"1","external_id":{"arxiv":["1704.08757"],"isi":["000437962900012"]},"language":[{"iso":"eng"}],"year":"2018","date_published":"2018-08-01T00:00:00Z","publication_status":"published","status":"public","citation":{"chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120."},"corr_author":"1"},{"oa":1,"abstract":[{"lang":"eng","text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game."}],"ec_funded":1,"publisher":"Elsevier","date_created":"2018-12-11T11:47:28Z","title":"Synthesis from component libraries with costs","publication":"Theoretical Computer Science","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-04-15T06:26:02Z","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"quality_controlled":"1","external_id":{"isi":["000424959200003"]},"language":[{"iso":"eng"}],"year":"2018","date_published":"2018-02-15T00:00:00Z","status":"public","publication_status":"published","corr_author":"1","citation":{"mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72."},"intvolume":" 712","author":[{"first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","last_name":"Avni"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"scopus_import":"1","isi":1,"department":[{"_id":"ToHe"}],"page":"50 - 72","article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","month":"02","day":"15","doi":"10.1016/j.tcs.2017.11.001","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"_id":"608","volume":712,"article_type":"original","publist_id":"7197"},{"arxiv":1,"date_updated":"2021-01-12T08:06:06Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1509.06286","open_access":"1"}],"oa_version":"Preprint","date_created":"2018-12-11T11:44:25Z","type":"book_chapter","title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","month":"05","publication":"Contemporary Computational Mathematics","article_processing_charge":"No","publisher":"Springer","oa":1,"department":[{"_id":"TaHa"}],"abstract":[{"text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. ","lang":"eng"}],"page":"131 - 134","publist_id":"7993","author":[{"last_name":"Bondarenko","first_name":"Andriy","full_name":"Bondarenko, Andriy"},{"id":"388D3134-F248-11E8-B48F-1D18A9856A87","full_name":"Mellit, Anton","first_name":"Anton","last_name":"Mellit"},{"full_name":"Prymak, Andriy","first_name":"Andriy","last_name":"Prymak"},{"full_name":"Radchenko, Danylo","first_name":"Danylo","last_name":"Radchenko"},{"last_name":"Viazovska","full_name":"Viazovska, Maryna","first_name":"Maryna"}],"year":"2018","_id":"61","date_published":"2018-05-23T00:00:00Z","status":"public","extern":"1","publication_status":"published","citation":{"mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7.","ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7","chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134."},"quality_controlled":"1","doi":"10.1007/978-3-319-72456-0_7","day":"23","language":[{"iso":"eng"}],"external_id":{"arxiv":["1509.06286"]}},{"page":"E6890-E6899","ddc":["570"],"type":"journal_article","month":"07","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"17","doi":"10.1073/pnas.1714610115","publication_identifier":{"issn":["0027-8424","1091-6490"]},"_id":"6109","volume":115,"abstract":[{"text":"Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels.","lang":"eng"}],"file":[{"file_name":"2018_PNAS_Laurent.pdf","file_size":1567765,"creator":"kschuh","checksum":"5e81665377441cdd8d99ab952c534319","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-19T13:01:58Z","file_id":"6110"}],"oa":1,"publisher":"National Academy of Sciences","title":"Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron","publication":"Proceedings of the National Academy of Sciences","date_created":"2019-03-19T12:41:33Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:09Z","pmid":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["29959203"]},"quality_controlled":"1","citation":{"mla":"Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:10.1073/pnas.1714610115.","ista":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.","ieee":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” Proceedings of the National Academy of Sciences, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.","ama":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899. doi:10.1073/pnas.1714610115","apa":"Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115","chicago":"Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115.","short":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899."