[{"citation":{"short":"É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete & Computational Geometry 53 (2015) 587–620.","ieee":"É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” Discrete & Computational Geometry, vol. 53, no. 3. Springer, pp. 587–620, 2015.","apa":"Colin De Verdière, É., Hubard, A., & de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9679-9","ama":"Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 2015;53(3):587-620. doi:10.1007/s00454-015-9679-9","mla":"Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:10.1007/s00454-015-9679-9.","ista":"Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 53(3), 587–620.","chicago":"Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9679-9."},"date_updated":"2021-01-12T06:52:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Colin De Verdière","full_name":"Colin De Verdière, Éric","first_name":"Éric"},{"last_name":"Hubard","full_name":"Hubard, Alfredo","first_name":"Alfredo"},{"full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay","first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5397","department":[{"_id":"UlWa"}],"title":"Discrete systolic inequalities and decompositions of triangulated surfaces","_id":"1730","type":"journal_article","status":"public","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","day":"02","page":"587 - 620","date_created":"2018-12-11T11:53:42Z","volume":53,"issue":"3","date_published":"2015-04-02T00:00:00Z","doi":"10.1007/s00454-015-9679-9","abstract":[{"lang":"eng","text":"How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations."}],"oa_version":"Preprint","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.4036"}],"scopus_import":1,"publisher":"Springer","quality_controlled":"1","intvolume":" 53","month":"04"},{"_id":"1728","status":"public","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","extern":1,"citation":{"ista":"Cohen M, Kicheva A, Ribeiro A, Blassberg R, Page K, Barnes C, Briscoe J. 2015. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 6.","chicago":"Cohen, Michael, Anna Kicheva, Ana Ribeiro, Robert Blassberg, Karen Page, Chris Barnes, and James Briscoe. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7709.","ama":"Cohen M, Kicheva A, Ribeiro A, et al. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 2015;6. doi:10.1038/ncomms7709","apa":"Cohen, M., Kicheva, A., Ribeiro, A., Blassberg, R., Page, K., Barnes, C., & Briscoe, J. (2015). Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7709","ieee":"M. Cohen et al., “Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","short":"M. Cohen, A. Kicheva, A. Ribeiro, R. Blassberg, K. Page, C. Barnes, J. Briscoe, Nature Communications 6 (2015).","mla":"Cohen, Michael, et al. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications, vol. 6, Nature Publishing Group, 2015, doi:10.1038/ncomms7709."},"date_updated":"2021-01-12T06:52:48Z","title":"Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms","author":[{"full_name":"Cohen, Michael H","last_name":"Cohen","first_name":"Michael"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Anna Kicheva","last_name":"Kicheva"},{"first_name":"Ana","full_name":"Ribeiro, Ana C","last_name":"Ribeiro"},{"full_name":"Blassberg, Robert A","last_name":"Blassberg","first_name":"Robert"},{"first_name":"Karen","last_name":"Page","full_name":"Page, Karen M"},{"last_name":"Barnes","full_name":"Barnes, Chris P","first_name":"Chris"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"}],"publist_id":"5399","acknowledgement":"C.P.B. gratefully acknowledges funding from the Wellcome Trust through a Research Career Development Fellowship (097319/Z/11/Z). This work was supported by the Medical Research Council (U117560541) and Wellcome Trust (WT098326MA, WT098325MA).","abstract":[{"lang":"eng","text":"In the vertebrate neural tube, the morphogen Sonic Hedgehog (Shh) establishes a characteristic pattern of gene expression. Here we quantify the Shh gradient in the developing mouse neural tube and show that while the amplitude of the gradient increases over time, the activity of the pathway transcriptional effectors, Gli proteins, initially increases but later decreases. Computational analysis of the pathway suggests three mechanisms that could contribute to this adaptation: transcriptional upregulation of the inhibitory receptor Ptch1, transcriptional downregulation of Gli and the differential stability of active and inactive Gli isoforms. Consistent with this, Gli2 protein expression is downregulated during neural tube patterning and adaptation continues when the pathway is stimulated downstream of Ptch1. Moreover, the Shh-induced upregulation of Gli2 transcription prevents Gli activity levels from adapting in a different cell type, NIH3T3 fibroblasts, despite the upregulation of Ptch1. Multiple mechanisms therefore contribute to the intracellular dynamics of Shh signalling, resulting in different signalling dynamics in different cell types."}],"intvolume":" 6","month":"04","quality_controlled":0,"publisher":"Nature Publishing Group","publication":"Nature Communications","day":"02","year":"2015","publication_status":"published","date_created":"2018-12-11T11:53:42Z","volume":6,"date_published":"2015-04-02T00:00:00Z","doi":"10.1038/ncomms7709"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad","date_created":"2018-12-11T11:53:44Z","doi":"10.1111/cgf.12576","date_published":"2015-05-01T00:00:00Z","page":"473 - 480","publication":"Computer Graphics Forum","day":"01","year":"2015","has_accepted_license":"1","title":"A dimension-reduced pressure solver for liquid simulations","author":[{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"},{"full_name":"Thürey, Nils","last_name":"Thürey","first_name":"Nils"},{"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":"5389","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:10.1111/cgf.12576.","short":"R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480.","ieee":"R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” Computer Graphics Forum, vol. 34, no. 2. Wiley, pp. 473–480, 2015.","ama":"Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 2015;34(2):473-480. doi:10.1111/cgf.12576","apa":"Ando, R., Thürey, N., & Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12576","chicago":"Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum. Wiley, 2015. https://doi.org/10.1111/cgf.12576.","ista":"Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480."},"intvolume":" 34","month":"05","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations."}],"issue":"2","volume":34,"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:15Z","file_size":6312352,"date_created":"2018-12-12T10:16:30Z","file_name":"IST-2016-607-v1+1_coarsegrid.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"590752bf977855b337a80f78a9bc2404","file_id":"5218"}],"publication_status":"published","pubrep_id":"607","status":"public","type":"journal_article","_id":"1735","file_date_updated":"2020-07-14T12:45:15Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2023-02-23T10:12:11Z"},{"_id":"1734","type":"journal_article","status":"public","citation":{"chicago":"Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum. Wiley-Blackwell, 2015. https://doi.org/10.1111/cgf.12594.","ista":"Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733.","mla":"Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:10.1111/cgf.12594.","ieee":"O. Klehm et al., “Recent advances in facial appearance capture,” Computer Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015.","short":"O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733.","ama":"Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. Computer Graphics Forum. 2015;34(2):709-733. doi:10.1111/cgf.12594","apa":"Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12594"},"date_updated":"2021-01-12T06:52:52Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5391","author":[{"last_name":"Klehm","full_name":"Klehm, Oliver","first_name":"Oliver"},{"first_name":"Fabrice","full_name":"Rousselle, Fabrice","last_name":"Rousselle"},{"first_name":"Marios","full_name":"Papas, Marios","last_name":"Papas"},{"last_name":"Bradley","full_name":"Bradley, Derek","first_name":"Derek"},{"first_name":"Christophe","full_name":"Hery, Christophe","last_name":"Hery"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"first_name":"Wojciech","last_name":"Jarosz","full_name":"Jarosz, Wojciech"},{"last_name":"Beeler","full_name":"Beeler, Thabo","first_name":"Thabo"}],"title":"Recent advances in facial appearance capture","department":[{"_id":"BeBi"}],"abstract":[{"text":"Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. "Image-based methods" try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. "Parametric methods" instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture.","lang":"eng"}],"oa_version":"None","main_file_link":[{"url":"https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf"}],"quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":1,"intvolume":" 34","month":"05","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Computer Graphics Forum","day":"01","page":"709 - 733","date_created":"2018-12-11T11:53:43Z","issue":"2","doi":"10.1111/cgf.12594","date_published":"2015-05-01T00:00:00Z","volume":34},{"publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":23,"abstract":[{"lang":"eng","text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/"}],"intvolume":" 23","month":"06","date_updated":"2021-01-12T06:53:12Z","department":[{"_id":"GaNo"}],"_id":"1789","type":"journal_article","status":"public","year":"2015","publication":"European Journal of Human Genetics","day":"15","page":"753 - 760","date_created":"2018-12-11T11:54:01Z","doi":"10.1038/ejhg.2014.165","date_published":"2015-06-15T00:00:00Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","citation":{"ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.","chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics. Nature Publishing Group, 2015. https://doi.org/10.1038/ejhg.2014.165.","ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 2015;23(6):753-760. doi:10.1038/ejhg.2014.165","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. Nature Publishing Group. https://doi.org/10.1038/ejhg.2014.165","ieee":"A. Kuechler et al., “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” European Journal of Human Genetics, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760.","mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:10.1038/ejhg.2014.165."