[{"_id":"1788","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:12Z","citation":{"apa":"Pitanti, A., Fink, J. M., Safavi Naeini, A., Hill, J., Lei, C., Tredicucci, A., & Painter, O. (2015). Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. Optical Society of America. https://doi.org/10.1364/OE.23.003196","ama":"Pitanti A, Fink JM, Safavi Naeini A, et al. Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. 2015;23(3):3196-3208. doi:10.1364/OE.23.003196","ieee":"A. Pitanti et al., “Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity,” Optics Express, vol. 23, no. 3. Optical Society of America, pp. 3196–3208, 2015.","short":"A. Pitanti, J.M. Fink, A. Safavi Naeini, J. Hill, C. Lei, A. Tredicucci, O. Painter, Optics Express 23 (2015) 3196–3208.","mla":"Pitanti, Alessandro, et al. “Strong Opto-Electro-Mechanical Coupling in a Silicon Photonic Crystal Cavity.” Optics Express, vol. 23, no. 3, Optical Society of America, 2015, pp. 3196–208, doi:10.1364/OE.23.003196.","ista":"Pitanti A, Fink JM, Safavi Naeini A, Hill J, Lei C, Tredicucci A, Painter O. 2015. Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. 23(3), 3196–3208.","chicago":"Pitanti, Alessandro, Johannes M Fink, Amir Safavi Naeini, Jeff Hill, Chan Lei, Alessandro Tredicucci, and Oskar Painter. “Strong Opto-Electro-Mechanical Coupling in a Silicon Photonic Crystal Cavity.” Optics Express. Optical Society of America, 2015. https://doi.org/10.1364/OE.23.003196."},"extern":1,"publist_id":"5325","author":[{"full_name":"Pitanti, Alessandro","last_name":"Pitanti","first_name":"Alessandro"},{"orcid":"0000-0001-8112-028X","full_name":"Johannes Fink","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"last_name":"Safavi Naeini","full_name":"Safavi-Naeini, Amir H","first_name":"Amir"},{"first_name":"Jeff","full_name":"Hill, Jeff T","last_name":"Hill"},{"full_name":"Lei, Chan U","last_name":"Lei","first_name":"Chan"},{"first_name":"Alessandro","full_name":"Tredicucci, Alessandro","last_name":"Tredicucci"},{"first_name":"Oskar","full_name":"Painter, Oskar J","last_name":"Painter"}],"title":"Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity","abstract":[{"text":"We fabricate and characterize a microscale silicon opto-electromechanical system whose mechanical motion is coupled capacitively to an electrical circuit and optically via radiation pressure to a photonic crystal cavity. To achieve large electromechanical interaction strength, we implement an inverse shadow mask fabrication scheme which obtains capacitor gaps as small as 30 nm while maintaining a silicon surface quality necessary for minimizing optical loss. Using the sensitive optical read-out of the photonic crystal cavity, we characterize the linear and nonlinear capacitive coupling to the fundamental ωm=2π = 63 MHz in-plane flexural motion of the structure, showing that the large electromechanical coupling in such devices may be suitable for realizing efficient microwave-to-optical signal conversion.","lang":"eng"}],"acknowledgement":"This work was supported by the DARPA MESO program, the AFOSR Hybrid Nanophotonics MURI, the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. AP gratefully acknowledge funding from EU through Marie Curie Actions, project NEMO (GA 298861). AT acknowledges partial financial support from the ERC through the advanced grant SoulMan","publisher":"Optical Society of America","quality_controlled":0,"month":"02","intvolume":" 23","year":"2015","publication_status":"published","day":"09","publication":"Optics Express","page":"3196 - 3208","issue":"3","doi":"10.1364/OE.23.003196","volume":23,"date_published":"2015-02-09T00:00:00Z","date_created":"2018-12-11T11:54:01Z"},{"year":"2015","has_accepted_license":"1","publication":"Scientific Reports","day":"12","date_created":"2018-12-11T11:54:06Z","doi":"10.1038/srep10781","date_published":"2015-06-12T00:00:00Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","citation":{"chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep10781.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781.","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports, vol. 5, 10781, Nature Publishing Group, 2015, doi:10.1038/srep10781.