},"file_date_updated":"2020-07-14T12:47:19Z","date_published":"2018-07-17T00:00:00Z","year":"2018","status":"public","publication_status":"published","extern":"1","has_accepted_license":"1","author":[{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"last_name":"Ch’ng","first_name":"QueeLim","full_name":"Ch’ng, QueeLim"},{"first_name":"Maëlle","full_name":"Jospin, Maëlle","last_name":"Jospin"},{"full_name":"Chen, Changchun","first_name":"Changchun","last_name":"Chen"},{"first_name":"Ramiro","full_name":"Lorenzo, Ramiro","last_name":"Lorenzo"},{"last_name":"de Bono","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","first_name":"Mario"}],"intvolume":" 115","issue":"29"},{"ddc":["570"],"type":"journal_article","month":"06","oa_version":"Published Version","_id":"6111","volume":14,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1371/journal.pgen.1007435","day":"07","publication_identifier":{"issn":["1553-7404"]},"article_number":"e1007435","publisher":"Public Library of Science","file":[{"date_created":"2019-03-19T13:18:01Z","file_id":"6112","access_level":"open_access","date_updated":"2020-07-14T12:47:19Z","checksum":"622036b945365dbc575bea2768aa9bc8","content_type":"application/pdf","relation":"main_file","file_name":"2018_PLOS_McLachlan.pdf","file_size":13011506,"creator":"kschuh"}],"abstract":[{"lang":"eng","text":"Neurons develop elaborate morphologies that provide a model for understanding cellular architecture. By studying C. elegans sensory dendrites, we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing neuron URX is not affected by these genes, suggesting it develops through a distinct mechanism. Here, we use a visual forward genetic screen to identify mutants that affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15 or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before: dendrites extend normally during embryogenesis but begin to overgrow as the animals reach adulthood, ultimately extending up to 150% of their normal length. SMA-1 is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts at the time of overgrowth, localizes at the dendrite ending, and requires its kinase activity, suggesting it acts locally in time and space to constrain dendrite growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which normally localizes at the dendrite ending, is localized throughout the overgrown region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond to expansion of a sensory compartment at the dendrite ending, reminiscent of the remodeling of sensory cilia or dendritic spines. Thus, in contrast to established pathways that promote dendrite growth during early development, our results reveal a distinct mechanism that constrains dendrite growth throughout the life of the animal, possibly by controlling the size of a sensory compartment at the dendrite ending."}],"oa":1,"pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:11Z","title":"A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism","publication":"PLOS Genetics","date_created":"2019-03-19T13:09:28Z","citation":{"chicago":"McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007435.","short":"I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018).","mla":"McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics, vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007435.","ieee":"I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism,” PLOS Genetics, vol. 14, no. 6. Public Library of Science, 2018.","ama":"McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 2018;14(6). doi:10.1371/journal.pgen.1007435","apa":"McLachlan, I. G., Beets, I., de Bono, M., & Heiman, M. G. (2018). A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007435","ista":"McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 14(6), e1007435."},"file_date_updated":"2020-07-14T12:47:19Z","date_published":"2018-06-07T00:00:00Z","year":"2018","publication_status":"published","status":"public","extern":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["29879119"]},"quality_controlled":"1","author":[{"full_name":"McLachlan, Ian G.","first_name":"Ian G.","last_name":"McLachlan"},{"first_name":"Isabel","full_name":"Beets, Isabel","last_name":"Beets"},{"last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"},{"full_name":"Heiman, Maxwell G.","first_name":"Maxwell G.","last_name":"Heiman"}],"intvolume":" 14","issue":"6","has_accepted_license":"1"},{"publication_identifier":{"isbn":["978-3-030-05287-4"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["978-3-030-05288-1"]},"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-05288-1_7","day":"22","publication_status":"published","volume":11255,"extern":"1","status":"public","year":"2018","_id":"6164","date_published":"2018-11-22T00:00:00Z","citation":{"short":"G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick, in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96.","chicago":"Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96. Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.","ista":"Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial Image Analysis, LNCS, vol. 11255, 82–96.","apa":"Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., & Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp. 82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7","ieee":"G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick, “Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255, pp. 82–96.","ama":"Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In: 19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7","mla":"Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255, Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7."