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25138099"]},"author":[{"last_name":"Kuechler","full_name":"Kuechler, Alma","first_name":"Alma"},{"first_name":"Alexander","full_name":"Zink, Alexander","last_name":"Zink"},{"first_name":"Thomas","last_name":"Wieland","full_name":"Wieland, Thomas"},{"full_name":"Lüdecke, Hermann","last_name":"Lüdecke","first_name":"Hermann"},{"first_name":"Kirsten","last_name":"Cremer","full_name":"Cremer, Kirsten"},{"first_name":"Leonardo","full_name":"Salviati, Leonardo","last_name":"Salviati"},{"last_name":"Magini","full_name":"Magini, Pamela","first_name":"Pamela"},{"first_name":"Kimia","full_name":"Najafi, Kimia","last_name":"Najafi"},{"first_name":"Christiane","last_name":"Zweier","full_name":"Zweier, Christiane"},{"last_name":"Czeschik","full_name":"Czeschik, Johanna","first_name":"Johanna"},{"first_name":"Stefan","last_name":"Aretz","full_name":"Aretz, Stefan"},{"first_name":"Sabine","last_name":"Endele","full_name":"Endele, Sabine"},{"first_name":"Federica","last_name":"Tamburrino","full_name":"Tamburrino, Federica"},{"full_name":"Pinato, Claudia","last_name":"Pinato","first_name":"Claudia"},{"first_name":"Maurizio","full_name":"Clementi, Maurizio","last_name":"Clementi"},{"first_name":"Jasmin","last_name":"Gundlach","full_name":"Gundlach, Jasmin"},{"last_name":"Maylahn","full_name":"Maylahn, Carina","first_name":"Carina"},{"first_name":"Laura","full_name":"Mazzanti, Laura","last_name":"Mazzanti"},{"last_name":"Wohlleber","full_name":"Wohlleber, Eva","first_name":"Eva"},{"first_name":"Thomas","full_name":"Schwarzmayr, Thomas","last_name":"Schwarzmayr"},{"last_name":"Kariminejad","full_name":"Kariminejad, Roxana","first_name":"Roxana"},{"first_name":"Avner","full_name":"Schlessinger, Avner","last_name":"Schlessinger"},{"first_name":"Dagmar","last_name":"Wieczorek","full_name":"Wieczorek, Dagmar"},{"last_name":"Strom","full_name":"Strom, Tim","first_name":"Tim"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Hartmut","full_name":"Engels, Hartmut","last_name":"Engels"}],"publist_id":"5324","title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome"},{"year":"2015","publication_status":"published","publication":"Optics Express","day":"09","page":"3196 - 3208","date_created":"2018-12-11T11:54:01Z","issue":"3","doi":"10.1364/OE.23.003196","volume":23,"date_published":"2015-02-09T00:00:00Z","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,"intvolume":" 23","month":"02","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."},"date_updated":"2021-01-12T06:53:12Z","extern":1,"publist_id":"5325","author":[{"full_name":"Pitanti, Alessandro","last_name":"Pitanti","first_name":"Alessandro"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X"},{"last_name":"Safavi Naeini","full_name":"Safavi-Naeini, Amir H","first_name":"Amir"},{"first_name":"Jeff","last_name":"Hill","full_name":"Hill, Jeff T"},{"first_name":"Chan","full_name":"Lei, Chan U","last_name":"Lei"},{"first_name":"Alessandro","last_name":"Tredicucci","full_name":"Tredicucci, Alessandro"},{"last_name":"Painter","full_name":"Painter, Oskar J","first_name":"Oskar"}],"title":"Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity","_id":"1788","type":"journal_article","status":"public"},{"month":"06","intvolume":" 5","scopus_import":1,"oa_version":"Published Version","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."}],"volume":5,"file":[{"file_name":"IST-2016-450-v1+1_srep10781.pdf","date_created":"2018-12-12T10:17:26Z","creator":"system","file_size":2449723,"date_updated":"2020-07-14T12:45:16Z","checksum":"7716f582f8c9d82d8f2bf80bf896b440","file_id":"5280","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"450","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":"1804","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:16Z","ddc":["530"],"date_updated":"2021-01-12T06:53:18Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"date_published":"2015-06-12T00:00:00Z","doi":"10.1038/srep10781","date_created":"2018-12-11T11:54:06Z","day":"12","publication":"Scientific Reports","has_accepted_license":"1","year":"2015","article_number":"10781","title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","last_name":"Altmeyer"},{"last_name":"Do","full_name":"Do, Younghae","first_name":"Younghae"},{"full_name":"Lai, Ying","last_name":"Lai","first_name":"Ying"}],"publist_id":"5306","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 2015;5. 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","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015)."}},{"type":"journal_article","status":"public","_id":"1803","author":[{"first_name":"Damien","last_name":"Rei","full_name":"Rei, Damien"},{"first_name":"Xenos","last_name":"Mason","full_name":"Mason, Xenos"},{"last_name":"Seo","full_name":"Seo, Jinsoo","first_name":"Jinsoo"},{"first_name":"Johannes","last_name":"Gräff","full_name":"Gräff, Johannes"},{"first_name":"Andrii","last_name":"Rudenko","full_name":"Rudenko, Andrii"},{"first_name":"Jùn","full_name":"Wang, Jùn","last_name":"Wang"},{"full_name":"Rueda, Richard","last_name":"Rueda","first_name":"Richard"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","full_name":"Sandra Siegert","orcid":"0000-0001-8635-0877","last_name":"Siegert"},{"first_name":"Sukhee","last_name":"Cho","full_name":"Cho, Sukhee"},{"full_name":"Canter, Rebecca G","last_name":"Canter","first_name":"Rebecca"},{"first_name":"Alison","full_name":"Mungenast, Alison E","last_name":"Mungenast"},{"last_name":"Deisseroth","full_name":"Deisseroth, Karl A","first_name":"Karl"},{"first_name":"Lihuei","full_name":"Tsai, Lihuei","last_name":"Tsai"}],"publist_id":"5307","title":"Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway","citation":{"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.","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.","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.","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.","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","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."},"date_updated":"2021-01-12T06:53:18Z","extern":1,"publisher":"National Academy of Sciences","quality_controlled":0,"intvolume":" 112","month":"06","abstract":[{"lang":"eng","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."}],"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","page":"7291 - 7296","date_created":"2018-12-11T11:54:06Z","date_published":"2015-06-09T00:00:00Z","doi":"10.1073/pnas.1415845112","issue":"23","volume":112,"publication_status":"published","year":"2015","publication":"PNAS","day":"09"},{"type":"journal_article","status":"public","_id":"1807","author":[{"first_name":"Michael","full_name":"Goldman, Michael","last_name":"Goldman"},{"last_name":"Royo-Letelier","full_name":"Royo-Letelier, Jimena","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","first_name":"Jimena"}],"publist_id":"5303","department":[{"_id":"RoSe"}],"title":"Sharp interface limit for two components Bose-Einstein condensates","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.","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","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","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"EDP Sciences","quality_controlled":"1","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1401.1727","open_access":"1"}],"month":"05","intvolume":" 21","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"}],"oa_version":"Preprint","page":"603 - 624","volume":21,"doi":"10.1051/cocv/2014040","issue":"3","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:54:07Z","publication_status":"published","year":"2015","day":"01","language":[{"iso":"eng"}],"publication":"ESAIM - Control, Optimisation and Calculus of Variations"},{"intvolume":" 18","month":"07","quality_controlled":0,"publisher":"Nature Publishing Group","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":[{"lang":"eng","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."}],"date_created":"2018-12-11T11:54:05Z","doi":"10.1038/nn.4023","volume":18,"date_published":"2015-07-01T00:00:00Z","page":"1008 - 1016","publication":"Nature Neuroscience","day":"01","publication_status":"published","year":"2015","status":"public","type":"journal_article","_id":"1802","title":"The schizophrenia risk gene product miR-137 alters presynaptic plasticity","author":[{"last_name":"Siegert","full_name":"Sandra Siegert","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"},{"first_name":"Jinsoo","last_name":"Seo","full_name":"Seo, Jinsoo"},{"first_name":"Ester","full_name":"Kwon, Ester J","last_name":"Kwon"},{"full_name":"Rudenko, Andrii","last_name":"Rudenko","first_name":"Andrii"},{"full_name":"Cho, Sukhee","last_name":"Cho","first_name":"Sukhee"},{"first_name":"Wenyuan","last_name":"Wang","full_name":"Wang, Wenyuan"},{"first_name":"Zachary","full_name":"Flood, Zachary C","last_name":"Flood"},{"last_name":"Martorell","full_name":"Martorell, Anthony J","first_name":"Anthony"},{"full_name":"Ericsson, Maria","last_name":"Ericsson","first_name":"Maria"},{"first_name":"Alison","full_name":"Mungenast, Alison E","last_name":"Mungenast"},{"full_name":"Tsai, Lihuei","last_name":"Tsai","first_name":"Lihuei"}],"publist_id":"5308","extern":1,"date_updated":"2021-01-12T06:53:18Z","citation":{"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.","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.","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","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."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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."},"title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","publist_id":"5298","author":[{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"publication":"Current Opinion in Microbiology","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:54:08Z","doi":"10.1016/j.mib.2015.05.008","date_published":"2015-06-01T00:00:00Z","page":"1 - 9","oa":1,"publisher":"Elsevier","quality_controlled":"1","ddc":["570"],"date_updated":"2021-01-12T06:53:21Z","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:17Z","_id":"1810","pubrep_id":"493","status":"public","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","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_id":"5277","date_updated":"2020-07-14T12:45:17Z","file_size":1047255,"creator":"system","date_created":"2018-12-12T10:17:23Z","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf"}],"publication_status":"published","ec_funded":1,"volume":27,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 27","month":"06","scopus_import":1},{"ddc":["530"],"date_updated":"2021-01-12T06:53:22Z","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"MiLe"}],"_id":"1812","pubrep_id":"446","status":"public","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","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"551f751a75b39b89a1db2f7f498f9a49","file_id":"5184","date_updated":"2020-07-14T12:45:17Z","file_size":1900925,"creator":"system","date_created":"2018-12-12T10:15:59Z","file_name":"IST-2016-446-v1+1_document.pdf"}],"publication_status":"published","volume":17,"issue":"4","oa_version":"Published Version","abstract":[{"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","lang":"eng"}],"intvolume":" 17","month":"04","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005.","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.","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","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.","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","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."},"title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","article_processing_charge":"No","author":[{"last_name":"Lahrz","full_name":"Lahrz, Martin","first_name":"Martin"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Ludwig","full_name":"Mathey, Ludwig","last_name":"Mathey"}],"publist_id":"5294","article_number":"045005","publication":"New Journal of Physics","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:54:09Z","date_published":"2015-04-01T00:00:00Z","doi":"10.1088/1367-2630/17/4/045005","oa":1,"quality_controlled":"1","publisher":"IOP Publishing Ltd."},{"department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:53:21Z","status":"public","type":"journal_article","_id":"1811","ec_funded":1,"issue":"5","volume":56,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 56","month":"05","main_file_link":[{"url":"http://arxiv.org/abs/1409.0110","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","author":[{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","last_name":"Safari","full_name":"Safari, Laleh"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"},{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"first_name":"Kari","full_name":"Jänkälä, Kari","last_name":"Jänkälä"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"}],"publist_id":"5295","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","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.","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","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","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.","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."