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep10781","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 2015;5. doi:10.1038/srep10781","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” Scientific Reports, vol. 5. Nature Publishing Group, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","last_name":"Altmeyer"},{"full_name":"Do, Younghae","last_name":"Do","first_name":"Younghae"},{"last_name":"Lai","full_name":"Lai, Ying","first_name":"Ying"}],"publist_id":"5306","title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","article_number":"10781","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7716f582f8c9d82d8f2bf80bf896b440","file_id":"5280","file_size":2449723,"date_updated":"2020-07-14T12:45:16Z","creator":"system","file_name":"IST-2016-450-v1+1_srep10781.pdf","date_created":"2018-12-12T10:17:26Z"}],"volume":5,"abstract":[{"lang":"eng","text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 5","month":"06","date_updated":"2021-01-12T06:53:18Z","ddc":["530"],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:16Z","_id":"1804","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"450","status":"public"},{"extern":1,"date_updated":"2021-01-12T06:53:18Z","citation":{"chicago":"Rei, Damien, Xenos Mason, Jinsoo Seo, Johannes Gräff, Andrii Rudenko, Jùn Wang, Richard Rueda, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1415845112.","ista":"Rei D, Mason X, Seo J, Gräff J, Rudenko A, Wang J, Rueda R, Siegert S, Cho S, Canter R, Mungenast A, Deisseroth K, Tsai L. 2015. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. 112(23), 7291–7296.","mla":"Rei, Damien, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” PNAS, vol. 112, no. 23, National Academy of Sciences, 2015, pp. 7291–96, doi:10.1073/pnas.1415845112.","ieee":"D. Rei et al., “Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway,” PNAS, vol. 112, no. 23. National Academy of Sciences, pp. 7291–7296, 2015.","short":"D. Rei, X. Mason, J. Seo, J. Gräff, A. Rudenko, J. Wang, R. Rueda, S. Siegert, S. Cho, R. Canter, A. Mungenast, K. Deisseroth, L. Tsai, PNAS 112 (2015) 7291–7296.","ama":"Rei D, Mason X, Seo J, et al. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. 2015;112(23):7291-7296. doi:10.1073/pnas.1415845112","apa":"Rei, D., Mason, X., Seo, J., Gräff, J., Rudenko, A., Wang, J., … Tsai, L. (2015). Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1415845112"},"title":"Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway","publist_id":"5307","author":[{"last_name":"Rei","full_name":"Rei, Damien","first_name":"Damien"},{"full_name":"Mason, Xenos","last_name":"Mason","first_name":"Xenos"},{"first_name":"Jinsoo","last_name":"Seo","full_name":"Seo, Jinsoo"},{"full_name":"Gräff, Johannes","last_name":"Gräff","first_name":"Johannes"},{"full_name":"Rudenko, Andrii","last_name":"Rudenko","first_name":"Andrii"},{"first_name":"Jùn","full_name":"Wang, Jùn","last_name":"Wang"},{"first_name":"Richard","last_name":"Rueda","full_name":"Rueda, Richard"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","full_name":"Sandra Siegert","orcid":"0000-0001-8635-0877","last_name":"Siegert"},{"last_name":"Cho","full_name":"Cho, Sukhee","first_name":"Sukhee"},{"first_name":"Rebecca","last_name":"Canter","full_name":"Canter, Rebecca G"},{"first_name":"Alison","last_name":"Mungenast","full_name":"Mungenast, Alison E"},{"full_name":"Deisseroth, Karl A","last_name":"Deisseroth","first_name":"Karl"},{"first_name":"Lihuei","last_name":"Tsai","full_name":"Tsai, Lihuei"}],"_id":"1803","status":"public","type":"journal_article","publication":"PNAS","day":"09","publication_status":"published","year":"2015","date_created":"2018-12-11T11:54:06Z","issue":"23","doi":"10.1073/pnas.1415845112","volume":112,"date_published":"2015-06-09T00:00:00Z","page":"7291 - 7296","acknowledgement":"AG047661; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nNS051874; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nSNSF; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung","abstract":[{"text":"Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.","lang":"eng"}],"intvolume":" 112","month":"06","quality_controlled":0,"publisher":"National Academy of Sciences"},{"oa_version":"Preprint","abstract":[{"text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.","lang":"eng"}],"month":"05","intvolume":" 21","scopus_import":1,"quality_controlled":"1","publisher":"EDP Sciences","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1401.1727","open_access":"1"}],"day":"01","publication":"ESAIM - Control, Optimisation and Calculus of Variations","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","volume":21,"issue":"3","doi":"10.1051/cocv/2014040","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:54:07Z","page":"603 - 624","_id":"1807","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624.","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences, 2015. https://doi.org/10.1051/cocv/2014040.","short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","apa":"Goldman, M., & Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences. https://doi.org/10.1051/cocv/2014040","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 2015;21(3):603-624. doi:10.1051/cocv/2014040","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:10.1051/cocv/2014040."