},"alternative_title":["LNCS"],"conference":{"location":"Porto, Portugal","name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2018-11-24","start_date":"2018-11-22"},"place":"Cham","intvolume":" 11255","author":[{"last_name":"Koshti","first_name":"Girish","full_name":"Koshti, Girish"},{"orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","first_name":"Ranita","last_name":"Biswas"},{"full_name":"Largeteau-Skapin, Gaëlle","first_name":"Gaëlle","last_name":"Largeteau-Skapin"},{"last_name":"Zrour","first_name":"Rita","full_name":"Zrour, Rita"},{"first_name":"Eric","full_name":"Andres, Eric","last_name":"Andres"},{"last_name":"Bhowmick","full_name":"Bhowmick, Partha","first_name":"Partha"}],"page":"82-96","abstract":[{"lang":"eng","text":"In this paper, we propose an algorithm to build discrete spherical shell having integer center and real-valued inner and outer radii on the face-centered cubic (FCC) grid. We address the problem by mapping it to a 2D scenario and building the shell layer by layer on hexagonal grids with additive manufacturing in mind. The layered hexagonal grids get shifted according to need as we move from one layer to another and forms the FCC grid in 3D. However, we restrict our computation strictly to 2D in order to utilize symmetry and simplicity."}],"article_processing_charge":"No","publisher":"Springer","date_created":"2019-03-21T12:16:58Z","oa_version":"None","publication":"19th International Workshop","month":"11","type":"conference","title":"Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-27T15:26:39Z"},{"oa":1,"abstract":[{"text":"Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions.","lang":"eng"}],"publisher":"Wiley","acknowledgement":"We would like to thank Susann Wicke for performing the genome-wide SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG) priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR 872/1-1). ","date_created":"2018-12-11T11:47:31Z","publication":"Journal of Evolutionary Biology","title":"Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance","pmid":1,"date_updated":"2023-09-11T14:06:04Z","main_file_link":[{"url":"https://doi.org/10.1111/jeb.13211","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["29150962"],"isi":["000419307000014"]},"status":"public","publication_status":"published","date_published":"2018-01-01T00:00:00Z","year":"2018","citation":{"ista":"Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 31(1), 159–171.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211","ama":"Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 2018;31(1):159-171. doi:10.1111/jeb.13211","ieee":"M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.","mla":"Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31, no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.","short":"M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018) 159–171.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211."},"issue":"1","intvolume":" 31","author":[{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978","first_name":"Megan","last_name":"Kutzer"},{"full_name":"Kurtz, Joachim","first_name":"Joachim","last_name":"Kurtz"},{"full_name":"Armitage, Sophie","first_name":"Sophie","last_name":"Armitage"}],"isi":1,"scopus_import":"1","page":"159 - 171","department":[{"_id":"SyCr"}],"article_processing_charge":"No","oa_version":"Published Version","month":"01","type":"journal_article","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"day":"01","doi":"10.1111/jeb.13211","volume":31,"_id":"617","article_type":"original","publist_id":"7187"},{"department":[{"_id":"BeBi"}],"abstract":[{"lang":"eng","text":"In the context of robotic manipulation and grasping, the shift from a view that is static (force closure of a single posture) and contact-deprived (only contact for force closure is allowed, everything else is obstacle) towards a view that is dynamic and contact-rich (soft manipulation) has led to an increased interest in soft hands. These hands can easily exploit environmental constraints and object surfaces without risk, and safely interact with humans, but present also some challenges. Designing them is difficult, as well as predicting, modelling, and “programming” their interactions with the objects and the environment. This paper tackles the problem of simulating them in a fast and effective way, leveraging on novel and existing simulation technologies. We present a triple-layered simulation framework where dynamic properties such as stiffness are determined from slow but accurate FEM simulation data once, and then condensed into a lumped parameter model that can be used to fast simulate soft fingers and soft hands. We apply our approach to the simulation of soft pneumatic fingers."