},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"052105","date_created":"2018-12-11T11:54:08Z","date_published":"2015-05-20T00:00:00Z","doi":"10.1063/1.4921227","publication":"Journal of Mathematical Physics","day":"20","year":"2015","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":"2018-12-11T11:54:09Z","date_published":"2015-05-18T00:00:00Z","volume":114,"issue":"20","doi":"10.1103/PhysRevLett.114.203001","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Physical Review Letters","day":"18","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"quality_controlled":"1","scopus_import":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":[{"first_name":"Richard","last_name":"Schmidt","full_name":"Schmidt, Richard"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"title":"Rotation of quantum impurities in the presence of a many-body environment","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:53:22Z","citation":{"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.","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1813","article_number":"203001"},{"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.","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).","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","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","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":"2021-01-12T06:53:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5302","author":[{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"department":[{"_id":"ToHe"}],"title":"Guest editors' introduction to special issue on computational methods in systems biology","_id":"1808","article_number":"7","type":"journal_article","status":"public","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"ACM Transactions on Modeling and Computer Simulation","day":"01","date_created":"2018-12-11T11:54:07Z","date_published":"2015-05-01T00:00:00Z","doi":"10.1145/2745799","volume":25,"issue":"2","oa_version":"None","publisher":"ACM","quality_controlled":"1","intvolume":" 25","month":"05"},{"title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","publist_id":"5289","author":[{"last_name":"Porazinski","full_name":"Porazinski, Sean","first_name":"Sean"},{"full_name":"Wang, Huijia","last_name":"Wang","first_name":"Huijia"},{"first_name":"Yoichi","last_name":"Asaoka","full_name":"Asaoka, Yoichi"},{"full_name":"Behrndt, Martin","last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Miyamoto","full_name":"Miyamoto, Tatsuo","first_name":"Tatsuo"},{"first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","last_name":"Morita"},{"full_name":"Hata, Shoji","last_name":"Hata","first_name":"Shoji"},{"first_name":"Takashi","last_name":"Sasaki","full_name":"Sasaki, Takashi"},{"last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yumi","full_name":"Osada, Yumi","last_name":"Osada"},{"first_name":"Satoshi","full_name":"Asaka, Satoshi","last_name":"Asaka"},{"full_name":"Momoi, Akihiro","last_name":"Momoi","first_name":"Akihiro"},{"first_name":"Sarah","last_name":"Linton","full_name":"Linton, Sarah"},{"first_name":"Joel","full_name":"Miesfeld, Joel","last_name":"Miesfeld"},{"last_name":"Link","full_name":"Link, Brian","first_name":"Brian"},{"first_name":"Takeshi","last_name":"Senga","full_name":"Senga, Takeshi"},{"first_name":"Atahualpa","full_name":"Castillo Morales, Atahualpa","last_name":"Castillo Morales"},{"first_name":"Araxi","full_name":"Urrutia, Araxi","last_name":"Urrutia"},{"first_name":"Nobuyoshi","full_name":"Shimizu, Nobuyoshi","last_name":"Shimizu"},{"full_name":"Nagase, Hideaki","last_name":"Nagase","first_name":"Hideaki"},{"first_name":"Shinya","last_name":"Matsuura","full_name":"Matsuura, Shinya"},{"first_name":"Stefan","last_name":"Bagby","full_name":"Bagby, Stefan"},{"first_name":"Hisato","full_name":"Kondoh, Hisato","last_name":"Kondoh"},{"first_name":"Hiroshi","full_name":"Nishina, Hiroshi","last_name":"Nishina"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Makoto","last_name":"Furutani Seiki","full_name":"Furutani Seiki, Makoto"}],"external_id":{"pmid":["25778702"]},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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."},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"date_published":"2015-03-16T00:00:00Z","doi":"10.1038/nature14215","date_created":"2018-12-11T11:54:10Z","page":"217 - 221","day":"16","publication":"Nature","year":"2015","status":"public","type":"journal_article","_id":"1817","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T06:53:23Z","month":"03","intvolume":" 521","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"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"}],"volume":521,"issue":"7551","language":[{"iso":"eng"}],"publication_status":"published"},{"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.","oa":1,"quality_controlled":"1","publisher":"AAAI Press","year":"2015","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","day":"01","page":"3496-3502","date_created":"2018-12-11T11:54:11Z","date_published":"2015-06-01T00:00:00Z","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"citation":{"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.","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.","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1411.3880"]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"first_name":"Raghav","full_name":"Gupta, Raghav","last_name":"Gupta"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"publist_id":"5286","title":"Optimal cost almost-sure reachability in POMDPs","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"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"alternative_title":["Artifical Intelligence"],"scopus_import":1,"intvolume":" 5","month":"06","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"1529"}]},"volume":5,"_id":"1820","conference":{"start_date":"2015-01-25","location":"Austin, TX, USA","end_date":"2015-01-30","name":"IAAI: Innovative Applications of Artificial Intelligence"},"type":"conference","status":"public","date_updated":"2023-02-23T10:02:57Z","department":[{"_id":"KrCh"}]},{"date_created":"2018-12-11T11:54:09Z","date_published":"2015-04-01T00:00:00Z","doi":"10.1145/2714572","publication":"ACM Transactions on Graphics","day":"01","year":"2015","has_accepted_license":"1","oa":1,"publisher":"ACM","quality_controlled":"1","title":"Water wave animation via wavefront parameter interpolation","publist_id":"5292","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","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572","apa":"Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572"},"project":[{"call_identifier":"FWF","_id":"25357BD2-B435-11E9-9278-68D0E5697425","name":"Deep Pictures: Creating Visual and Haptic Vector Images","grant_number":"P 24352-N23"},{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"27","ec_funded":1,"volume":34,"issue":"3","language":[{"iso":"eng"}],"file":[{"file_size":23712153,"date_updated":"2020-07-14T12:45:17Z","creator":"system","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","date_created":"2018-12-12T10:12:15Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"67c9f4fa370def68cdf31299e48bc91f","file_id":"4933"}],"publication_status":"published","intvolume":" 34","month":"04","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:17Z","ddc":["000"],"date_updated":"2023-02-23T10:15:40Z","pubrep_id":"575","status":"public","type":"journal_article","_id":"1814"},{"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","page":"6401 - 6406","date_created":"2018-12-11T11:54:11Z","date_published":"2015-05-19T00:00:00Z","doi":"10.1073/pnas.1421515112","year":"2015","publication":"PNAS","day":"19","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"external_id":{"pmid":["25941385"]},"publist_id":"5288","author":[{"last_name":"Polechova","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"Limits to adaptation along environmental gradients","citation":{"ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 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.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"scopus_import":1,"intvolume":" 112","month":"05","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Submitted Version","ec_funded":1,"volume":112,"issue":"20","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1818","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:53:24Z"},{"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187.","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.","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","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."},"title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","publist_id":"5287","author":[{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Friml","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ"}],"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..","quality_controlled":"1","publisher":"Elsevier","publication":"Molecular Plant","day":"03","year":"2015","date_created":"2018-12-11T11:54:11Z","date_published":"2015-08-03T00:00:00Z","doi":"10.1016/j.molp.2015.03.007","page":"1175 - 1187","_id":"1819","status":"public","type":"journal_article","date_updated":"2021-01-12T06:53:24Z","department":[{"_id":"JiFr"}],"oa_version":"None","abstract":[{"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.","lang":"eng"}],"intvolume":" 8","month":"08","scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":8,"issue":"8"},{"date_created":"2018-12-11T11:54:12Z","date_published":"2015-04-01T00:00:00Z","doi":"10.15252/msb.20156098","publication":"Molecular Systems Biology","day":"01","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","title":"Systematic discovery of drug interaction mechanisms","publist_id":"5283","author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” Molecular Systems Biology, vol. 11, no. 4. Nature Publishing Group, 2015.","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.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807."},"project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"article_number":"807","ec_funded":1,"volume":11,"issue":"4","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:34Z","file_name":"IST-2015-395-v1+1_807.full.pdf","date_updated":"2020-07-14T12:45:17Z","file_size":1273573,"creator":"system","checksum":"4289b518fbe2166682fb1a1ef9b405f3","file_id":"5087","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":" 11","month":"04","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."}],"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ToBo"}],"ddc":["570"],"date_updated":"2021-01-12T06:53:26Z","pubrep_id":"395","status":"public","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","_id":"1823"},{"_id":"1824","status":"public","pubrep_id":"451","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)"},"ddc":["530"],"date_updated":"2021-01-12T06:53:26Z","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"LaEr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"04","intvolume":" 6","scopus_import":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"c4cffb5c8b245e658a34eac71a03e7cc","file_id":"5245","creator":"system","file_size":1151501,"date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-451-v1+1_ncomms7977.pdf","date_created":"2018-12-12T10:16:54Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6,"article_number":"6977","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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)."