},"date_updated":"2021-01-12T06:53:20Z","department":[{"_id":"RoSe"}],"title":"Sharp interface limit for two components Bose-Einstein condensates","publist_id":"5303","author":[{"full_name":"Goldman, Michael","last_name":"Goldman","first_name":"Michael"},{"last_name":"Royo-Letelier","full_name":"Royo-Letelier, Jimena","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","first_name":"Jimena"}]},{"_id":"1802","status":"public","type":"journal_article","extern":1,"citation":{"apa":"Siegert, S., Seo, J., Kwon, E., Rudenko, A., Cho, S., Wang, W., … Tsai, L. (2015). The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.4023","ama":"Siegert S, Seo J, Kwon E, et al. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. 2015;18:1008-1016. doi:10.1038/nn.4023","short":"S. Siegert, J. Seo, E. Kwon, A. Rudenko, S. Cho, W. Wang, Z. Flood, A. Martorell, M. Ericsson, A. Mungenast, L. Tsai, Nature Neuroscience 18 (2015) 1008–1016.","ieee":"S. Siegert et al., “The schizophrenia risk gene product miR-137 alters presynaptic plasticity,” Nature Neuroscience, vol. 18. Nature Publishing Group, pp. 1008–1016, 2015.","mla":"Siegert, Sandra, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” Nature Neuroscience, vol. 18, Nature Publishing Group, 2015, pp. 1008–16, doi:10.1038/nn.4023.","ista":"Siegert S, Seo J, Kwon E, Rudenko A, Cho S, Wang W, Flood Z, Martorell A, Ericsson M, Mungenast A, Tsai L. 2015. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. 18, 1008–1016.","chicago":"Siegert, Sandra, Jinsoo Seo, Ester Kwon, Andrii Rudenko, Sukhee Cho, Wenyuan Wang, Zachary Flood, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” Nature Neuroscience. Nature Publishing Group, 2015. https://doi.org/10.1038/nn.4023."},"date_updated":"2021-01-12T06:53:18Z","title":"The schizophrenia risk gene product miR-137 alters presynaptic plasticity","publist_id":"5308","author":[{"last_name":"Siegert","full_name":"Sandra Siegert","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"},{"last_name":"Seo","full_name":"Seo, Jinsoo","first_name":"Jinsoo"},{"full_name":"Kwon, Ester J","last_name":"Kwon","first_name":"Ester"},{"full_name":"Rudenko, Andrii","last_name":"Rudenko","first_name":"Andrii"},{"last_name":"Cho","full_name":"Cho, Sukhee","first_name":"Sukhee"},{"full_name":"Wang, Wenyuan","last_name":"Wang","first_name":"Wenyuan"},{"last_name":"Flood","full_name":"Flood, Zachary C","first_name":"Zachary"},{"first_name":"Anthony","last_name":"Martorell","full_name":"Martorell, Anthony J"},{"last_name":"Ericsson","full_name":"Ericsson, Maria","first_name":"Maria"},{"full_name":"Mungenast, Alison E","last_name":"Mungenast","first_name":"Alison"},{"full_name":"Tsai, Lihuei","last_name":"Tsai","first_name":"Lihuei"}],"acknowledgement":"S.S. was supported by a Human Frontier Science Program (HFSP) long-term postdoctoral fellowship and a Swiss National Science Foundation fellowship for prospective researchers. E.J.K. was supported by a Simons Foundation Postdoctoral Fellowship. A.R. was supported by a NARSAD Young Investigator Award. This work was supported by a Seed Grant from the Simons Center for the Social Brain and US National Institutes of Health grant RO1 MH 091115 to L.-H.T.","abstract":[{"text":"Noncoding variants in the human MIR137 gene locus increase schizophrenia risk with genome-wide significance. However, the functional consequence of these risk alleles is unknown. Here we examined induced human neurons harboring the minor alleles of four disease-associated single nucleotide polymorphisms in MIR137. We observed increased MIR137 levels compared to those in major allele–carrying cells. microRNA-137 gain of function caused downregulation of the presynaptic target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic vesicle pool distribution, impaired induction of mossy fiber long-term potentiation and deficits in hippocampus-dependent learning and memory. By sequestering endogenous miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement of Syt1 expression partially restored synaptic plasticity, demonstrating the importance of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by which miR-137 dysregulation can impair synaptic plasticity in the hippocampus.","lang":"eng"}],"month":"07","intvolume":" 18","quality_controlled":0,"publisher":"Nature Publishing Group","day":"01","publication":"Nature Neuroscience","year":"2015","publication_status":"published","doi":"10.1038/nn.4023","volume":18,"date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:54:05Z","page":"1008 - 1016"},{"volume":27,"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_id":"5277","creator":"system","date_updated":"2020-07-14T12:45:17Z","file_size":1047255,"date_created":"2018-12-12T10:17:23Z","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 27","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.","lang":"eng"}],"department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:17Z","ddc":["570"],"date_updated":"2021-01-12T06:53:21Z","status":"public","pubrep_id":"493","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1810","doi":"10.1016/j.mib.2015.05.008","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:54:08Z","page":"1 - 9","day":"01","publication":"Current Opinion in