}],"scopus_import":"1","isi":1,"publisher":"IEEE","article_processing_charge":"No","type":"conference","title":"Efficient FEM-based simulation of soft robots modeled as kinematic chains","month":"09","oa_version":"None","date_created":"2019-04-04T09:50:38Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-19T14:49:03Z","doi":"10.1109/icra.2018.8461106","day":"10","external_id":{"isi":["000446394503031"]},"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781538630815"]},"conference":{"start_date":"2018-05-21","name":"ICRA: International Conference on Robotics and Automation","end_date":"2018-05-25","location":"Brisbane, Australia"},"citation":{"chicago":"Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.","short":"M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018.","mla":"Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106.","ista":"Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains. ICRA: International Conference on Robotics and Automation, 8461106.","ieee":"M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled as kinematic chains,” presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia, 2018.","apa":"Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock, O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots modeled as kinematic chains. Presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106","ama":"Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106"},"year":"2018","_id":"6195","date_published":"2018-09-10T00:00:00Z","publication_status":"published","status":"public","author":[{"last_name":"Pozzi","full_name":"Pozzi, Maria","first_name":"Maria"},{"id":"3FB91342-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","first_name":"Eder","last_name":"Miguel Villalba"},{"full_name":"Deimel, Raphael","first_name":"Raphael","last_name":"Deimel"},{"first_name":"Monica","full_name":"Malvezzi, Monica","last_name":"Malvezzi"},{"last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"last_name":"Brock","first_name":"Oliver","full_name":"Brock, Oliver"},{"full_name":"Prattichizzo, Domenico","first_name":"Domenico","last_name":"Prattichizzo"}],"article_number":"8461106"},{"_id":"62","volume":8,"day":"24","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1038/s41598-018-32628-3","publist_id":"7992","article_number":"14247","article_type":"original","article_processing_charge":"No","department":[{"_id":"MaJö"}],"scopus_import":"1","ddc":["570"],"isi":1,"type":"journal_article","month":"09","oa_version":"Published Version","citation":{"short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3","mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3."},"file_date_updated":"2020-07-14T12:47:24Z","date_published":"2018-09-24T00:00:00Z","year":"2018","status":"public","publication_status":"published","language":[{"iso":"eng"}],"external_id":{"isi":["000445336600015"]},"quality_controlled":"1","author":[{"first_name":"Ali","full_name":"Shabazi, Ali","last_name":"Shabazi"},{"last_name":"Kinnison","full_name":"Kinnison, Jeffery","first_name":"Jeffery"},{"last_name":"Vescovi","first_name":"Rafael","full_name":"Vescovi, Rafael"},{"last_name":"Du","full_name":"Du, Ming","first_name":"Ming"},{"last_name":"Hill","first_name":"Robert","full_name":"Hill, Robert"},{"last_name":"Jösch","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","first_name":"Maximilian A"},{"full_name":"Takeno, Marc","first_name":"Marc","last_name":"Takeno"},{"last_name":"Zeng","full_name":"Zeng, Hongkui","first_name":"Hongkui"},{"full_name":"Da Costa, Nuno","first_name":"Nuno","last_name":"Da Costa"},{"last_name":"Grutzendler","first_name":"Jaime","full_name":"Grutzendler, Jaime"},{"first_name":"Narayanan","full_name":"Kasthuri, Narayanan","last_name":"Kasthuri"},{"first_name":"Walter","full_name":"Scheirer, Walter","last_name":"Scheirer"}],"intvolume":" 8","issue":"1","has_accepted_license":"1","publisher":"Nature Publishing Group","abstract":[{"lang":"eng","text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively."}],"file":[{"file_id":"5699","date_created":"2018-12-17T12:22:24Z","date_updated":"2020-07-14T12:47:24Z","access_level":"open_access","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2","content_type":"application/pdf","relation":"main_file","file_name":"2018_ScientificReports_Shahbazi.pdf","file_size":4141645,"creator":"dernst"}],"oa":1,"date_updated":"2023-09-11T14:02:55Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Flexible learning-free segmentation and reconstruction of neural volumes","related_material":{"link":[{"url":"http://doi.org/10.1038/s41598-018-36220-7","relation":"erratum"}]},"publication":"Scientific Reports","date_created":"2018-12-11T11:44:25Z","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357."