},"title":"Evolutionary games of condensates in coupled birth-death processes","publist_id":"5282","author":[{"full_name":"Knebel, Johannes","last_name":"Knebel","first_name":"Johannes"},{"first_name":"Markus","last_name":"Weber","full_name":"Weber, Markus"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H"},{"last_name":"Frey","full_name":"Frey, Erwin","first_name":"Erwin"}],"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"24","publication":"Nature Communications","has_accepted_license":"1","year":"2015","date_published":"2015-04-24T00:00:00Z","doi":"10.1038/ncomms7977","date_created":"2018-12-11T11:54:13Z"},{"title":"Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies","external_id":{"pmid":["25870402"]},"publist_id":"5272","author":[{"full_name":"Kappeler, Peter","last_name":"Kappeler","first_name":"Peter"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"full_name":"Nunn, Charles","last_name":"Nunn","first_name":"Charles"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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).","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","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","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.","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.","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."},"article_number":"20140116","date_created":"2018-12-11T11:54:15Z","doi":"10.1098/rstb.2014.0116","date_published":"2015-05-01T00:00:00Z","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","day":"01","year":"2015","oa":1,"publisher":"Royal Society","quality_controlled":"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.","department":[{"_id":"SyCr"}],"date_updated":"2021-01-12T06:53:29Z","status":"public","type":"journal_article","_id":"1831","volume":370,"issue":"1669","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 370","month":"05","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","pmid":1,"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"}]},{"doi":"10.1007/s10955-015-1238-5","date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:54:14Z","page":"163 - 167","day":"01","publication":"Journal of Statistical Physics","year":"2015","publisher":"Springer","quality_controlled":"1","oa":1,"title":"Invariant measures of genetic recombination process","publist_id":"5276","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pirogov","full_name":"Pirogov, Sergey","first_name":"Sergey"},{"last_name":"Rybko","full_name":"Rybko, Aleksandr","first_name":"Aleksandr"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"issue":"1","volume":160,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 160","scopus_import":1,"main_file_link":[{"url":"arxiv.org/abs/1406.5313","open_access":"1"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:53:28Z","status":"public","type":"journal_article","_id":"1828"},{"publisher":"Springer","quality_controlled":"1","doi":"10.1007/978-3-662-46669-8_5","date_published":"2015-04-01T00:00:00Z","date_created":"2018-12-11T11:54:16Z","page":"105 - 131","day":"01","year":"2015","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"Segment abstraction for worst-case execution time analysis","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Laura","full_name":"Kovács, Laura","last_name":"Kovács"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakob","last_name":"Zwirchmayr","full_name":"Zwirchmayr, Jakob"}],"publist_id":"5266","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032 (2015) 105–131.","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.","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","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","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.","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."},"month":"04","intvolume":" 9032","alternative_title":["LNCS"],"scopus_import":1,"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."}],"volume":9032,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"conference","conference":{"end_date":"2015-04-18","location":"London, United Kingdom","start_date":"2015-04-11","name":"ESOP: European Symposium on Programming"},"series_title":"Lecture Notes in Computer Science","_id":"1836","department":[{"_id":"ToHe"}],"date_updated":"2020-08-11T10:09:32Z"},{"year":"2015","day":"01","page":"517 - 532","date_created":"2018-12-11T11:54:17Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-662-46681-0_50","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by the European Commission through an ERC Start grant (279307: Graph Games) and project STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR 14 AVACS and project ASDPS(JA 2357/2-1).","oa":1,"publisher":"Springer","citation":{"ista":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis for concurrent reactive programs with partial information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer. “Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,” 9035:517–32. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_50.","ieee":"R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.","short":"R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532.","apa":"Bloem, R., Chatterjee, K., Jacobs, S., & Könighofer, R. (2015). Assume-guarantee synthesis for concurrent reactive programs with partial information (Vol. 9035, pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_50","ama":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:10.1007/978-3-662-46681-0_50","mla":"Bloem, Roderick, et al. Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information. Vol. 9035, Springer, 2015, pp. 517–32, doi:10.1007/978-3-662-46681-0_50."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Swen","last_name":"Jacobs","full_name":"Jacobs, Swen"},{"last_name":"Könighofer","full_name":"Könighofer, Robert","first_name":"Robert"}],"publist_id":"5264","title":"Assume-guarantee synthesis for concurrent reactive programs with partial information","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":9035,"abstract":[{"lang":"eng","text":"Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples."}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1411.4604","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 9035","month":"01","date_updated":"2021-01-12T06:53:32Z","department":[{"_id":"KrCh"}],"_id":"1838","conference":{"start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"type":"conference","status":"public"},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":9035,"abstract":[{"text":"We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.03093"}],"alternative_title":["LNCS"],"intvolume":" 9035","month":"01","date_updated":"2020-01-21T13:18:52Z","department":[{"_id":"KrCh"}],"series_title":"Lecture Notes in Computer Science","_id":"1839","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom"},"type":"conference","status":"public","year":"2015","day":"01","page":"181 - 187","date_created":"2018-12-11T11:54:18Z","doi":"10.1007/978-3-662-46681-0_12","date_published":"2015-01-01T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_12.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187.","mla":"Brázdil, Tomáš, et al. Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives. Vol. 9035, Springer, 2015, pp. 181–87, doi:10.1007/978-3-662-46681-0_12.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer, pp. 181–187, 2015.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:10.1007/978-3-662-46681-0_12","apa":"Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2015). Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_12"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vojtěch","full_name":"Forejt, Vojtěch","last_name":"Forejt"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"}],"publist_id":"5263","title":"Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}]},{"date_created":"2018-12-11T11:54:17Z","doi":"10.1017/jfm.2015.184","date_published":"2015-04-08T00:00:00Z","publication":"Journal of Fluid Mechanics","day":"08","year":"2015","oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","title":"Subcritical versus supercritical transition to turbulence in curved pipes","external_id":{"arxiv":["1508.06559"]},"article_processing_charge":"No","publist_id":"5265","author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","last_name":"Kühnen","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob"},{"first_name":"P","full_name":"Braunshier, P","last_name":"Braunshier"},{"first_name":"M","full_name":"Schwegel, M","last_name":"Schwegel"},{"first_name":"Hendrik","last_name":"Kuhlmann","full_name":"Kuhlmann, Hendrik"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 770(5), R3.","chicago":"Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics. Cambridge University Press, 2015. https://doi.org/10.1017/jfm.2015.184.","apa":"Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., & Hof, B. (2015). Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2015.184","ama":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 2015;770(5). doi:10.1017/jfm.2015.184","short":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015).","ieee":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical versus supercritical transition to turbulence in curved pipes,” Journal of Fluid Mechanics, vol. 770, no. 5. Cambridge University Press, 2015.","mla":"Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics, vol. 770, no. 5, R3, Cambridge University Press, 2015, doi:10.1017/jfm.2015.184."},"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin"}],"article_number":"R3","ec_funded":1,"volume":770,"issue":"5","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 770","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1508.06559","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.","lang":"eng"}],"department":[{"_id":"BjHo"}],"date_updated":"2021-01-12T06:53:31Z","status":"public","article_type":"original","type":"journal_article","_id":"1837"},{"department":[{"_id":"LifeSc"}],"date_updated":"2021-01-12T06:53:36Z","status":"public","type":"journal_article","article_type":"original","_id":"1848","volume":137,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 137","month":"09","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497860/"}],"scopus_import":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis.","lang":"eng"}],"title":"FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors","external_id":{"pmid":["25716227"]},"article_processing_charge":"No","publist_id":"5253","author":[{"last_name":"Schwamb","full_name":"Schwamb, Bettina","first_name":"Bettina"},{"full_name":"Pick, Robert","last_name":"Pick","first_name":"Robert"},{"first_name":"Sara","last_name":"Fernández","full_name":"Fernández, Sara"},{"first_name":"Kirsten","full_name":"Völp, Kirsten","last_name":"Völp"},{"last_name":"Heering","full_name":"Heering, Jan","first_name":"Jan"},{"full_name":"Dötsch, Volker","last_name":"Dötsch","first_name":"Volker"},{"first_name":"Susanne","full_name":"Bösser, Susanne","last_name":"Bösser"},{"first_name":"Jennifer","last_name":"Jung","full_name":"Jung, Jennifer"},{"first_name":"Rasa","last_name":"Beinoravičiute Kellner","full_name":"Beinoravičiute Kellner, Rasa"},{"last_name":"Wesely","full_name":"Wesely, Josephine","first_name":"Josephine"},{"last_name":"Zörnig","full_name":"Zörnig, Inka","first_name":"Inka"},{"first_name":"Matthias","full_name":"Hammerschmidt, Matthias","last_name":"Hammerschmidt"},{"full_name":"Nowak, Matthias","last_name":"Nowak","id":"30845DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"full_name":"Penzel, Roland","last_name":"Penzel","first_name":"Roland"},{"first_name":"Kurt","last_name":"Zatloukal","full_name":"Zatloukal, Kurt"},{"first_name":"Stefan","full_name":"Joos, Stefan","last_name":"Joos"},{"last_name":"Rieker","full_name":"Rieker, Ralf","first_name":"Ralf"},{"first_name":"Abbas","full_name":"Agaimy, Abbas","last_name":"Agaimy"},{"first_name":"Stephan","full_name":"Söder, Stephan","last_name":"Söder"},{"first_name":"Kmarie","full_name":"Reid Lombardo, Kmarie","last_name":"Reid Lombardo"},{"first_name":"Michael","last_name":"Kendrick","full_name":"Kendrick, Michael"},{"first_name":"Michael","full_name":"Bardsley, Michael","last_name":"Bardsley"},{"last_name":"Hayashi","full_name":"Hayashi, Yujiro","first_name":"Yujiro"},{"first_name":"David","last_name":"Asuzu","full_name":"Asuzu, David"},{"full_name":"Syed, Sabriya","last_name":"Syed","first_name":"Sabriya"},{"first_name":"Tamás","full_name":"Ördög, Tamás","last_name":"Ördög"},{"first_name":"Martin","full_name":"Zörnig, Martin","last_name":"Zörnig"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Schwamb B, Pick R, Fernández S, Völp K, Heering J, Dötsch V, Bösser S, Jung J, Beinoravičiute Kellner R, Wesely J, Zörnig I, Hammerschmidt M, Nowak M, Penzel R, Zatloukal K, Joos S, Rieker R, Agaimy A, Söder S, Reid Lombardo K, Kendrick M, Bardsley M, Hayashi Y, Asuzu D, Syed S, Ördög T, Zörnig M. 2015. