[{"publisher":"Springer Nature","citation":{"ama":"Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete spherical circles. In: <i>Combinatorial Image Analysis</i>. Vol 9448. Cham: Springer Nature; 2016:86-100. doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity and Smoothness of Discrete Spherical Circles.” In <i>Combinatorial Image Analysis</i>, 9448:86–100. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2016, pp. 86–100.","apa":"Biswas, R., Bhowmick, P., &#38; Brimkov, V. E. (2016). On the connectivity and smoothness of discrete spherical circles. In <i>Combinatorial image analysis</i> (Vol. 9448, pp. 86–100). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>","mla":"Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical Circles.” <i>Combinatorial Image Analysis</i>, vol. 9448, Springer Nature, 2016, pp. 86–100, doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness of discrete spherical circles,” in <i>Combinatorial image analysis</i>, vol. 9448, Cham: Springer Nature, 2016, pp. 86–100.","ista":"Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100."},"article_processing_charge":"No","extern":"1","title":"On the connectivity and smoothness of discrete spherical circles","type":"book_chapter","status":"public","date_created":"2019-01-08T20:45:19Z","doi":"10.1007/978-3-319-26145-4_7","_id":"5809","page":"86-100","intvolume":"      9448","quality_controlled":"1","department":[{"_id":"HeEd"}],"place":"Cham","author":[{"first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"},{"last_name":"Brimkov","first_name":"Valentin E.","full_name":"Brimkov, Valentin E."}],"abstract":[{"text":"A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness.","lang":"eng"}],"volume":9448,"date_published":"2016-01-06T00:00:00Z","month":"01","publication":"Combinatorial image analysis","oa_version":"None","day":"06","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2016","language":[{"iso":"eng"}],"publication_status":"published","conference":{"location":"Kolkata, India","name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2015-11-27","start_date":"2015-11-24"},"date_updated":"2022-01-28T08:13:03Z","publication_identifier":{"isbn":["978-3-319-26144-7"],"eissn":["1611-3349"],"eisbn":["978-3-319-26145-4"],"issn":["0302-9743"]}},{"date_created":"2018-12-11T11:51:59Z","file":[{"date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","access_level":"open_access","file_size":1216360,"file_id":"5272","date_created":"2018-12-12T10:17:19Z","creator":"system","relation":"main_file","checksum":"c27d898598a1e3d7f629607a309254e1"}],"publisher":"PeerJ","scopus_import":1,"day":"01","year":"2016","language":[{"iso":"eng"}],"publication":"PeerJ","issue":"3","file_date_updated":"2020-07-14T12:44:53Z","abstract":[{"text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow.","lang":"eng"}],"volume":2016,"date_published":"2016-01-01T00:00:00Z","author":[{"last_name":"Tartally","first_name":"András","full_name":"Tartally, András"},{"first_name":"Andreas","last_name":"Kelager","full_name":"Kelager, Andreas"},{"first_name":"Matthias","last_name":"Fürst","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nash","first_name":"David","full_name":"Nash, David"}],"_id":"1431","intvolume":"      2016","doi":"10.7717/peerj.1865","department":[{"_id":"SyCr"}],"quality_controlled":"1","citation":{"ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” <i>PeerJ</i>, vol. 2016, no. 3. PeerJ, 2016.","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.","short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. 2016;2016(3). doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>","chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” <i>PeerJ</i>. PeerJ, 2016. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>.","apa":"Tartally, A., Kelager, A., Fürst, M., &#38; Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” <i>PeerJ</i>, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>."},"type":"journal_article","status":"public","pubrep_id":"584","tmp":{"short":"CC BY (4.0)","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)"},"title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5767","oa_version":"Published Version","month":"01","ddc":["570"],"date_updated":"2021-01-12T06:50:41Z","oa":1,"publication_status":"published","has_accepted_license":"1","article_number":"1865"},{"file":[{"date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","file_size":4510512,"access_level":"open_access","file_id":"5355","creator":"system","date_created":"2018-12-12T10:18:33Z","relation":"main_file","checksum":"7e84d0392348c874d473b62f1042de22"}],"publisher":"Nature Publishing Group","scopus_import":1,"date_created":"2018-12-11T11:51:59Z","project":[{"grant_number":"P24909-B24","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548"}],"file_date_updated":"2020-07-14T12:44:53Z","date_published":"2016-05-13T00:00:00Z","volume":7,"abstract":[{"lang":"eng","text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network."