},{"oa_version":"Published Version","type":"journal_article","month":"01","article_processing_charge":"No","scopus_import":"1","isi":1,"department":[{"_id":"DaSi"}],"article_number":"jcs207696","publist_id":"7184","_id":"620","volume":131,"day":"04","doi":"10.1242/jcs.207696","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"date_updated":"2023-09-11T12:57:13Z","date_created":"2018-12-11T11:47:32Z","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","publication":"Journal of Cell Science","publisher":"Company of Biologists","oa":1,"abstract":[{"text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.","lang":"eng"}],"intvolume":" 131","issue":"1","author":[{"last_name":"Yamamoto","first_name":"Wataru","full_name":"Yamamoto, Wataru"},{"full_name":"Wada, Suguru","first_name":"Suguru","last_name":"Wada"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"full_name":"Aoshima, Kaito","first_name":"Kaito","last_name":"Aoshima"},{"first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"},{"last_name":"Toshima","full_name":"Toshima, Junko","first_name":"Junko"},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"year":"2018","date_published":"2018-01-04T00:00:00Z","publication_status":"published","status":"public","citation":{"ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696","mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000424786900012"],"pmid":["29192062"]}},{"author":[{"last_name":"Gammerdinger","first_name":"William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J"},{"last_name":"Kocher","first_name":"Thomas","full_name":"Kocher, Thomas"}],"intvolume":" 9","issue":"10","has_accepted_license":"1","citation":{"ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI. https://doi.org/10.3390/genes9100480","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI, 2018.","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI, 2018, doi:10.3390/genes9100480.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI, 2018. https://doi.org/10.3390/genes9100480."},"file_date_updated":"2020-07-14T12:47:27Z","year":"2018","date_published":"2018-10-04T00:00:00Z","status":"public","publication_status":"published","external_id":{"isi":["000448656700018"]},"language":[{"iso":"eng"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T06:50:01Z","title":"Unusual diversity of sex chromosomes in African cichlid fishes","publication":"Genes","date_created":"2018-12-11T11:44:26Z","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","publisher":"MDPI","ec_funded":1,"abstract":[{"text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.","lang":"eng"}],"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:27Z","file_id":"5743","date_created":"2018-12-18T09:54:46Z","file_name":"2018_Genes_Gammerdinger.pdf","file_size":1415791,"creator":"dernst","checksum":"bec527692e2c9b56919c0429634ff337","content_type":"application/pdf","relation":"main_file"}],"oa":1,"publist_id":"7991","article_number":"480","_id":"63","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"volume":9,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"04","doi":"10.3390/genes9100480","type":"journal_article","month":"10","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"BeVi"}],"scopus_import":"1","ddc":["570"],"isi":1},{"date_created":"2019-04-17T10:53:38Z","title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","related_material":{"link":[{"url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","description":"News on IST Homepage","relation":"press_release"}]},"publication":"Physical Review Letters","date_updated":"2025-04-15T07:59:29Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa":1,"abstract":[{"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.","lang":"eng"}],"publisher":"American Physical Society","intvolume":" 121","issue":"16","author":[{"last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777"},{"last_name":"Tscherbul","full_name":"Tscherbul, Timur","first_name":"Timur"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"year":"2018","date_published":"2018-10-16T00:00:00Z","publication_status":"published","status":"public","citation":{"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.","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","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","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."},"oa_version":"Preprint","type":"journal_article","month":"10","scopus_import":"1","isi":1,"department":[{"_id":"MiLe"}],"article_processing_charge":"No","article_number":"165301","day":"16","doi":"10.1103/physrevlett.121.165301","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"6339","volume":121},{"day":"20","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.21769/bioprotoc.3018","publication_identifier":{"issn":["2331-8325"]},"volume":8,"_id":"6354","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_type":"original","article_number":"e3018","department":[{"_id":"MiSi"}],"ddc":["570"],"article_processing_charge":"Yes","month":"09","type":"journal_article","DOAJ_listed":"1","oa_version":"Published Version","external_id":{"pmid":["34395806"]},"language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:28Z","citation":{"short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018."