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 137(6), 1318–1329.","chicago":"Schwamb, Bettina, Robert Pick, Sara Fernández, Kirsten Völp, Jan Heering, Volker Dötsch, Susanne Bösser, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer. Wiley, 2015. https://doi.org/10.1002/ijc.29498.","ama":"Schwamb B, Pick R, Fernández S, et al. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 2015;137(6):1318-1329. doi:10.1002/ijc.29498","apa":"Schwamb, B., Pick, R., Fernández, S., Völp, K., Heering, J., Dötsch, V., … Zörnig, M. (2015). FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.29498","ieee":"B. Schwamb et al., “FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors,” International Journal of Cancer, vol. 137, no. 6. Wiley, pp. 1318–1329, 2015.","short":"B. Schwamb, R. Pick, S. Fernández, K. Völp, J. Heering, V. Dötsch, S. Bösser, J. Jung, R. Beinoravičiute Kellner, J. Wesely, I. Zörnig, M. Hammerschmidt, M. Nowak, R. Penzel, K. Zatloukal, S. Joos, R. Rieker, A. Agaimy, S. Söder, K. Reid Lombardo, M. Kendrick, M. Bardsley, Y. Hayashi, D. Asuzu, S. Syed, T. Ördög, M. Zörnig, International Journal of Cancer 137 (2015) 1318–1329.","mla":"Schwamb, Bettina, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer, vol. 137, no. 6, Wiley, 2015, pp. 1318–29, doi:10.1002/ijc.29498."},"date_created":"2018-12-11T11:54:20Z","doi":"10.1002/ijc.29498","date_published":"2015-09-01T00:00:00Z","page":"1318 - 1329","publication":"International Journal of Cancer","day":"01","year":"2015","oa":1,"quality_controlled":"1","publisher":"Wiley"},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS."}],"intvolume":" 52","month":"04","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_id":"7854","checksum":"fb4037ddc4fc05f33080dd3547ede350","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2015_ActaInfo_Benes.pdf","date_created":"2020-05-15T08:57:44Z","file_size":488482,"date_updated":"2020-07-14T12:45:19Z","creator":"dernst"}],"publication_status":"published","ec_funded":1,"issue":"2-3","volume":52,"_id":"1846","status":"public","article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2021-01-12T06:53:35Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:19Z","oa":1,"publisher":"Springer","quality_controlled":"1","publication":"Acta Informatica","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:54:20Z","date_published":"2015-04-01T00:00:00Z","doi":"10.1007/s00236-015-0215-4","page":"269 - 297","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. 2015. Refinement checking on parametric modal transition systems. Acta Informatica. 52(2–3), 269–297.","chicago":"Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert, and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica. Springer, 2015. https://doi.org/10.1007/s00236-015-0215-4.","ama":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking on parametric modal transition systems. Acta Informatica. 2015;52(2-3):269-297. doi:10.1007/s00236-015-0215-4","apa":"Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., & Srba, J. (2015). Refinement checking on parametric modal transition systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-015-0215-4","ieee":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement checking on parametric modal transition systems,” Acta Informatica, vol. 52, no. 2–3. Springer, pp. 269–297, 2015.","short":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297.","mla":"Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:10.1007/s00236-015-0215-4."},"title":"Refinement checking on parametric modal transition systems","article_processing_charge":"No","author":[{"first_name":"Nikola","full_name":"Beneš, Nikola","last_name":"Beneš"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"full_name":"Larsen, Kim","last_name":"Larsen","first_name":"Kim"},{"full_name":"Möller, Mikael","last_name":"Möller","first_name":"Mikael"},{"full_name":"Sickert, Salomon","last_name":"Sickert","first_name":"Salomon"},{"last_name":"Srba","full_name":"Srba, Jiří","first_name":"Jiří"}],"publist_id":"5255"},{"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:19Z","ddc":["570"],"date_updated":"2021-10-08T09:07:34Z","pubrep_id":"822","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","_id":"1845","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"6","volume":85,"language":[{"iso":"eng"}],"file":[{"file_size":411832,"date_updated":"2020-07-14T12:45:19Z","creator":"system","file_name":"IST-2017-822-v1+1_Perspective_Fig__Final.pdf","date_created":"2018-12-12T10:16:07Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"d1808550e376a0eca2a950fda017cfa6","file_id":"5192"},{"file_name":"IST-2017-822-v1+2_Perspective_Final2.pdf","date_created":"2018-12-12T10:16:07Z","file_size":100769,"date_updated":"2020-07-14T12:45:19Z","creator":"system","checksum":"a279f4ae61e6c8f33d68f69a0d02097d","file_id":"5193","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","intvolume":" 85","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression.","lang":"eng"}],"title":"Excitement about inhibitory presynaptic terminals","article_processing_charge":"No","publist_id":"5256","author":[{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael"},{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory presynaptic terminals,” Neuron, vol. 85, no. 6. Elsevier, pp. 1149–1151, 2015.","short":"D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151.","ama":"Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic terminals. Neuron. 2015;85(6):1149-1151. doi:10.1016/j.neuron.2015.03.006","apa":"Vandael, D. H., Espinoza Martinez, C., & Jonas, P. M. (2015). Excitement about inhibitory presynaptic terminals. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.03.006","mla":"Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.” Neuron, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:10.1016/j.neuron.2015.03.006.","ista":"Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151.","chicago":"Vandael, David H, Claudia Espinoza Martinez, and Peter M Jonas. “Excitement about Inhibitory Presynaptic Terminals.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.03.006."},"date_created":"2018-12-11T11:54:19Z","doi":"10.1016/j.neuron.2015.03.006","date_published":"2015-03-18T00:00:00Z","page":"1149 - 1151","publication":"Neuron","day":"18","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"date_updated":"2021-01-12T06:53:33Z","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"_id":"1840","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0018-9286"]},"volume":60,"issue":"4","oa_version":"Preprint","abstract":[{"text":"In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.","lang":"eng"}],"intvolume":" 60","month":"04","main_file_link":[{"url":"http://arxiv.org/abs/1304.6603","open_access":"1"}],"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:10.1109/TAC.2014.2364971.","apa":"Geiger, B., Petrov, T., Kubin, G., & Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2014.2364971","ama":"Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022. doi:10.1109/TAC.2014.2364971","ieee":"B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” IEEE Transactions on Automatic Control, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015.","short":"B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.","chicago":"Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2014.2364971.","ista":"Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022."},"title":"Optimal Kullback-Leibler aggregation via information bottleneck","publist_id":"5262","author":[{"last_name":"Geiger","full_name":"Geiger, Bernhard","first_name":"Bernhard"},{"first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"},{"last_name":"Kubin","full_name":"Kubin, Gernot","first_name":"Gernot"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"}],"publication":"IEEE Transactions on Automatic Control","day":"01","year":"2015","date_created":"2018-12-11T11:54:18Z","doi":"10.1109/TAC.2014.2364971","date_published":"2015-04-01T00:00:00Z","page":"1010 - 1022","acknowledgement":"This work was supported by the Austrian Research Association under Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2 128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n","oa":1,"quality_controlled":"1","publisher":"IEEE"},{"quality_controlled":"1","publisher":"IEEE","oa":1,"year":"2015","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","page":"919 - 930","doi":"10.1109/TPAMI.2014.2363465","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:54:18Z","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"apa":"Kolmogorov, V. (2015). A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2014.2363465","ama":"Kolmogorov V. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2015;37(5):919-930. doi:10.1109/TPAMI.2014.2363465","short":"V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930.","ieee":"V. Kolmogorov, “A new look at reweighted message passing,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5. IEEE, pp. 919–930, 2015.","mla":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, IEEE, 2015, pp. 919–30, doi:10.1109/TPAMI.2014.2363465.","ista":"Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 37(5), 919–930.","chicago":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2015. https://doi.org/10.1109/TPAMI.2014.2363465."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5261","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"}],"title":"A new look at reweighted message passing","abstract":[{"text":"We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1309.5655","open_access":"1"}],"month":"05","intvolume":" 37","publication_status":"published","language":[{"iso":"eng"}],"issue":"5","volume":37,"ec_funded":1,"_id":"1841","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:33Z","department":[{"_id":"VlKo"}]},{"author":[{"last_name":"Himschoot","full_name":"Himschoot, Ellie","first_name":"Ellie"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","last_name":"Friml","first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"publist_id":"5252","department":[{"_id":"JiFr"}],"title":"Calcium is an organizer of cell polarity in plants","citation":{"chicago":"Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017.","ista":"Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(9), 2168–2172.","mla":"Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017.","apa":"Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017","ama":"Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017","short":"E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172.","ieee":"E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015."