}],"author":[{"last_name":"Mishra","first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","full_name":"Mishra, Rajiv Kumar"},{"id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","last_name":"Kim","first_name":"Sooyun"},{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","last_name":"Guzmán","first_name":"José","orcid":"0000-0003-2209-5242"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"year":"2016","language":[{"iso":"eng"}],"day":"13","publication":"Nature Communications","ec_funded":1,"citation":{"ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>.","apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552."},"pubrep_id":"582","status":"public","type":"journal_article","title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","tmp":{"short":"CC BY (4.0)","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)"},"intvolume":"         7","_id":"1432","doi":"10.1038/ncomms11552","department":[{"_id":"PeJo"}],"quality_controlled":"1","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","has_accepted_license":"1","article_number":"11552","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"dissertation_contains","id":"1396","status":"public"}]},"publist_id":"5766","month":"05","oa_version":"Published Version","date_updated":"2023-09-07T11:55:25Z","ddc":["570"],"oa":1,"publication_status":"published"},{"oa":1,"publication_status":"published","date_updated":"2021-01-12T06:50:42Z","oa_version":"Preprint","month":"08","publist_id":"5764","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","department":[{"_id":"LaEr"}],"doi":"10.1016/j.jfa.2016.04.006","_id":"1434","page":"672 - 719","intvolume":"       271","title":"Local stability of the free additive convolution","type":"journal_article","status":"public","citation":{"apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2016). Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>.","ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. 2016;271(3):672-719. doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” <i>Journal of Functional Analysis</i>, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719."},"ec_funded":1,"publication":"Journal of Functional Analysis","day":"01","year":"2016","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-3036-1475","last_name":"Bao","first_name":"Zhigang","full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0003-0954-3231","first_name":"Kevin","last_name":"Schnelli","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"volume":271,"abstract":[{"text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B   are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B   on scales down to N−2/3N−2/3.","lang":"eng"}],"date_published":"2016-08-01T00:00:00Z","issue":"3","date_created":"2018-12-11T11:52:00Z","project":[{"grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"scopus_import":1,"publisher":"Academic Press","main_file_link":[{"url":"http://arxiv.org/abs/1508.05905","open_access":"1"}]},{"citation":{"ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” <i>Neural Plasticity</i>, vol. 2016. Hindawi Publishing Corporation, 2016.","apa":"Guzmán, J., &#38; Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. Hindawi Publishing Corporation. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>.","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. 2016;2016. doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>","chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>. Hindawi Publishing Corporation, 2016. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>.","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016)."},"pubrep_id":"580","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","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)"},"title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","intvolume":"      2016","_id":"1435","doi":"10.1155/2016/1207393","department":[{"_id":"PeJo"}],"quality_controlled":"1","has_accepted_license":"1","article_number":"1207393","publist_id":"5762","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"01","oa_version":"Published Version","ddc":["570"],"date_updated":"2021-01-12T06:50:43Z","oa":1,"publication_status":"published","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:54Z","file_size":1395180,"access_level":"open_access","file_name":"IST-2016-580-v1+1_1207393.pdf","file_id":"4740","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","relation":"main_file","date_created":"2018-12-12T10:09:17Z","creator":"system"}],"publisher":"Hindawi Publishing Corporation","scopus_import":1,"date_created":"2018-12-11T11:52:00Z","file_date_updated":"2020-07-14T12:44:54Z","date_published":"2016-01-01T00:00:00Z","abstract":[{"text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.","lang":"eng"}],"volume":2016,"author":[{"full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán"},{"last_name":"Gerevich","first_name":"Zoltan","full_name":"Gerevich, Zoltan"}],"language":[{"iso":"eng"}],"year":"2016","day":"01","publication":"Neural Plasticity"},{"has_accepted_license":"1","month":"01","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5763","oa":1,"publication_status":"published","ddc":["510","530"],"date_updated":"2021-01-12T06:50:43Z","citation":{"ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., &#38; Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>.","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>.","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. 