},"corr_author":"1","OA_type":"gold","publication_status":"published","status":"public","date_published":"2018-09-20T00:00:00Z","year":"2018","has_accepted_license":"1","author":[{"last_name":"Fan","full_name":"Fan, Shuxia","first_name":"Shuxia"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"},{"first_name":"Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","last_name":"Gärtner"}],"issue":"18","intvolume":" 8","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"OA_place":"publisher","file":[{"date_updated":"2020-07-14T12:47:28Z","access_level":"open_access","file_id":"6360","date_created":"2019-04-30T08:04:33Z","creator":"dernst","file_name":"2018_BioProtocol_Fan.pdf","file_size":2928337,"content_type":"application/pdf","relation":"main_file","checksum":"d4588377e789da7f360b553ae02c5119"}],"oa":1,"publisher":"Bio-Protocol","ec_funded":1,"publication":"Bio-Protocol","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"title":"Platelet migration and bacterial trapping assay under flow","acknowledgement":"This protocol was adapted from a previously published study (Gaertner et al., 2017). We thank Michael Lorenz for his excellent assistance in bacteria culture. This work was funded by the DFG SFB 914 (S.M. [B02 and Z01]), the DFG SFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Centre for Cardiovascular Research (DZHK) (MHA 1.4VD [S.M.]), FP7 program (project 260309, PRESTIGE [S.M.]), FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.), Marie Sklodowska Curie Individual Fellowship (EU project 747687, LamelliaActin [F.G.]).","date_created":"2019-04-29T09:40:33Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-20T07:43:06Z"},{"page":"1038-1042","month":"10","type":"journal_article","oa_version":"Preprint","volume":14,"_id":"6368","doi":"10.1038/s41567-018-0210-0","day":"01","publication_identifier":{"issn":["1745-2473","1745-2481"]},"publisher":"Springer Nature","abstract":[{"text":"An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.06535"}],"date_updated":"2021-01-12T08:07:15Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication":"Nature Physics","title":"Harnessing electro-optic correlations in an efficient mechanical converter","date_created":"2019-05-03T09:17:20Z","citation":{"chicago":"Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S. Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0210-0.","short":"A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M. Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042.","mla":"Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics, vol. 14, no. 10, Springer Nature, 2018, pp. 1038–42, doi:10.1038/s41567-018-0210-0.","apa":"Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N. S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0210-0","ieee":"A. P. Higginbotham et al., “Harnessing electro-optic correlations in an efficient mechanical converter,” Nature Physics, vol. 14, no. 10. Springer Nature, pp. 1038–1042, 2018.","ama":"Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 2018;14(10):1038-1042. doi:10.1038/s41567-018-0210-0","ista":"Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM, Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 14(10), 1038–1042."},"extern":"1","status":"public","publication_status":"published","year":"2018","date_published":"2018-10-01T00:00:00Z","external_id":{"arxiv":["1712.06535"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"},{"last_name":"Burns","full_name":"Burns, P. S.","first_name":"P. S."},{"last_name":"Urmey","first_name":"M. D.","full_name":"Urmey, M. D."},{"full_name":"Peterson, R. W.","first_name":"R. W.","last_name":"Peterson"},{"last_name":"Kampel","first_name":"N. S.","full_name":"Kampel, N. S."},{"full_name":"Brubaker, B. M.","first_name":"B. M.","last_name":"Brubaker"},{"full_name":"Smith, G.","first_name":"G.","last_name":"Smith"},{"last_name":"Lehnert","first_name":"K. W.","full_name":"Lehnert, K. W."},{"full_name":"Regal, C. A.","first_name":"C. A.","last_name":"Regal"}],"issue":"10","intvolume":" 14"},{"article_number":"220301","_id":"6369","volume":97,"doi":"10.1103/physrevb.97.220301","day":"04","publication_identifier":{"issn":["2469-9950","2469-9969"]},"type":"journal_article","month":"06","oa_version":"Preprint","author":[{"last_name":"Rosenthal","first_name":"Eric I.","full_name":"Rosenthal, Eric I."},{"last_name":"Ehrlich","full_name":"Ehrlich, Nicole K.","first_name":"Nicole K."},{"last_name":"Rudner","first_name":"Mark S.","full_name":"Rudner, Mark S."},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","first_name":"Andrew P"},{"last_name":"Lehnert","full_name":"Lehnert, K. W.","first_name":"K. W."