},"date_updated":"2021-01-12T06:53:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1849","page":"2168 - 2172","date_created":"2018-12-11T11:54:21Z","issue":"9","volume":1853,"date_published":"2015-09-01T00:00:00Z","doi":"10.1016/j.bbamcr.2015.02.017","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","day":"01","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"intvolume":" 1853","month":"09","abstract":[{"text":"Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.","lang":"eng"}],"acknowledgement":"The contributing authors were supported by the Ghent University Special Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33 and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), and the Research Foundation Flanders (to S.V.).","oa_version":"None"},{"type":"journal_article","status":"public","_id":"1847","publist_id":"5254","author":[{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","last_name":"Grones"},{"first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","last_name":"Friml"}],"title":"ABP1: Finally docking","department":[{"_id":"JiFr"}],"citation":{"short":"P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358.","ieee":"P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.","ama":"Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013","apa":"Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2014.12.013","mla":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013.","ista":"Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.","chicago":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013."},"date_updated":"2021-01-12T06:53:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":1,"publisher":"Elsevier","month":"03","intvolume":" 8","oa_version":"None","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).","page":"356 - 358","date_published":"2015-03-02T00:00:00Z","doi":"10.1016/j.molp.2014.12.013","volume":8,"issue":"3","date_created":"2018-12-11T11:54:20Z","publication_status":"published","year":"2015","day":"02","publication":"Molecular Plant","language":[{"iso":"eng"}]},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2018-12-11T11:54:21Z","date_published":"2015-05-07T00:00:00Z","doi":"10.1016/j.jtbi.2015.02.018","page":"54 - 64","publication":"Journal of Theoretical Biology","day":"07","year":"2015","has_accepted_license":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:10.1016/j.jtbi.2015.02.018.","apa":"Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” Journal of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018.","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64."},"intvolume":" 372","month":"05","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.","lang":"eng"}],"ec_funded":1,"volume":372,"issue":"5","language":[{"iso":"eng"}],"file":[{"file_id":"5326","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-329-v1+1_manuscript.pdf","date_created":"2018-12-12T10:18:07Z","creator":"system","file_size":1546914,"date_updated":"2020-07-14T12:45:19Z"}],"publication_status":"published","pubrep_id":"329","status":"public","type":"journal_article","_id":"1850","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"ddc":["576"],"date_updated":"2021-01-12T06:53:37Z"},{"page":"1015 - 1026","date_published":"2015-02-09T00:00:00Z","doi":"10.1111/evo.12618","date_created":"2018-12-11T11:54:21Z","has_accepted_license":"1","year":"2015","day":"09","publication":"Evolution","quality_controlled":"1","publisher":"Wiley","oa":1,"author":[{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kisdi","full_name":"Kisdi, Eva","first_name":"Eva"},{"last_name":"Gyllenberg","full_name":"Gyllenberg, Mats","first_name":"Mats"}],"publist_id":"5249","external_id":{"pmid":["25662095"]},"article_processing_charge":"No","title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","citation":{"chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12618.","ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026.","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:10.1111/evo.12618.","ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 2015;69(4):1015-1026. doi:10.1111/evo.12618","apa":"Priklopil, T., Kisdi, E., & Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. Wiley. https://doi.org/10.1111/evo.12618","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” Evolution, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"volume":69,"issue":"4","ec_funded":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","file_id":"7855","file_size":967214,"date_updated":"2020-07-14T12:45:19Z","creator":"dernst","file_name":"2015_Evolution_Priklopil.pdf","date_created":"2020-05-15T09:05:34Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"02","intvolume":" 69","abstract":[{"lang":"eng","text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them."}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:19Z","date_updated":"2022-06-07T10:52:37Z","ddc":["570"],"article_type":"original","type":"journal_article","status":"public","_id":"1851"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \\emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut.\r\nIn this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes.\r\nWe show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. "}],"month":"06","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1408.6804","open_access":"1"}],"quality_controlled":"1","scopus_import":1,"publisher":"IEEE","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015","ec_funded":1,"date_created":"2018-12-11T11:54:24Z","date_published":"2015-06-01T00:00:00Z","doi":"10.1109/CVPR.2015.7298890","page":"2737 - 2745","_id":"1859","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"status":"public","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2015-06-07","end_date":"2015-06-12","location":"Boston, MA, USA"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:40Z","citation":{"mla":"Shah, Neel, et al. A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle. IEEE, 2015, pp. 2737–45, doi:10.1109/CVPR.2015.7298890.","ama":"Shah N, Kolmogorov V, Lampert C. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. In: IEEE; 2015:2737-2745. doi:10.1109/CVPR.2015.7298890","apa":"Shah, N., Kolmogorov, V., & Lampert, C. (2015). A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle (pp. 2737–2745). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7298890","ieee":"N. Shah, V. Kolmogorov, and C. Lampert, “A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 2737–2745.","short":"N. Shah, V. Kolmogorov, C. Lampert, in:, IEEE, 2015, pp. 2737–2745.","chicago":"Shah, Neel, Vladimir Kolmogorov, and Christoph Lampert. “A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle,” 2737–45. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298890.","ista":"Shah N, Kolmogorov V, Lampert C. 2015. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. CVPR: Computer Vision and Pattern Recognition, 2737–2745."},"department":[{"_id":"VlKo"},{"_id":"ChLa"}],"title":"A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle","author":[{"full_name":"Shah, Neel","last_name":"Shah","first_name":"Neel","id":"31ABAF80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"publist_id":"5240"},{"doi":"10.1109/CVPR.2015.7298746","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:54:24Z","ec_funded":1,"page":"1401 - 1409","day":"01","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","month":"06","quality_controlled":"1","scopus_import":1,"publisher":"IEEE","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.cv-foundation.org/openaccess/content_cvpr_2015/papers/Royer_Classifier_Adaptation_at_2015_CVPR_paper.pdf"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback."}],"title":"Classifier adaptation at prediction time","department":[{"_id":"ChLa"}],"author":[{"full_name":"Royer, Amélie","last_name":"Royer","first_name":"Amélie"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5239","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Royer, Amélie, and Christoph Lampert. Classifier Adaptation at Prediction Time. IEEE, 2015, pp. 1401–09, doi:10.1109/CVPR.2015.7298746.","short":"A. Royer, C. Lampert, in:, IEEE, 2015, pp. 1401–1409.","ieee":"A. Royer and C. Lampert, “Classifier adaptation at prediction time,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 1401–1409.","ama":"Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409. doi:10.1109/CVPR.2015.7298746","apa":"Royer, A., & Lampert, C. (2015). Classifier adaptation at prediction time (pp. 1401–1409). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298746","chicago":"Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction Time,” 1401–9. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298746.","ista":"Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR: Computer Vision and Pattern Recognition, 1401–1409."},"date_updated":"2021-01-12T06:53:41Z","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"status":"public","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","location":"Boston, MA, United States","start_date":"2015-06-07"},"_id":"1860"},{"type":"conference","conference":{"start_date":"2015-06-07","end_date":"2015-06-12","location":"Boston, MA, United States","name":"CVPR: Computer Vision and Pattern Recognition"},"status":"public","_id":"1858","publist_id":"5241","author":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"external_id":{"arxiv":["1406.5362"]},"department":[{"_id":"ChLa"}],"title":"Predicting the future behavior of a time-varying probability distribution","date_updated":"2021-01-12T06:53:40Z","citation":{"mla":"Lampert, Christoph. Predicting the Future Behavior of a Time-Varying Probability Distribution. IEEE, 2015, pp. 942–50, doi:10.1109/CVPR.2015.7298696.","short":"C. Lampert, in:, IEEE, 2015, pp. 942–950.","ieee":"C. Lampert, “Predicting the future behavior of a time-varying probability distribution,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 942–950.","ama":"Lampert C. Predicting the future behavior of a time-varying probability distribution. In: IEEE; 2015:942-950. doi:10.1109/CVPR.2015.7298696","apa":"Lampert, C. (2015). Predicting the future behavior of a time-varying probability distribution (pp. 942–950). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298696","chicago":"Lampert, Christoph. “Predicting the Future Behavior of a Time-Varying Probability Distribution,” 942–50. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298696.","ista":"Lampert C. 2015. Predicting the future behavior of a time-varying probability distribution. CVPR: Computer Vision and Pattern Recognition, 942–950."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","quality_controlled":"1","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1406.5362","open_access":"1"}],"oa":1,"month":"10","abstract":[{"text":"We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time.","lang":"eng"}],"oa_version":"Preprint","page":"942 - 950","doi":"10.1109/CVPR.2015.7298696","date_published":"2015-10-15T00:00:00Z","date_created":"2018-12-11T11:54:24Z","publication_status":"published","year":"2015","day":"15","language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:17:31Z","citation":{"short":"A. Pentina, V. Sharmanska, C. Lampert, in:, IEEE, 2015, pp. 5492–5500.","ieee":"A. Pentina, V. Sharmanska, and C. Lampert, “Curriculum learning of multiple tasks,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 5492–5500.","ama":"Pentina A, Sharmanska V, Lampert C. Curriculum learning of multiple tasks. In: IEEE; 2015:5492-5500. doi:10.1109/CVPR.2015.7299188","apa":"Pentina, A., Sharmanska, V., & Lampert, C. (2015). Curriculum learning of multiple tasks (pp. 5492–5500). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7299188","mla":"Pentina, Anastasia, et al. Curriculum Learning of Multiple Tasks. IEEE, 2015, pp. 5492–500, doi:10.1109/CVPR.2015.7299188.","ista":"Pentina A, Sharmanska V, Lampert C. 2015. Curriculum learning of multiple tasks. CVPR: Computer Vision and Pattern Recognition, 5492–5500.","chicago":"Pentina, Anastasia, Viktoriia Sharmanska, and Christoph Lampert. “Curriculum Learning of Multiple Tasks,” 5492–5500. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299188."},"title":"Curriculum learning of multiple tasks","department":[{"_id":"ChLa"}],"publist_id":"5243","author":[{"full_name":"Pentina, Anastasia","last_name":"Pentina","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"_id":"1857","status":"public","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","location":"Boston, MA, United States","end_date":"2015-06-12","start_date":"2015-06-07"},"day":"01","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","date_published":"2015-06-01T00:00:00Z","doi":"10.1109/CVPR.2015.7299188","date_created":"2018-12-11T11:54:23Z","page":"5492 - 5500","oa_version":"Preprint","abstract":[{"text":"Sharing information between multiple tasks enables algorithms to achieve good generalization performance even from small amounts of training data. However, in a realistic scenario of multi-task learning not all tasks are equally related to each other, hence it could be advantageous to transfer information only between the most related tasks. In this work we propose an approach that processes multiple tasks in a sequence with sharing between subsequent tasks instead of solving all tasks jointly. Subsequently, we address the question of curriculum learning of tasks, i.e. finding the best order of tasks to be learned. Our approach is based on a generalization bound criterion for choosing the task order that optimizes the average expected classification performance over all tasks. Our experimental results show that learning multiple related tasks sequentially can be more effective than learning them jointly, the order in which tasks are being solved affects the overall performance, and that our model is able to automatically discover the favourable order of tasks. ","lang":"eng"}],"month":"06","quality_controlled":"1","publisher":"IEEE","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1412.1353","open_access":"1"}]},{"pubrep_id":"836","status":"public","type":"journal_article","_id":"1867","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T06:53:43Z","intvolume":" 36","month":"02","scopus_import":1,"oa_version":"None","abstract":[{"text":"Cultured mammalian cells essential are model systems in basic biology research, production platforms of proteins for medical use, and testbeds in synthetic biology. Flavin cofactors, in particular flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are critical for cellular redox reactions and sense light in naturally occurring photoreceptors and optogenetic tools. Here, we quantified flavin contents of commonly used mammalian cell lines. We first compared three procedures for extraction of free and noncovalently protein-bound flavins and verified extraction using fluorescence spectroscopy. For separation, two CE methods with different BGEs were established, and detection was performed by LED-induced fluorescence with limit of detections (LODs 0.5-3.8 nM). We found that riboflavin (RF), FMN, and FAD contents varied significantly between cell lines. RF (3.1-14 amol/cell) and FAD (2.2-17.0 amol/cell) were the predominant flavins, while FMN (0.46-3.4 amol/cell) was found at markedly lower levels. Observed flavin contents agree with those previously extracted from mammalian tissues, yet reduced forms of RF were detected that were not described previously. Quantification of flavins in mammalian cell lines will allow a better understanding of cellular redox reactions and optogenetic tools.","lang":"eng"}],"ec_funded":1,"issue":"4","volume":36,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012"}],"title":"Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection","author":[{"first_name":"Jens","last_name":"Hühner","full_name":"Hühner, Jens"},{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"last_name":"Neusüß","full_name":"Neusüß, Christian","first_name":"Christian"},{"full_name":"Lämmerhofer, Michael","last_name":"Lämmerhofer","first_name":"Michael"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5230","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hühner, Jens, Álvaro Inglés Prieto, Christian Neusüß, Michael Lämmerhofer, and Harald L Janovjak. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis. Wiley, 2015. https://doi.org/10.1002/elps.201400451.","ista":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. 2015. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 36(4), 518–525.","mla":"Hühner, Jens, et al. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis, vol. 36, no. 4, Wiley, 2015, pp. 518–25, doi:10.1002/elps.201400451.","apa":"Hühner, J., Inglés Prieto, Á., Neusüß, C., Lämmerhofer, M., & Janovjak, H. L. (2015). Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. Wiley. https://doi.org/10.1002/elps.201400451","ama":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 2015;36(4):518-525. doi:10.1002/elps.201400451","short":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, H.L. Janovjak, Electrophoresis 36 (2015) 518–525.","ieee":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, and H. L. Janovjak, “Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection,” Electrophoresis, vol. 36, no. 4. Wiley, pp. 518–525, 2015."},"quality_controlled":"1","publisher":"Wiley","date_created":"2018-12-11T11:54:26Z","doi":"10.1002/elps.201400451","date_published":"2015-02-01T00:00:00Z","page":"518 - 525","publication":"Electrophoresis","day":"01","year":"2015"},{"date_created":"2018-12-11T11:54:26Z","doi":"10.1242/dev.115832","date_published":"2015-02-15T00:00:00Z","page":"702 - 711","publication":"Development","day":"15","year":"2015","publisher":"Company of Biologists","quality_controlled":"1","acknowledgement":"W.G. is a post-doctoral fellow of the Research Foundation Flanders. H.S.R. is supported by Employment of Best Young Scientists for International Cooperation Empowerment [CZ.1.07/2.3.00/30.0037], co-financed by the European Social Fund and the state budget of the Czech Republic. Mi.S. was funded by the Ramón y Cajal program. This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], project ‘CEITEC – Central European Institute of Technology’ [CZ.1.05/1.1.00/02.0068], the European Social Fund [CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GACR [GA13-40637S] to J.F. We acknowledge funding from the Biological and Biotechnological Science Research Council (BBSRC) and Engineering Physics Science Research Council (EPSRC) to R.S. and M.B","title":"Plant embryogenesis requires AUX/LAX-mediated auxin influx","author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"first_name":"Bernard","full_name":"Cannoot, Bernard","last_name":"Cannoot"},{"full_name":"Soriano, Mercedes","last_name":"Soriano","first_name":"Mercedes"},{"first_name":"Ranjan","full_name":"Swarup, Ranjan","last_name":"Swarup"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"last_name":"Bennett","full_name":"Bennett, Malcolm","first_name":"Malcolm"},{"full_name":"Boutilier, Kim","last_name":"Boutilier","first_name":"Kim"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"publist_id":"5231","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Robert, Hélène, et al. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 702–11, doi:10.1242/dev.115832.","apa":"Robert, H., Grunewald, W., Sauer, M., Cannoot, B., Soriano, M., Swarup, R., … Friml, J. (2015). Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. Company of Biologists. https://doi.org/10.1242/dev.115832","ama":"Robert H, Grunewald W, Sauer M, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 2015;142(4):702-711. doi:10.1242/dev.115832","ieee":"H. Robert et al., “Plant embryogenesis requires AUX/LAX-mediated auxin influx,” Development, vol. 142, no. 4. Company of Biologists, pp. 702–711, 2015.","short":"H. Robert, W. Grunewald, M. Sauer, B. Cannoot, M. Soriano, R. Swarup, D. Weijers, M. Bennett, K. Boutilier, J. Friml, Development 142 (2015) 702–711.","chicago":"Robert, Hélène, Wim Grunewald, Michael Sauer, Bernard Cannoot, Mercedes Soriano, Ranjan Swarup, Dolf Weijers, Malcolm Bennett, Kim Boutilier, and Jiří Friml. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.115832.","ista":"Robert H, Grunewald W, Sauer M, Cannoot B, Soriano M, Swarup R, Weijers D, Bennett M, Boutilier K, Friml J. 2015. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 142(4), 702–711."},"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ec_funded":1,"issue":"4","volume":142,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 142","month":"02","scopus_import":1,"oa_version":"None","abstract":[{"text":"The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.","lang":"eng"}],"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:43Z","status":"public","type":"journal_article","_id":"1865"},{"type":"journal_article","status":"public","_id":"1868","article_number":"022906","author":[{"first_name":"Youngyong","full_name":"Park, Youngyong","last_name":"Park"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","last_name":"Altmeyer"},{"full_name":"Lai, Yingcheng","last_name":"Lai","first_name":"Yingcheng"},{"full_name":"Lee, Gyuwon","last_name":"Lee","first_name":"Gyuwon"}],"publist_id":"5229","department":[{"_id":"BjHo"}],"title":"Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances","citation":{"ieee":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, and G. Lee, “Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances,” Physical Review E, vol. 91, no. 2. American Physical Society, 2015.","short":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, G. Lee, Physical Review E 91 (2015).","ama":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 2015;91(2). doi:10.1103/PhysRevE.91.022906","apa":"Park, Y., Do, Y., Altmeyer, S., Lai, Y., & Lee, G. (2015). Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.91.022906","mla":"Park, Youngyong, et al. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E, vol. 91, no. 2, 022906, American Physical Society, 2015, doi:10.1103/PhysRevE.91.022906.","ista":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. 2015. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 91(2), 022906.","chicago":"Park, Youngyong, Younghae Do, Sebastian Altmeyer, Yingcheng Lai, and Gyuwon Lee. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.91.022906."