2016;105(1):1-30. doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30."},"title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"pubrep_id":"581","status":"public","type":"journal_article","doi":"10.1016/j.matpur.2015.09.003","intvolume":"       105","_id":"1436","page":"1 - 30","quality_controlled":"1","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:44:54Z","issue":"1","author":[{"full_name":"Bach, Volker","first_name":"Volker","last_name":"Bach"},{"full_name":"Breteaux, Sébastien","first_name":"Sébastien","last_name":"Breteaux"},{"orcid":"0000-0002-9166-5889","first_name":"Sören P","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"},{"full_name":"Tzaneteas, Tim","first_name":"Tim","last_name":"Tzaneteas"}],"date_published":"2016-01-01T00:00:00Z","volume":105,"abstract":[{"text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system.","lang":"eng"}],"publication":"Journal de Mathématiques Pures et Appliquées","year":"2016","language":[{"iso":"eng"}],"day":"01","ec_funded":1,"file":[{"file_size":658491,"access_level":"open_access","file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:54Z","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","relation":"main_file","date_created":"2018-12-12T10:10:36Z","creator":"system","file_id":"4825"}],"publisher":"Elsevier","scopus_import":1,"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"date_created":"2018-12-11T11:52:00Z"},{"arxiv":1,"alternative_title":["POPL"],"date_updated":"2024-03-25T23:30:18Z","oa":1,"publication_status":"published","conference":{"name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","end_date":"2016-01-22","location":"St. Petersburg, FL, USA"},"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5441"},{"id":"5442","relation":"earlier_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"821"},{"status":"public","id":"6009","relation":"later_version"},{"id":"8934","relation":"dissertation_contains","status":"public"}]},"publist_id":"5761","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"01","status":"public","type":"conference","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747."},"department":[{"_id":"KrCh"}],"quality_controlled":"1","_id":"1437","page":"733 - 747","doi":"10.1145/2837614.2837624","external_id":{"arxiv":["1510.07565"]},"volume":"20-22","abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks."}],"date_published":"2016-01-11T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","last_name":"Goharshady","first_name":"Amir","orcid":"0000-0003-1702-6584"},{"orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"ec_funded":1,"day":"11","language":[{"iso":"eng"}],"year":"2016","scopus_import":1,"publisher":"ACM","main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"date_created":"2018-12-11T11:52:01Z"},{"_id":"1438","page":"327 - 342","doi":"10.1145/2837614.2837639","external_id":{"arxiv":["1510.08517"]},"department":[{"_id":"KrCh"}],"acknowledgement":"Supported by the Natural Science Foundation of China (NSFC) under Grant No. 61532019 ","quality_controlled":"1","citation":{"ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 327–342.","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.","apa":"Chatterjee, K., Fu, H., Novotný, P., &#38; Hasheminezhad, R. (2016). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs</i>. Vol. 20–22, ACM, 2016, pp. 327–42, doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>.","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. In: Vol 20-22. ACM; 2016:327-342. doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342."},"type":"conference","status":"public","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","publist_id":"5760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","id":"5993","status":"public"}]},"oa_version":"Preprint","month":"01","date_updated":"2023-09-19T14:38:41Z","oa":1,"publication_status":"published","conference":{"location":"St. Petersburg, FL, USA","end_date":"2016-01-22","start_date":"2016-01-20","name":"POPL: Principles of Programming Languages"},"arxiv":1,"alternative_title":["POPL"],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"date_created":"2018-12-11T11:52:01Z","publisher":"ACM","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08517"}],"scopus_import":1,"day":"11","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"volume":"20-22","abstract":[{"lang":"eng","text":"In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism."}],"date_published":"2016-01-11T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu"},{"last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"},{"last_name":"Hasheminezhad","first_name":"Rouzbeh","full_name":"Hasheminezhad, Rouzbeh"}]},{"citation":{"short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>.","apa":"Dragoi, C., Henzinger, T. A., &#38; Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>","mla":"Dragoi, Cezara, et al. <i>PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms</i>. Vol. 20–22, ACM, 2016, pp. 400–15, doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>.","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415."