Microbiology","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"Elsevier","oa":1,"title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","author":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"publist_id":"5298","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology. Elsevier, 2015. https://doi.org/10.1016/j.mib.2015.05.008.","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. Elsevier. https://doi.org/10.1016/j.mib.2015.05.008","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 2015;27:1-9. doi:10.1016/j.mib.2015.05.008","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” Current Opinion in Microbiology, vol. 27. Elsevier, pp. 1–9, 2015.","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology, vol. 27, Elsevier, 2015, pp. 1–9, doi:10.1016/j.mib.2015.05.008."},"project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}]},{"date_updated":"2021-01-12T06:53:22Z","ddc":["530"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:45:17Z","_id":"1812","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"446","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-446-v1+1_document.pdf","date_created":"2018-12-12T10:15:59Z","file_size":1900925,"date_updated":"2020-07-14T12:45:17Z","creator":"system","file_id":"5184","checksum":"551f751a75b39b89a1db2f7f498f9a49","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":17,"issue":"4","abstract":[{"lang":"eng","text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 17","month":"04","citation":{"mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics, vol. 17, no. 4, 045005, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/4/045005.","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 2015;17(4). doi:10.1088/1367-2630/17/4/045005","apa":"Lahrz, M., Lemeshko, M., & Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/4/045005","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” New Journal of Physics, vol. 17, no. 4. IOP Publishing Ltd., 2015.","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/4/045005.","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Lahrz, Martin","last_name":"Lahrz","first_name":"Martin"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"Ludwig","last_name":"Mathey","full_name":"Mathey, Ludwig"}],"publist_id":"5294","title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","article_number":"045005","year":"2015","has_accepted_license":"1","publication":"New Journal of Physics","day":"01","date_created":"2018-12-11T11:54:09Z","doi":"10.1088/1367-2630/17/4/045005","date_published":"2015-04-01T00:00:00Z","oa":1,"publisher":"IOP Publishing Ltd.","quality_controlled":"1"},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"052105","publist_id":"5295","author":[{"full_name":"Safari, Laleh","last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"},{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"first_name":"Kari","full_name":"Jänkälä, Kari","last_name":"Jänkälä"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"}],"title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","citation":{"ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” Journal of Mathematical Physics, vol. 56, no. 5. American Institute of Physics, 2015.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., & Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4921227","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 2015;56(5). doi:10.1063/1.4921227","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:10.1063/1.4921227.","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4921227."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"American Institute of Physics","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","date_created":"2018-12-11T11:54:08Z","doi":"10.1063/1.4921227","date_published":"2015-05-20T00:00:00Z","year":"2015","publication":"Journal of Mathematical Physics","day":"20","type":"journal_article","status":"public","_id":"1811","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:53:21Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"scopus_import":1,"intvolume":" 56","month":"05","abstract":[{"text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"volume":56,"issue":"5","publication_status":"published","language":[{"iso":"eng"}]},{"date_created":"2018-12-11T11:54:09Z","volume":114,"date_published":"2015-05-18T00:00:00Z","doi":"10.1103/PhysRevLett.114.203001","issue":"20","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Physical Review Letters","day":"18","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.03447"}],"oa":1,"scopus_import":1,"quality_controlled":"1","publisher":"American Physical Society","intvolume":" 114","month":"05","abstract":[{"lang":"eng","text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system."