}],"intvolume":" 97","issue":"22","citation":{"ista":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 97(22), 220301.","ieee":"E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W. Lehnert, “Topological phase transition measured in a dissipative metamaterial,” Physical Review B, vol. 97, no. 22. American Physical Society (APS), 2018.","ama":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 2018;97(22). doi:10.1103/physrevb.97.220301","apa":"Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., & Lehnert, K. W. (2018). Topological phase transition measured in a dissipative metamaterial. Physical Review B. American Physical Society (APS). https://doi.org/10.1103/physrevb.97.220301","mla":"Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B, vol. 97, no. 22, 220301, American Physical Society (APS), 2018, doi:10.1103/physrevb.97.220301.","short":"E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert, Physical Review B 97 (2018).","chicago":"Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham, and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B. American Physical Society (APS), 2018. https://doi.org/10.1103/physrevb.97.220301."},"date_published":"2018-06-04T00:00:00Z","year":"2018","extern":"1","publication_status":"published","status":"public","language":[{"iso":"eng"}],"external_id":{"arxiv":["1802.02243"]},"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.02243","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:07:16Z","arxiv":1,"title":"Topological phase transition measured in a dissipative metamaterial","publication":"Physical Review B","date_created":"2019-05-03T09:29:49Z","publisher":"American Physical Society (APS)","abstract":[{"lang":"eng","text":"We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before."}],"oa":1},{"department":[{"_id":"TaHa"}],"page":"E8135 - E8142","scopus_import":"1","isi":1,"article_processing_charge":"No","type":"journal_article","month":"08","oa_version":"Preprint","doi":"10.1073/pnas.1805847115","day":"28","publication_identifier":{"issn":["0027-8424"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"_id":"64","volume":115,"article_type":"original","publist_id":"7990","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"oa":1,"publisher":"National Academy of Sciences","ec_funded":1,"title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2018-12-11T11:44:26Z","date_updated":"2025-06-03T11:21:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1806.09153","open_access":"1"}],"arxiv":1,"external_id":{"arxiv":["1806.09153"],"isi":["000442861600009"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142."},"year":"2018","date_published":"2018-08-28T00:00:00Z","status":"public","publication_status":"published","author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"first_name":"Aldo","full_name":"Guzmán Sáenz, Aldo","last_name":"Guzmán Sáenz"},{"last_name":"Prieto","full_name":"Prieto, Y","first_name":"Y"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","last_name":"Shkolnikov"},{"full_name":"Kalinina, V","first_name":"V","last_name":"Kalinina"},{"last_name":"Lupercio","first_name":"Ernesto","full_name":"Lupercio, Ernesto"}],"intvolume":" 115","issue":"35"},{"quality_controlled":"1","external_id":{"isi":["000440822900011"]},"language":[{"iso":"eng"}],"year":"2018","date_published":"2018-06-06T00:00:00Z","publication_status":"published","status":"public","file_date_updated":"2020-07-14T12:47:32Z","citation":{"apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20170896","ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2018;2015(7):1869–1890. doi:10.1084/jem.20170896","ieee":"F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.","ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896.","short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896."},"has_accepted_license":"1","intvolume":" 2015","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","issue":"7","author":[{"last_name":"Moalli","full_name":"Moalli, Federica","first_name":"Federica"},{"full_name":"Ficht, Xenia","first_name":"Xenia","last_name":"Ficht"},{"last_name":"Germann","first_name":"Philipp","full_name":"Germann, Philipp"},{"full_name":"Vladymyrov, Mykhailo","first_name":"Mykhailo","last_name":"Vladymyrov"},{"last_name":"Stolp","full_name":"Stolp, Bettina","first_name":"Bettina"},{"last_name":"de Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"de Vries, Ingrid","first_name":"Ingrid"},{"last_name":"Lyck","full_name":"Lyck, Ruth","first_name":"Ruth"},{"last_name":"Balmer","first_name":"Jasmin","full_name":"Balmer, Jasmin"},{"last_name":"Fiocchi","first_name":"Amleto","full_name":"Fiocchi, Amleto"},{"full_name":"Kreutzfeldt, Mario","first_name":"Mario","last_name":"Kreutzfeldt"},{"last_name":"Merkler","full_name":"Merkler, Doron","first_name":"Doron"},{"last_name":"Iannacone","full_name":"Iannacone, Matteo","first_name":"Matteo"},{"last_name":"Ariga","first_name":"Akitaka","full_name":"Ariga, Akitaka"},{"first_name":"Michael H.","full_name":"Stoffel, Michael H.","last_name":"Stoffel"},{"last_name":"Sharpe","first_name":"James","full_name":"Sharpe, James"},{"last_name":"Bähler","first_name":"Martin","full_name":"Bähler, Martin"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"full_name":"Diz-Muñoz, Alba","first_name":"Alba","last_name":"Diz-Muñoz"},{"full_name":"Stein, Jens V.","first_name":"Jens