},"type":"conference","status":"public","title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","_id":"1439","page":"400 - 415","doi":"10.1145/2837614.2837650","department":[{"_id":"ToHe"}],"acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","quality_controlled":"1","alternative_title":["ACM SIGPLAN Notices"],"publist_id":"5759","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"01","date_updated":"2021-01-12T06:50:45Z","oa":1,"publication_status":"published","conference":{"location":"St. Petersburg, FL, USA","start_date":"2016-01-20","end_date":"2016-01-22","name":"POPL: Principles of Programming Languages"},"publisher":"ACM","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01251199/"}],"scopus_import":1,"date_created":"2018-12-11T11:52:01Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification."}],"volume":"20-22","date_published":"2016-01-11T00:00:00Z","author":[{"last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","full_name":"Dragoi, Cezara"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736"}],"day":"11","year":"2016","language":[{"iso":"eng"}],"ec_funded":1},{"acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).","quality_controlled":"1","department":[{"_id":"HaJa"}],"date_created":"2018-12-11T11:52:02Z","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303564"},{"name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"}],"doi":"10.1016/j.str.2016.01.002","page":"213 - 215","_id":"1440","intvolume":"        24","title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","scopus_import":1,"status":"public","type":"journal_article","publisher":"Cell Press","citation":{"short":"H.L. Janovjak, Structure 24 (2016) 213–215.","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. 2016;24(2):213-215. doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>","mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>.","ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215.","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” <i>Structure</i>, vol. 24, no. 2. Cell Press, pp. 213–215, 2016."},"publication_status":"published","date_updated":"2021-01-12T06:50:46Z","ec_funded":1,"month":"02","oa_version":"None","publication":"Structure","publist_id":"5756","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"02","language":[{"iso":"eng"}],"year":"2016","author":[{"first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"volume":24,"date_published":"2016-02-02T00:00:00Z","issue":"2"},{"citation":{"ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 55(21), 6339–6342.","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>.","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &#38; Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. 2016;55(21):6339-6342. doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>."},"title":"A phytochrome sensory domain permits receptor activation by red light","pubrep_id":"840","type":"journal_article","status":"public","doi":"10.1002/anie.201601736","intvolume":"        55","_id":"1441","page":"6339 - 6342","quality_controlled":"1","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","department":[{"_id":"HaJa"}],"has_accepted_license":"1","month":"05","oa_version":"Submitted Version","publist_id":"5755","related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"ddc":["571","576"],"date_updated":"2023-09-07T12:49:08Z","file":[{"creator":"system","date_created":"2018-12-12T10:17:03Z","relation":"main_file","checksum":"26da07960e57ac4750b54179197ce57f","file_id":"5255","file_name":"IST-2017-840-v1+1_reichhart.pdf","file_size":1268662,"access_level":"open_access","date_updated":"2020-07-14T12:44:55Z","content_type":"application/pdf"}],"publisher":"Wiley","scopus_import":1,"date_created":"2018-12-11T11:52:02Z","project":[{"grant_number":"303564","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:44:55Z","issue":"21","author":[{"first_name":"Eva","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5409-8571","first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine","last_name":"Tichy"},{"last_name":"Mckenzie","first_name":"Catherine","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L"}],"date_published":"2016-05-17T00:00:00Z","abstract":[{"text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.","lang":"eng"}],"volume":55,"publication":"Angewandte Chemie - International Edition","year":"2016","language":[{"iso":"eng"}],"day":"17","ec_funded":1},{"issue":"1","file_date_updated":"2020-07-14T12:44:55Z","date_published":"2016-04-01T00:00:00Z","volume":107,"abstract":[{"text":"The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index.","lang":"eng"}],"author":[{"full_name":"Calatrava Moreno, Maria","first_name":"Maria","last_name":"Calatrava Moreno"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger","first_name":"Thomas"},{"full_name":"Werthner, Hannes","first_name":"Hannes","last_name":"Werthner"}],"year":"2016","language":[{"iso":"eng"}],"day":"01","publication":"Scientometrics","file":[{"date_updated":"2020-07-14T12:44:55Z","content_type":"application/pdf","file_name":"IST-2016-530-v1+1_s11192-016-1842-4.pdf","access_level":"open_access","file_size":806035,"file_id":"4848","creator":"system","date_created":"2018-12-12T10:10:56Z","checksum":"32d46268588b87d9b686492018e6a2b2","relation":"main_file"}],"publisher":"Springer","scopus_import":"1","date_created":"2018-12-11T11:52:04Z","has_accepted_license":"1","related_material":{"link":[{"url":"https://doi.org/10.1007/s11192-016-1902-9","relation":"erratum"}]},"publist_id":"5750","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","month":"04","date_updated":"2021-11-16T08:29:11Z","ddc":["000"],"publication_status":"published","oa":1,"citation":{"ama":"Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. 