}],"oa_version":"Preprint","publist_id":"5293","author":[{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"title":"Rotation of quantum impurities in the presence of a many-body environment","department":[{"_id":"MiLe"}],"citation":{"short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” Physical Review Letters, vol. 114, no. 20. American Physical Society, 2015.","ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 2015;114(20). doi:10.1103/PhysRevLett.114.203001","apa":"Schmidt, R., & Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.203001","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.203001.","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.203001."},"date_updated":"2021-01-12T06:53:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1813","article_number":"203001"},{"intvolume":" 25","month":"05","publisher":"ACM","quality_controlled":"1","oa_version":"None","date_created":"2018-12-11T11:54:07Z","date_published":"2015-05-01T00:00:00Z","doi":"10.1145/2745799","volume":25,"issue":"2","language":[{"iso":"eng"}],"publication":"ACM Transactions on Modeling and Computer Simulation","day":"01","publication_status":"published","year":"2015","status":"public","type":"journal_article","article_number":"7","_id":"1808","department":[{"_id":"ToHe"}],"title":"Guest editors' introduction to special issue on computational methods in systems biology","publist_id":"5302","author":[{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:20Z","citation":{"mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 7, ACM, 2015, doi:10.1145/2745799.","apa":"Gupta, A., & Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2745799","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2745799","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2745799.","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7."}},{"date_updated":"2021-01-12T06:53:23Z","department":[{"_id":"CaHe"}],"_id":"1817","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":521,"issue":"7551","abstract":[{"text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"month":"03","intvolume":" 521","citation":{"chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215.","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:10.1038/nature14215.","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","ieee":"S. Porazinski et al., “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015."},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Porazinski, Sean","last_name":"Porazinski","first_name":"Sean"},{"full_name":"Wang, Huijia","last_name":"Wang","first_name":"Huijia"},{"full_name":"Asaoka, Yoichi","last_name":"Asaoka","first_name":"Yoichi"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Behrndt, Martin","last_name":"Behrndt"},{"full_name":"Miyamoto, Tatsuo","last_name":"Miyamoto","first_name":"Tatsuo"},{"full_name":"Morita, Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi"},{"first_name":"Shoji","last_name":"Hata","full_name":"Hata, Shoji"},{"first_name":"Takashi","full_name":"Sasaki, Takashi","last_name":"Sasaki"},{"last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"first_name":"Yumi","last_name":"Osada","full_name":"Osada, Yumi"},{"first_name":"Satoshi","full_name":"Asaka, Satoshi","last_name":"Asaka"},{"first_name":"Akihiro","full_name":"Momoi, Akihiro","last_name":"Momoi"},{"last_name":"Linton","full_name":"Linton, Sarah","first_name":"Sarah"},{"full_name":"Miesfeld, Joel","last_name":"Miesfeld","first_name":"Joel"},{"last_name":"Link","full_name":"Link, Brian","first_name":"Brian"},{"first_name":"Takeshi","last_name":"Senga","full_name":"Senga, Takeshi"},{"full_name":"Castillo Morales, Atahualpa","last_name":"Castillo Morales","first_name":"Atahualpa"},{"first_name":"Araxi","last_name":"Urrutia","full_name":"Urrutia, Araxi"},{"first_name":"Nobuyoshi","full_name":"Shimizu, Nobuyoshi","last_name":"Shimizu"},{"full_name":"Nagase, Hideaki","last_name":"Nagase","first_name":"Hideaki"},{"first_name":"Shinya","full_name":"Matsuura, Shinya","last_name":"Matsuura"},{"full_name":"Bagby, Stefan","last_name":"Bagby","first_name":"Stefan"},{"first_name":"Hisato","last_name":"Kondoh","full_name":"Kondoh, Hisato"},{"full_name":"Nishina, Hiroshi","last_name":"Nishina","first_name":"Hiroshi"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"full_name":"Furutani Seiki, Makoto","last_name":"Furutani Seiki","first_name":"Makoto"}],"publist_id":"5289","external_id":{"pmid":["25778702"]},"title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","year":"2015","day":"16","publication":"Nature","page":"217 - 221","date_published":"2015-03-16T00:00:00Z","doi":"10.1038/nature14215","date_created":"2018-12-11T11:54:10Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1},{"oa":1,"quality_controlled":"1","publisher":"AAAI Press","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","date_created":"2018-12-11T11:54:11Z","date_published":"2015-06-01T00:00:00Z","page":"3496-3502","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","day":"01","year":"2015","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"title":"Optimal cost almost-sure reachability in POMDPs","external_id":{"arxiv":["1411.3880"]},"publist_id":"5286","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , vol. 5, AAAI Press, 2015, pp. 3496–502.