V.","last_name":"Stein"}],"oa":1,"abstract":[{"text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations.","lang":"eng"}],"file":[{"file_id":"6498","date_created":"2019-05-28T12:40:05Z","date_updated":"2020-07-14T12:47:32Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"86ae5331f9bfced9a6358a790a04bef4","creator":"kschuh","file_size":3841660,"file_name":"2018_rupress_Moalli.pdf"}],"publisher":"Rockefeller University Press","date_created":"2019-05-28T12:36:47Z","title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","publication":"The Journal of Experimental Medicine","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-19T14:52:08Z","publication_identifier":{"issn":["0022-1007"],"eissn":["1540-9538"]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"day":"06","doi":"10.1084/jem.20170896","_id":"6497","volume":2015,"scopus_import":"1","ddc":["570"],"isi":1,"department":[{"_id":"MiSi"}],"page":"1869–1890","article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","month":"06"},{"article_processing_charge":"No","scopus_import":"1","ddc":["580"],"isi":1,"department":[{"_id":"JoDa"}],"oa_version":"Published Version","type":"journal_article","month":"09","_id":"6499","volume":19,"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"day":"01","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.15252/embr.201845836","article_number":"e45836","publisher":"Embo Press","oa":1,"file":[{"file_id":"6500","date_created":"2019-05-28T13:17:19Z","access_level":"open_access","date_updated":"2020-07-14T12:47:32Z","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","content_type":"application/pdf","relation":"main_file","file_name":"2018_embo_Truckenbrodt.pdf","file_size":2005572,"creator":"kschuh"}],"abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-12-11T11:48:40Z","date_created":"2019-05-28T13:16:08Z","title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","publication":"EMBO reports","date_published":"2018-09-01T00:00:00Z","year":"2018","status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:47:32Z","citation":{"ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 2018;19(9). doi:10.15252/embr.201845836","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” EMBO reports, vol. 19, no. 9. Embo Press, 2018.","apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., & Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.201845836","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, Embo Press, 2018, doi:10.15252/embr.201845836.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports. Embo Press, 2018. https://doi.org/10.15252/embr.201845836."},"quality_controlled":"1","external_id":{"isi":["000443682200009"]},"language":[{"iso":"eng"}],"intvolume":" 19","issue":"9","author":[{"first_name":"Sven M","full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt"},{"last_name":"Maidorn","first_name":"Manuel","full_name":"Maidorn, Manuel"},{"full_name":"Crzan, Dagmar","first_name":"Dagmar","last_name":"Crzan"},{"last_name":"Wildhagen","full_name":"Wildhagen, Hanna","first_name":"Hanna"},{"full_name":"Kabatas, Selda","first_name":"Selda","last_name":"Kabatas"},{"last_name":"Rizzoli","first_name":"Silvio O","full_name":"Rizzoli, Silvio O"}],"has_accepted_license":"1"},{"day":"01","conference":{"start_date":"2018-12-02","location":"Montreal, Canada","name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2018-12-08"},"_id":"6558","volume":2018,"department":[{"_id":"DaAl"}],"page":"4613-4623","scopus_import":"1","isi":1,"article_processing_charge":"No","type":"conference","month":"12","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"isi":["000461823304061"],"arxiv":["1803.08917"]},"quality_controlled":"1","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances in Neural Information Processing Systems, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: Advances in Neural Information Processing Systems. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","apa":"Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic gradient descent. In Advances in Neural Information Processing Systems (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623.","chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In Advances in Neural Information Processing Systems, 2018:4613–23. Neural Information Processing Systems Foundation, 2018.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623."},"date_published":"2018-12-01T00:00:00Z","year":"2018","publication_status":"published","status":"public","author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"first_name":"Zeyuan","full_name":"Allen-Zhu, Zeyuan","last_name":"Allen-Zhu"},{"last_name":"Li","full_name":"Li, Jerry","first_name":"Jerry"}],"intvolume":" 2018","abstract":[{"text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity.","lang":"eng"}],"oa":1,"publisher":"Neural Information Processing Systems Foundation","title":"Byzantine stochastic gradient descent","publication":"Advances in Neural Information Processing Systems","date_created":"2019-06-13T08:22:37Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"date_updated":"2023-09-19T15:12:45Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08917"}]}]