},"date_updated":"2021-01-12T06:53:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"quality_controlled":"1","publisher":"American Physical Society","intvolume":" 91","month":"02","abstract":[{"text":"We investigate high-dimensional nonlinear dynamical systems exhibiting multiple resonances under adiabatic parameter variations. Our motivations come from experimental considerations where time-dependent sweeping of parameters is a practical approach to probing and characterizing the bifurcations of the system. The question is whether bifurcations so detected are faithful representations of the bifurcations intrinsic to the original stationary system. Utilizing a harmonically forced, closed fluid flow system that possesses multiple resonances and solving the Navier-Stokes equation under proper boundary conditions, we uncover the phenomenon of the early effect. Specifically, as a control parameter, e.g., the driving frequency, is adiabatically increased from an initial value, resonances emerge at frequency values that are lower than those in the corresponding stationary system. The phenomenon is established by numerical characterization of physical quantities through the resonances, which include the kinetic energy and the vorticity field, and a heuristic analysis based on the concept of instantaneous frequency. A simple formula is obtained which relates the resonance points in the time-dependent and time-independent systems. Our findings suggest that, in general, any true bifurcation of a nonlinear dynamical system can be unequivocally uncovered through adiabatic parameter sweeping, in spite of a shift in the bifurcation point, which is of value to experimental studies of nonlinear dynamical systems.","lang":"eng"}],"oa_version":"None","date_created":"2018-12-11T11:54:27Z","date_published":"2015-02-09T00:00:00Z","issue":"2","doi":"10.1103/PhysRevE.91.022906","volume":91,"year":"2015","publication_status":"published","publication_identifier":{"issn":["1539-3755"]},"publication":"Physical Review E","language":[{"iso":"eng"}],"day":"09"},{"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"title":"The Altshuler–Shklovskii formulas for random band matrices II: The general case","publist_id":"5233","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Antti","full_name":"Knowles, Antti","last_name":"Knowles"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Erdös L, Knowles A. 2015. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 16(3), 709–799.","chicago":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare. Springer, 2015. https://doi.org/10.1007/s00023-014-0333-5.","ieee":"L. Erdös and A. Knowles, “The Altshuler–Shklovskii formulas for random band matrices II: The general case,” Annales Henri Poincare, vol. 16, no. 3. Springer, pp. 709–799, 2015.","short":"L. Erdös, A. Knowles, Annales Henri Poincare 16 (2015) 709–799.","apa":"Erdös, L., & Knowles, A. (2015). The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-014-0333-5","ama":"Erdös L, Knowles A. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 2015;16(3):709-799. doi:10.1007/s00023-014-0333-5","mla":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare, vol. 16, no. 3, Springer, 2015, pp. 709–99, doi:10.1007/s00023-014-0333-5."},"publisher":"Springer","oa":1,"doi":"10.1007/s00023-014-0333-5","date_published":"2015-03-01T00:00:00Z","date_created":"2018-12-11T11:54:26Z","page":"709 - 799","day":"01","publication":"Annales Henri Poincare","year":"2015","status":"public","type":"journal_article","_id":"1864","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:53:42Z","month":"03","intvolume":" 16","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1309.5107","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas.\r\n"}],"volume":16,"issue":"3","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:41Z","citation":{"ista":"Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.","chicago":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2688906.","short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ieee":"J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.","ama":"Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2688906","apa":"Ruess, J., & Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2688906","mla":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 8, ACM, 2015, doi:10.1145/2688906."},"title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publist_id":"5238","author":[{"orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","last_name":"Ruess","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lygeros","full_name":"Lygeros, John","first_name":"John"}],"article_number":"8","_id":"1861","status":"public","type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"ACM Transactions on Modeling and Computer Simulation","publication_status":"published","year":"2015","doi":"10.1145/2688906","date_published":"2015-02-01T00:00:00Z","volume":25,"issue":"2","date_created":"2018-12-11T11:54:25Z","oa_version":"None","acknowledgement":"HYCON2; EC; European Commission\r\n","abstract":[{"text":"Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of themolecular interactions cannot be ignored. This has motivated recent research effort into methods for parameter inference and experiment design for such models. The major difficulty is that such methods usually require one to iteratively solve the chemical master equation that governs the time evolution of the probability distribution of the system. This, however, is rarely possible, and even approximation techniques remain limited to relatively small and simple systems. An alternative explored in this article is to base methods on only some low-order moments of the entire probability distribution. We summarize the theory behind such moment-based methods for parameter inference and experiment design and provide new case studies where we investigate their performance.","lang":"eng"}],"month":"02","intvolume":" 25","scopus_import":1,"publisher":"ACM","quality_controlled":"1"},{"oa_version":"None","publisher":"ACM","scopus_import":1,"month":"01","intvolume":" 58","year":"2015","publication_status":"published","day":"28","publication":"Communications of the ACM","language":[{"iso":"eng"}],"page":"86-86","issue":"2","date_published":"2015-01-28T00:00:00Z","doi":"10.1145/2701001","volume":58,"date_created":"2018-12-11T11:54:26Z","_id":"1866","type":"journal_article","status":"public","citation":{"chicago":"Henzinger, Thomas A, and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM. ACM, 2015. https://doi.org/10.1145/2701001.","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 86–86.","mla":"Henzinger, Thomas A., and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM, vol. 58, no. 2, ACM, 2015, pp. 86–86, doi:10.1145/2701001.","ama":"Henzinger TA, Raskin J. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 2015;58(2):86-86. doi:10.1145/2701001","apa":"Henzinger, T. A., & Raskin, J. (2015). The equivalence problem for finite automata: Technical perspective. Communications of the ACM. ACM. https://doi.org/10.1145/2701001","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","ieee":"T. A. Henzinger and J. Raskin, “The equivalence problem for finite automata: Technical perspective,” Communications of the ACM, vol. 58, no. 2. ACM, pp. 86–86, 2015."},"date_updated":"2021-01-12T06:53:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Jean","last_name":"Raskin","full_name":"Raskin, Jean"}],"publist_id":"5232","department":[{"_id":"ToHe"}],"title":"The equivalence problem for finite automata: Technical perspective"},{"issue":"1","volume":128,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"24c779f4cd9d549ca6833e26f486be27","file_id":"4852","creator":"system","file_size":1688844,"date_updated":"2020-07-14T12:45:19Z","file_name":"IST-2016-563-v1+1_1.full.pdf","date_created":"2018-12-12T10:11:00Z"}],"scopus_import":1,"intvolume":" 128","month":"01","abstract":[{"text":"The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:19Z","date_updated":"2021-01-12T06:53:45Z","ddc":["570"],"type":"journal_article","pubrep_id":"563","status":"public","_id":"1871","page":"1 - 7","date_created":"2018-12-11T11:54:28Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1242/jcs.159418","year":"2015","has_accepted_license":"1","publication":"Journal of Cell Science","day":"01","oa":1,"publisher":"Company of Biologists","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GAČR [grant number GA13-40637S]","publist_id":"5225","author":[{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"title":"Auxin transporters and binding proteins at a glance","citation":{"mla":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science, vol. 128, no. 1, Company of Biologists, 2015, pp. 1–7, doi:10.1242/jcs.159418.","ieee":"P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,” Journal of Cell Science, vol. 128, no. 1. Company of Biologists, pp. 1–7, 2015.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.","apa":"Grones, P., & Friml, J. (2015). Auxin transporters and binding proteins at a glance. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.159418","ama":"Grones P, Friml J. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 2015;128(1):1-7. doi:10.1242/jcs.159418","chicago":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.159418.","ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"1874","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:46Z","citation":{"chicago":"Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus. Wiley, 2015. https://doi.org/10.1002/hipo.22407.","ista":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 25(7), 838–857.","mla":"Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus, vol. 25, no. 7, Wiley, 2015, pp. 838–57, doi:10.1002/hipo.22407.","ama":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 2015;25(7):838-857. doi:10.1002/hipo.22407","apa":"Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., & Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22407","ieee":"C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter, “A three-plane architectonic atlas of the rat hippocampal region,” Hippocampus, vol. 25, no. 7. Wiley, pp. 838–857, 2015.","short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857."},"title":"A three-plane architectonic atlas of the rat hippocampal region","department":[{"_id":"JoCs"}],"author":[{"last_name":"Boccara","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte","first_name":"Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kjønigsen","full_name":"Kjønigsen, Lisa","first_name":"Lisa"},{"first_name":"Ingvild","full_name":"Hammer, Ingvild","last_name":"Hammer"},{"first_name":"Jan","last_name":"Bjaalie","full_name":"Bjaalie, Jan"},{"last_name":"Leergaard","full_name":"Leergaard, Trygve","first_name":"Trygve"},{"first_name":"Menno","full_name":"Witter, Menno","last_name":"Witter"}],"publist_id":"5222","oa_version":"None","abstract":[{"lang":"eng","text":"The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource."}],"intvolume":" 25","month":"07","publisher":"Wiley","scopus_import":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Hippocampus","day":"01","publication_status":"published","year":"2015","date_created":"2018-12-11T11:54:29Z","doi":"10.1002/hipo.22407","issue":"7","volume":25,"date_published":"2015-07-01T00:00:00Z","page":"838 - 857"},{"abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples."}],"oa_version":"Preprint","publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1408.2058","open_access":"1"}],"month":"04","intvolume":" 221","year":"2015","publication_status":"published","day":"01","publication":"Artificial Intelligence","language":[{"iso":"eng"}],"page":"46 - 72","date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.artint.2014.12.009","volume":221,"date_created":"2018-12-11T11:54:28Z","_id":"1873","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:46Z","citation":{"ista":"Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72.","chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009.","short":"K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.","ieee":"K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.","apa":"Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009","ama":"Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009","mla":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence, vol. 221, Elsevier, 2015, pp. 46–72, doi:10.1016/j.artint.2014.12.009."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5224","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"}],"external_id":{"arxiv":["1408.2058"]},"department":[{"_id":"KrCh"}],"title":"POMDPs under probabilistic semantics"}]