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . Vol 5. AAAI Press; 2015:3496-3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502."},"intvolume":" 5","month":"06","main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"alternative_title":["Artifical Intelligence"],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.","lang":"eng"}],"ec_funded":1,"volume":5,"related_material":{"record":[{"status":"public","id":"1529","relation":"later_version"}]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","conference":{"name":"IAAI: Innovative Applications of Artificial Intelligence","start_date":"2015-01-25","end_date":"2015-01-30","location":"Austin, TX, USA"},"type":"conference","_id":"1820","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T10:02:57Z"},{"publisher":"ACM","quality_controlled":"1","oa":1,"date_published":"2015-04-01T00:00:00Z","doi":"10.1145/2714572","date_created":"2018-12-11T11:54:09Z","day":"01","publication":"ACM Transactions on Graphics","has_accepted_license":"1","year":"2015","project":[{"grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images","call_identifier":"FWF","_id":"25357BD2-B435-11E9-9278-68D0E5697425"},{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"article_number":"27","title":"Water wave animation via wavefront parameter interpolation","author":[{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"publist_id":"5292","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM, 2015, doi:10.1145/2714572.","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","apa":"Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572.","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27."},"month":"04","intvolume":" 34","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms."}],"volume":34,"issue":"3","ec_funded":1,"file":[{"creator":"system","file_size":23712153,"date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","date_created":"2018-12-12T10:12:15Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4933","checksum":"67c9f4fa370def68cdf31299e48bc91f"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"575","type":"journal_article","_id":"1814","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2023-02-23T10:15:40Z"},{"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"citation":{"mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112.","apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25941385"]},"author":[{"last_name":"Polechova","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"publist_id":"5288","title":"Limits to adaptation along environmental gradients","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","year":"2015","publication":"PNAS","day":"19","page":"6401 - 6406","date_created":"2018-12-11T11:54:11Z","date_published":"2015-05-19T00:00:00Z","doi":"10.1073/pnas.1421515112","_id":"1818","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:24Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"scopus_import":1,"intvolume":" 112","month":"05","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"20","volume":112},{"type":"journal_article","status":"public","_id":"1819","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:24Z","scopus_import":1,"intvolume":" 8","month":"08","abstract":[{"lang":"eng","text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity."}],"oa_version":"None","ec_funded":1,"volume":8,"issue":"8","publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"author":[{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596"}],"publist_id":"5287","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","citation":{"chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2015.03.007.","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007.","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","page":"1175 - 1187","date_created":"2018-12-11T11:54:11Z","date_published":"2015-08-03T00:00:00Z","doi":"10.1016/j.molp.2015.03.007","year":"2015","publication":"Molecular Plant","day":"03"},{"title":"Systematic discovery of drug interaction mechanisms","author":[{"full_name":"Chevereau, Guillaume","last_name":"Chevereau","first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5283","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Chevereau, G., & Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.15252/msb.20156098","ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 2015;11(4). doi:10.15252/msb.20156098","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” Molecular Systems Biology, vol. 11, no. 4. Nature Publishing Group, 2015.","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:10.15252/msb.20156098.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology. Nature Publishing Group, 2015. https://doi.org/10.15252/msb.20156098."