2016;107(1):213-232. doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>","short":"M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016) 213–232.","chicago":"Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>.","mla":"Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>, vol. 107, no. 1, Springer, 2016, pp. 213–32, doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>.","apa":"Calatrava Moreno, M., Auzinger, T., &#38; Werthner, H. (2016). On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. Springer. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>","ieee":"M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data,” <i>Scientometrics</i>, vol. 107, no. 1. Springer, pp. 213–232, 2016.","ista":"Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232."},"article_processing_charge":"No","pubrep_id":"530","status":"public","type":"journal_article","title":"On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data","tmp":{"short":"CC BY (4.0)","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)"},"intvolume":"       107","_id":"1446","page":"213 - 232","doi":"10.1007/s11192-016-1842-4","department":[{"_id":"BeBi"}],"quality_controlled":"1"},{"date_updated":"2021-01-12T06:50:49Z","publication_status":"published","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5748","oa_version":"Preprint","month":"06","status":"public","type":"journal_article","title":"Entropic Ricci curvature bounds for discrete interacting systems","citation":{"ista":"Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 26(3), 1774–1806.","ieee":"M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting systems,” <i>The Annals of Applied Probability</i>, vol. 26, no. 3. Institute of Mathematical Statistics, pp. 1774–1806, 2016.","mla":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>, vol. 26, no. 3, Institute of Mathematical Statistics, 2016, pp. 1774–806, doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>.","apa":"Fathi, M., &#38; Maas, J. (2016). Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>","ama":"Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. 2016;26(3):1774-1806. doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>","short":"M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.","chicago":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>."},"department":[{"_id":"JaMa"}],"quality_controlled":"1","acknowledgement":"Supported by the German Research Foundation through the Collaborative Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center for Mathematics. Part of this work has been done while M. Fathi visited J. Maas at the University of Bonn in July 2014.We would like to thank the referees for their careful reading of the manuscript. ","intvolume":"        26","page":"1774 - 1806","_id":"1448","doi":"10.1214/15-AAP1133","date_published":"2016-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities."}],"volume":26,"author":[{"full_name":"Fathi, Max","first_name":"Max","last_name":"Fathi"},{"orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"}],"issue":"3","language":[{"iso":"eng"}],"year":"2016","day":"01","publication":"The Annals of Applied Probability","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00562"}],"publisher":"Institute of Mathematical Statistics","date_created":"2018-12-11T11:52:05Z"},{"volume":5,"abstract":[{"text":"The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.","lang":"eng"}],"date_published":"2016-02-25T00:00:00Z","author":[{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"last_name":"Furuya","first_name":"Eri","full_name":"Furuya, Eri"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"last_name":"Kanno","first_name":"Chisa","full_name":"Kanno, Chisa"},{"full_name":"Sakamoto, Yuta","last_name":"Sakamoto","first_name":"Yuta"},{"last_name":"Ebihara","first_name":"Masashi","full_name":"Ebihara, Masashi"},{"orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"},{"first_name":"Jiro","last_name":"Toshima","full_name":"Toshima, Jiro"}],"issue":"February 2016","file_date_updated":"2020-07-14T12:44:56Z","ec_funded":1,"day":"25","year":"2016","language":[{"iso":"eng"}],"publication":"eLife","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:44:56Z","content_type":"application/pdf","file_name":"IST-2016-529-v1+1_elife-10276-v1.pdf","access_level":"open_access","file_size":5198001,"file_id":"4793","creator":"system","date_created":"2018-12-12T10:10:08Z","checksum":"d1cc44870580756ba8badd8e41adfdb5","relation":"main_file"}],"publisher":"eLife Sciences Publications","date_created":"2018-12-11T11:52:14Z","project":[{"grant_number":"334077","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions"}],"article_number":"e10276","has_accepted_license":"1","date_updated":"2021-01-12T06:50:59Z","ddc":["570"],"oa":1,"publication_status":"published","publist_id":"5721","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"02","status":"public","type":"journal_article","pubrep_id":"529","title":"Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton","tmp":{"short":"CC BY (4.0)","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)"},"citation":{"ista":"Toshima J, Furuya E, Nagano M, Kanno C, Sakamoto Y, Ebihara M, Siekhaus DE, Toshima J. 2016. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 5(February 2016), e10276.","ieee":"J. Toshima <i>et al.</i>, “Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,” <i>eLife</i>, vol. 5, no. February 2016. eLife Sciences Publications, 2016.","apa":"Toshima, J., Furuya, E., Nagano, M., Kanno, C., Sakamoto, Y., Ebihara, M., … Toshima, J. (2016). Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.10276\">https://doi.org/10.7554/eLife.10276</a>","mla":"Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” <i>ELife</i>, vol. 5, no. February 2016, e10276, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.10276\">10.7554/eLife.10276</a>.","short":"J. Toshima, E. Furuya, M. Nagano, C. Kanno, Y. Sakamoto, M. Ebihara, D.E. Siekhaus, J. Toshima, ELife 5 (2016).","chicago":"Toshima, Junko, Eri Furuya, Makoto Nagano, Chisa Kanno, Yuta Sakamoto, Masashi Ebihara, Daria E Siekhaus, and Jiro Toshima. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.10276\">https://doi.org/10.7554/eLife.10276</a>.","ama":"Toshima J, Furuya E, Nagano M, et al. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. <i>eLife</i>. 2016;5(February 2016). doi:<a href=\"https://doi.org/10.7554/eLife.10276\">10.7554/eLife.10276</a>"},"department":[{"_id":"DaSi"}],"quality_controlled":"1","_id":"1475","intvolume":"         5","doi":"10.7554/eLife.10276"},{"title":"Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis","pubrep_id":"767","type":"journal_article","status":"public","citation":{"ista":"Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W, Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 129(2), 367–379.","ieee":"J. Toshima <i>et al.</i>, “Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis,” <i>Journal of Cell Science</i>, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.","ama":"Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. 2016;129(2):367-379. doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>","chicago":"Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano, Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>.","short":"J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto, D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.","apa":"Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., … Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>","mla":"Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>."},"quality_controlled":"1","acknowledgement":"We are grateful to Anthony Bretscher (Cornell University, NY) for providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported by the European Union [grant number PCIG12-GA-2012-334077].","department":[{"_id":"DaSi"}],"doi":"10.1242/jcs.176651","intvolume":"       129","page":"367 - 379","_id":"1476","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["570","576"],"date_updated":"2021-01-12T06:51:00Z","oa_version":"Published Version","month":"01","publist_id":"5720","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"file":[{"checksum":"2da0a09149a9ed956cdf79a95c17f08a","relation":"main_file","date_created":"2018-12-12T10:11:08Z","creator":"system","file_id":"4861","file_size":7176912,"access_level":"open_access","file_name":"IST-2017-767-v1+1_367.full.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:56Z"}],"publisher":"Company of Biologists","project":[{"name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","call_identifier":"FP7"}],"date_created":"2018-12-11T11:52:14Z","author":[{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"first_name":"Chika","last_name":"Horikomi","full_name":"Horikomi, Chika"},{"first_name":"Asuka","last_name":"Okada","full_name":"Okada, Asuka"},{"full_name":"Hatori, Makiko","first_name":"Makiko","last_name":"Hatori"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"last_name":"Masuda","first_name":"Atsushi","full_name":"Masuda, Atsushi"},{"first_name":"Wataru","last_name":"Yamamoto","full_name":"Yamamoto, Wataru"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"date_published":"2016-01-15T00:00:00Z","abstract":[{"text":"The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis","lang":"eng"}],"volume":129,"file_date_updated":"2020-07-14T12:44:56Z","issue":"2","ec_funded":1,"publication":"Journal of Cell Science","language":[{"iso":"eng"}],"year":"2016","day":"15"},{"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"date_created":"2018-12-11T11:52:15Z","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2802"}],"scopus_import":1,"publication":"Journal of Computer and System Sciences","day":"01","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"issue":"5","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tracol, Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","first_name":"Mathieu","last_name":"Tracol"}],"volume":82,"abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples."}],"date_published":"2016-08-01T00:00:00Z","doi":"10.1016/j.jcss.2016.02.009","external_id":{"arxiv":["1309.2802"]},"_id":"1477","page":"878 - 911","intvolume":"        82","quality_controlled":"1","department":[{"_id":"KrCh"}],"citation":{"ista":"Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 82(5), 878–911.","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with ω-regular objectives,” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.","short":"K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences 82 (2016) 878–911.","ama":"Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. 2016;82(5):878-911. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>.","mla":"Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2016). What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>"},"title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","type":"journal_article","status":"public","oa_version":"Preprint","month":"08","related_material":{"record":[{"status":"public","id":"2295","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"5400"}]},"publist_id":"5718","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","date_updated":"2023-02-23T12:24:38Z","arxiv":1},{"scopus_import":1,"file":[{"access_level":"open_access","file_size":965607,"file_name":"IST-2016-579-v1+1_njp_18_3_035002.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:56Z","relation":"main_file","checksum":"4f959eabc19d2a2f518318a450a4d424","date_created":"2018-12-12T10:17:22Z","creator":"system","file_id":"5276"}],"publisher":"IOP Publishing Ltd.","date_created":"2018-12-11T11:52:15Z","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27"}],"author":[{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"},{"first_name":"Simone","last_name":"Warzel","full_name":"Warzel, Simone"}],"date_published":"2016-02-29T00:00:00Z","abstract":[{"text":"We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.","lang":"eng"}],"volume":18,"file_date_updated":"2020-07-14T12:44:56Z","issue":"3","publication":"New Journal of Physics","language":[{"iso":"eng"}],"year":"2016","day":"29","title":"Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas","tmp":{"short":"CC BY (4.0)","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)"},"pubrep_id":"579","type":"journal_article","status":"public","citation":{"mla":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>, vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>.","apa":"Seiringer, R., &#38; Warzel, S. (2016). Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>","chicago":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>.","short":"R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).","ama":"Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. 2016;18(3). doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>","ieee":"R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas,” <i>New Journal of Physics</i>, vol. 18, no. 3. IOP Publishing Ltd., 2016.","ista":"Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002."},"quality_controlled":"1","department":[{"_id":"RoSe"}],"doi":"10.1088/1367-2630/18/3/035002","intvolume":"        18","_id":"1478","article_number":"035002","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["510","530"],"date_updated":"2021-01-12T06:51:01Z","month":"02","oa_version":"Published Version","publist_id":"5716","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"citation":{"mla":"Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>, vol. 25, no. 3, Springer, 2016, pp. 567–605, doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>.","apa":"Krenn, S., Pietrzak, K. Z., Wadia, A., &#38; Wichs, D. (2016). A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. Springer. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25 (2016) 567–605.","ama":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. 2016;25(3):567-605. doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>","ista":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605.","ieee":"S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the chain rule for conditional HILL entropy,” <i>Computational Complexity</i>, vol. 25, no. 3. Springer, pp. 567–605, 2016."