},"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"},{"call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics","grant_number":"303507"}],"article_number":"807","doi":"10.15252/msb.20156098","date_published":"2015-04-01T00:00:00Z","date_created":"2018-12-11T11:54:12Z","day":"01","publication":"Molecular Systems Biology","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:17Z","ddc":["570"],"date_updated":"2021-01-12T06:53:26Z","status":"public","pubrep_id":"395","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1823","volume":11,"issue":"4","ec_funded":1,"file":[{"date_created":"2018-12-12T10:14:34Z","file_name":"IST-2015-395-v1+1_807.full.pdf","creator":"system","date_updated":"2020-07-14T12:45:17Z","file_size":1273573,"checksum":"4289b518fbe2166682fb1a1ef9b405f3","file_id":"5087","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 11","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways."}]},{"abstract":[{"text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"04","intvolume":" 6","publication_status":"published","file":[{"checksum":"c4cffb5c8b245e658a34eac71a03e7cc","file_id":"5245","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:54Z","file_name":"IST-2016-451-v1+1_ncomms7977.pdf","date_updated":"2020-07-14T12:45:17Z","file_size":1151501,"creator":"system"}],"language":[{"iso":"eng"}],"volume":6,"_id":"1824","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"451","date_updated":"2021-01-12T06:53:26Z","ddc":["530"],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:45:17Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"24","publication":"Nature Communications","date_published":"2015-04-24T00:00:00Z","doi":"10.1038/ncomms7977","date_created":"2018-12-11T11:54:13Z","article_number":"6977","citation":{"mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications, vol. 6, 6977, Nature Publishing Group, 2015, doi:10.1038/ncomms7977.","apa":"Knebel, J., Weber, M., Krüger, T. H., & Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7977","ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 2015;6. doi:10.1038/ncomms7977","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).","chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7977.","ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5282","author":[{"full_name":"Knebel, Johannes","last_name":"Knebel","first_name":"Johannes"},{"full_name":"Weber, Markus","last_name":"Weber","first_name":"Markus"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"},{"first_name":"Erwin","last_name":"Frey","full_name":"Frey, Erwin"}],"title":"Evolutionary games of condensates in coupled birth-death processes"},{"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/","open_access":"1"}],"month":"05","intvolume":" 370","abstract":[{"text":"This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"volume":370,"issue":"1669","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1831","department":[{"_id":"SyCr"}],"date_updated":"2021-01-12T06:53:29Z","publisher":"Royal Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank the German Research Foundation (DFG), the Ministry of Science and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for their support of the 9. Göttinger Freilandtage in 2013, a conference at which most contributions to this issue were first presented, the referees of the contributions to this issue for their constructive comments, Meggan Craft for comments, and Helen Eaton for her support in producing this theme issue.","doi":"10.1098/rstb.2014.0116","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:54:15Z","year":"2015","day":"01","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","article_number":"20140116","publist_id":"5272","author":[{"first_name":"Peter","last_name":"Kappeler","full_name":"Kappeler, Peter"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Charles","last_name":"Nunn","full_name":"Nunn, Charles"}],"external_id":{"pmid":["25870402"]},"title":"Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies","citation":{"chicago":"Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rstb.2014.0116.","ista":"Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669), 20140116.","mla":"Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:10.1098/rstb.2014.0116.","apa":"Kappeler, P., Cremer, S., & Nunn, C. (2015). Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2014.0116","ama":"Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0116","ieee":"P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, 2015.","short":"P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"1","volume":160,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory."}],"intvolume":" 160","month":"07","main_file_link":[{"url":"arxiv.org/abs/1406.5313","open_access":"1"}],"scopus_import":1,"date_updated":"2021-01-12T06:53:28Z","department":[{"_id":"HeEd"}],"_id":"1828","status":"public","type":"journal_article","publication":"Journal of Statistical Physics","day":"01","year":"2015","date_created":"2018-12-11T11:54:14Z","doi":"10.1007/s10955-015-1238-5","date_published":"2015-07-01T00:00:00Z","page":"163 - 167","oa":1,"quality_controlled":"1","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics. Springer, 2015. https://doi.org/10.1007/s10955-015-1238-5.","ista":"Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167.","mla":"Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics, vol. 160, no. 1, Springer, 2015, pp. 163–67, doi:10.1007/s10955-015-1238-5.","ama":"Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination process. Journal of Statistical Physics. 2015;160(1):163-167. doi:10.1007/s10955-015-1238-5","apa":"Akopyan, A., Pirogov, S., & Rybko, A. (2015). Invariant measures of genetic recombination process. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-015-1238-5","ieee":"A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination process,” Journal of Statistical Physics, vol. 160, no. 1. Springer, pp. 163–167, 2015.","short":"A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015) 163–167."},"title":"Invariant measures of genetic recombination process","article_processing_charge":"No","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"first_name":"Sergey","last_name":"Pirogov","full_name":"Pirogov, Sergey"},{"first_name":"Aleksandr","last_name":"Rybko","full_name":"Rybko, Aleksandr"}],"publist_id":"5276","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"Segment abstraction for worst-case execution time analysis","publist_id":"5266","author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kovács","full_name":"Kovács, Laura","first_name":"Laura"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"},{"first_name":"Jakob","last_name":"Zwirchmayr","full_name":"Zwirchmayr, Jakob"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment abstraction for worst-case execution time analysis. 9032, 105–131.","chicago":"Cerny, Pavol, Thomas A Henzinger, Laura Kovács, Arjun Radhakrishna, and Jakob Zwirchmayr. “Segment Abstraction for Worst-Case Execution Time Analysis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46669-8_5.","apa":"Cerny, P., Henzinger, T. A., Kovács, L., Radhakrishna, A., & Zwirchmayr, J. (2015). Segment abstraction for worst-case execution time analysis. Presented at the ESOP: European Symposium on Programming, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46669-8_5","ama":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. Segment abstraction for worst-case execution time analysis. 2015;9032:105-131. doi:10.1007/978-3-662-46669-8_5","ieee":"P. Cerny, T. A. Henzinger, L. Kovács, A. Radhakrishna, and J. Zwirchmayr, “Segment abstraction for worst-case execution time analysis,” vol. 9032. Springer, pp. 105–131, 2015.","short":"P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032 (2015) 105–131.","mla":"Cerny, Pavol, et al. Segment Abstraction for Worst-Case Execution Time Analysis. Vol. 9032, Springer, 2015, pp. 105–31, doi:10.1007/978-3-662-46669-8_5."},"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:54:16Z","doi":"10.1007/978-3-662-46669-8_5","date_published":"2015-04-01T00:00:00Z","page":"105 - 131","day":"01","year":"2015","status":"public","conference":{"name":"ESOP: European Symposium on Programming","start_date":"2015-04-11","location":"London, United Kingdom","end_date":"2015-04-18"},"type":"conference","_id":"1836","series_title":"Lecture Notes in Computer Science","department":[{"_id":"ToHe"}],"date_updated":"2020-08-11T10:09:32Z","intvolume":" 9032","month":"04","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"None","abstract":[{"lang":"eng","text":"In the standard framework for worst-case execution time (WCET) analysis of programs, the main data structure is a single instance of integer linear programming (ILP) that represents the whole program. The instance of this NP-hard problem must be solved to find an estimate forWCET, and it must be refined if the estimate is not tight.We propose a new framework for WCET analysis, based on abstract segment trees (ASTs) as the main data structure. The ASTs have two advantages. First, they allow computing WCET by solving a number of independent small ILP instances. Second, ASTs store more expressive constraints, thus enabling a more efficient and precise refinement procedure. In order to realize our framework algorithmically, we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework to obtain parametric estimates of WCET. We experimentally evaluate our approach on a set of examples from WCET benchmark suites and linear-algebra packages. We show that our analysis, with comparable effort, provides WCET estimates that in many cases significantly improve those computed by existing tools."}],"ec_funded":1,"volume":9032,"language":[{"iso":"eng"}],"publication_status":"published"}]