},"pubrep_id":"766","type":"journal_article","status":"public","title":"A counterexample to the chain rule for conditional HILL entropy","tmp":{"short":"CC BY (4.0)","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)"},"intvolume":"        25","page":"567 - 605","_id":"1479","doi":"10.1007/s00037-015-0120-9","department":[{"_id":"KrPi"}],"quality_controlled":"1","acknowledgement":"This work was partly funded by the European Research Council under ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n","has_accepted_license":"1","publist_id":"5715","related_material":{"record":[{"id":"2940","relation":"earlier_version","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"09","ddc":["004"],"date_updated":"2023-02-23T11:05:09Z","oa":1,"publication_status":"published","publisher":"Springer","file":[{"date_updated":"2020-07-14T12:44:56Z","content_type":"application/pdf","file_name":"IST-2017-766-v1+1_678.pdf","file_size":483258,"access_level":"open_access","file_id":"5012","date_created":"2018-12-12T10:13:29Z","creator":"system","checksum":"7659296174fa75f5f0364f31f46f4bcf","relation":"main_file"}],"scopus_import":1,"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668"}],"date_created":"2018-12-11T11:52:16Z","issue":"3","file_date_updated":"2020-07-14T12:44:56Z","date_published":"2016-09-01T00:00:00Z","volume":25,"abstract":[{"text":"Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.","lang":"eng"}],"author":[{"id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","full_name":"Krenn, Stephan","first_name":"Stephan","last_name":"Krenn","orcid":"0000-0003-2835-9093"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"first_name":"Akshay","last_name":"Wadia","full_name":"Wadia, Akshay"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"year":"2016","language":[{"iso":"eng"}],"day":"01","publication":"Computational Complexity","ec_funded":1},{"citation":{"ista":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties. Proceedings of the London Mathematical Society. 112(1), 27–56.","ieee":"M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1. Oxford University Press, pp. 27–56, 2016.","apa":"Michałek, M., Sturmfels, B., Uhler, C., &#38; Zwiernik, P. (2016). Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>","mla":"Michałek, Mateusz, et al. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1, Oxford University Press, 2016, pp. 27–56, doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>.","chicago":"Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>.","ama":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. 2016;112(1):27-56. doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>","short":"M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London Mathematical Society 112 (2016) 27–56."},"main_file_link":[{"url":"http://arxiv.org/abs/1412.6185","open_access":"1"}],"publisher":"Oxford University Press","status":"public","type":"journal_article","title":"Exponential varieties","scopus_import":1,"intvolume":"       112","_id":"1480","page":"27 - 56","doi":"10.1112/plms/pdv066","date_created":"2018-12-11T11:52:16Z","department":[{"_id":"CaUh"}],"quality_controlled":"1","issue":"1","date_published":"2016-01-07T00:00:00Z","volume":112,"abstract":[{"lang":"eng","text":"Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. "}],"author":[{"first_name":"Mateusz","last_name":"Michałek","full_name":"Michałek, Mateusz"},{"last_name":"Sturmfels","first_name":"Bernd","full_name":"Sturmfels, Bernd"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"},{"full_name":"Zwiernik, Piotr","first_name":"Piotr","last_name":"Zwiernik"}],"language":[{"iso":"eng"}],"year":"2016","publist_id":"5714","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"07","oa_version":"Preprint","month":"01","publication":"Proceedings of the London Mathematical Society","date_updated":"2021-01-12T06:51:02Z","oa":1,"publication_status":"published"},{"author":[{"full_name":"Adibi, Milad","last_name":"Adibi","first_name":"Milad"},{"full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"full_name":"Fleck, Christian","last_name":"Fleck","first_name":"Christian"}],"volume":11,"abstract":[{"lang":"eng","text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation."}],"date_published":"2016-02-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:57Z","issue":"2","publication":"PLoS One","day":"01","year":"2016","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Public Library of Science","file":[{"file_id":"5066","checksum":"6066146e527335030f83aa5924ab72a6","relation":"main_file","creator":"system","date_created":"2018-12-12T10:14:16Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:57Z","file_size":4297148,"access_level":"open_access","file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF"}],"date_created":"2018-12-11T11:52:17Z","article_number":"e0147830","has_accepted_license":"1","oa":1,"publication_status":"published","date_updated":"2021-01-12T06:51:03Z","ddc":["570"],"oa_version":"Published Version","month":"02","publist_id":"5711","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","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)"},"title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","type":"journal_article","status":"public","pubrep_id":"521","citation":{"ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” <i>PLoS One</i>, vol. 11, no. 2. Public Library of Science, 2016.","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>.","apa":"Adibi, M., Yoshida, S., Weijers, D., &#38; Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>.","ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. 2016;11(2). doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016)."},"acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","quality_controlled":"1","department":[{"_id":"JiFr"}],"doi":"10.1371/journal.pone.0147830","_id":"1482","intvolume":"        11"}]