[{"month":"11","publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":3963728,"creator":"dernst","date_updated":"2022-05-24T08:41:41Z","date_created":"2022-05-24T08:41:41Z","file_name":"2014_JournNeuroscience_Matsukawa.pdf","file_id":"11410","checksum":"6913e9bc26e9fc1c0441a739a4199229","success":1}],"day":"19","oa_version":"Published Version","author":[{"first_name":"Hiroshi","full_name":"Matsukawa, Hiroshi","last_name":"Matsukawa"},{"last_name":"Akiyoshi Nishimura","full_name":"Akiyoshi Nishimura, Sachiko","first_name":"Sachiko"},{"first_name":"Qi","full_name":"Zhang, Qi","last_name":"Zhang"},{"last_name":"Luján","full_name":"Luján, Rafael","first_name":"Rafael"},{"full_name":"Yamaguchi, Kazuhiko","first_name":"Kazuhiko","last_name":"Yamaguchi"},{"first_name":"Hiromichi","full_name":"Goto, Hiromichi","last_name":"Goto"},{"last_name":"Yaguchi","first_name":"Kunio","full_name":"Yaguchi, Kunio"},{"last_name":"Hashikawa","full_name":"Hashikawa, Tsutomu","first_name":"Tsutomu"},{"full_name":"Sano, Chie","first_name":"Chie","last_name":"Sano"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"},{"first_name":"Toshiaki","full_name":"Nakashiba, Toshiaki","last_name":"Nakashiba"},{"last_name":"Itohara","full_name":"Itohara, Shigeyoshi","first_name":"Shigeyoshi"}],"type":"journal_article","status":"public","pmid":1,"has_accepted_license":"1","intvolume":"        34","scopus_import":"1","issue":"47","article_processing_charge":"No","date_updated":"2022-05-24T08:54:54Z","oa":1,"title":"Netrin-G/NGL complexes encode functional synaptic diversification","publication":"Journal of Neuroscience","language":[{"iso":"eng"}],"ddc":["570"],"abstract":[{"lang":"eng","text":"Synaptic cell adhesion molecules are increasingly gaining attention for conferring specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic adhesion molecules that distribute on distinct axons, and their presence restricts the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific subdendritic segments of target neurons. However, the neural circuits and functional roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify excitatory synapses in independent hippocampal pathways. In the hippocampal CA1 area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G mutant synapses displayed opposing phenotypes in long-term and short-term plasticity through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic membranes. Our findings show that netrin-G/NGL interactions differentially control synaptic plasticity in distinct circuits via retrograde signaling mechanisms and explain how synaptic inputs are diversified to control neuronal activity."}],"external_id":{"pmid":["25411505"]},"publication_status":"published","date_published":"2014-11-19T00:00:00Z","publisher":"Society for Neuroscience","quality_controlled":"1","volume":34,"department":[{"_id":"RySh"}],"page":"15779 - 15792","year":"2014","acknowledgement":"This work was supported by “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)” initiated by the Council for Science and Technology Policy.","date_created":"2018-12-11T11:55:14Z","citation":{"apa":"Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K., Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic diversification. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">https://doi.org/10.1523/JNEUROSCI.1141-14.2014</a>","short":"H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792.","ama":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode functional synaptic diversification. <i>Journal of Neuroscience</i>. 2014;34(47):15779-15792. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">10.1523/JNEUROSCI.1141-14.2014</a>","ieee":"H. Matsukawa <i>et al.</i>, “Netrin-G/NGL complexes encode functional synaptic diversification,” <i>Journal of Neuroscience</i>, vol. 34, no. 47. Society for Neuroscience, pp. 15779–15792, 2014.","ista":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H, Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 34(47), 15779–15792.","mla":"Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” <i>Journal of Neuroscience</i>, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">10.1523/JNEUROSCI.1141-14.2014</a>.","chicago":"Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján, Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2014. <a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">https://doi.org/10.1523/JNEUROSCI.1141-14.2014</a>."},"publist_id":"5054","doi":"10.1523/JNEUROSCI.1141-14.2014","_id":"2018","article_type":"original","file_date_updated":"2022-05-24T08:41:41Z"},{"type":"journal_article","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.1552"}],"day":"17","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"12","author":[{"first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder"}],"publication":"Mathematical Physics, Analysis and Geometry","language":[{"iso":"eng"}],"intvolume":"        17","scopus_import":1,"title":"Phase transition in the density of states of quantum spin glasses","oa":1,"date_updated":"2021-01-12T06:54:45Z","issue":"3-4","page":"441 - 464","department":[{"_id":"LaEr"}],"quality_controlled":"1","volume":17,"publisher":"Springer","date_published":"2014-12-17T00:00:00Z","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"abstract":[{"lang":"eng","text":"We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory."}],"publication_status":"published","doi":"10.1007/s11040-014-9164-3","_id":"2019","ec_funded":1,"publist_id":"5053","date_created":"2018-12-11T11:55:15Z","citation":{"mla":"Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:<a href=\"https://doi.org/10.1007/s11040-014-9164-3\">10.1007/s11040-014-9164-3</a>.","ista":"Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464.","chicago":"Erdös, László, and Dominik J Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s11040-014-9164-3\">https://doi.org/10.1007/s11040-014-9164-3</a>.","short":"L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464.","ama":"Erdös L, Schröder DJ. Phase transition in the density of states of quantum spin glasses. <i>Mathematical Physics, Analysis and Geometry</i>. 2014;17(3-4):441-464. doi:<a href=\"https://doi.org/10.1007/s11040-014-9164-3\">10.1007/s11040-014-9164-3</a>","ieee":"L. Erdös and D. J. Schröder, “Phase transition in the density of states of quantum spin glasses,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 17, no. 3–4. Springer, pp. 441–464, 2014.","apa":"Erdös, L., &#38; Schröder, D. J. (2014). Phase transition in the density of states of quantum spin glasses. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-014-9164-3\">https://doi.org/10.1007/s11040-014-9164-3</a>"},"year":"2014"},{"quality_controlled":"1","volume":111,"page":"8850 - 8855","department":[{"_id":"SiHi"}],"date_published":"2014-06-17T00:00:00Z","status":"public","type":"journal_article","publisher":"National Academy of Sciences","author":[{"last_name":"Ali","first_name":"Shah","full_name":"Ali, Shah"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"last_name":"Saadat","first_name":"Lily","full_name":"Saadat, Lily"},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"},{"last_name":"Weissman","first_name":"Irving","full_name":"Weissman, Irving"},{"last_name":"Ardehali","full_name":"Ardehali, Reza","first_name":"Reza"}],"publication_status":"published","abstract":[{"text":"The mammalian heart has long been considered a postmitotic organ, implying that the total number of cardiomyocytes is set at birth. Analysis of cell division in the mammalian heart is complicated by cardiomyocyte binucleation shortly after birth, which makes it challenging to interpret traditional assays of cell turnover [Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009) Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry technique recently calculated the low, discrete rate of cardiomyocyte generation in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level understanding of postnatal cardiomyogenesis remains limited. Herein, we provide a new line of evidence for the differentiated α-myosin heavy chain-expressing cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic analysis with double markers” mouse model. We show limited, life-long, symmetric division of cardiomyocytes as a rare event that is evident in utero but significantly diminishes after the first month of life in mice; daughter cardiomyocytes divide very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore, ligation of the left anterior descending coronary artery, which causes a myocardial infarction in the mosaic analysis with double-marker mice, did not increase the rate of cardiomyocyte division above the basal level for up to 4 wk after the injury. The clonal analysis described here provides direct evidence of postnatal mammalian cardiomyogenesis.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"17","month":"06","language":[{"iso":"eng"}],"_id":"2020","doi":"10.1073/pnas.1408233111","publication":"PNAS","publist_id":"5052","date_created":"2018-12-11T11:55:15Z","citation":{"apa":"Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., &#38; Ardehali, R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1408233111\">https://doi.org/10.1073/pnas.1408233111</a>","short":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855.","ama":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. <i>PNAS</i>. 2014;111(24):8850-8855. doi:<a href=\"https://doi.org/10.1073/pnas.1408233111\">10.1073/pnas.1408233111</a>","ieee":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” <i>PNAS</i>, vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014.","chicago":"Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman, and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1408233111\">https://doi.org/10.1073/pnas.1408233111</a>.","ista":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 111(24), 8850–8855.","mla":"Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” <i>PNAS</i>, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:<a href=\"https://doi.org/10.1073/pnas.1408233111\">10.1073/pnas.1408233111</a>."},"title":"Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice","year":"2014","issue":"24","date_updated":"2021-01-12T06:54:46Z","intvolume":"       111","scopus_import":1},{"publication":"Science","doi":"10.1126/science.1258996","_id":"2021","language":[{"iso":"eng"}],"intvolume":"       346","scopus_import":1,"issue":"6209","year":"2014","oa":1,"date_updated":"2021-01-12T06:54:47Z","date_created":"2018-12-11T11:55:15Z","title":"Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling","publist_id":"5051","citation":{"apa":"William, J., Hippenmeyer, S., &#38; Luo, L. (2014). Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1258996\">https://doi.org/10.1126/science.1258996</a>","ieee":"J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling,” <i>Science</i>, vol. 346, no. 6209. American Association for the Advancement of Science, pp. 626–629, 2014.","ama":"William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. <i>Science</i>. 2014;346(6209):626-629. doi:<a href=\"https://doi.org/10.1126/science.1258996\">10.1126/science.1258996</a>","short":"J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629.","mla":"William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” <i>Science</i>, vol. 346, no. 6209, American Association for the Advancement of Science, 2014, pp. 626–29, doi:<a href=\"https://doi.org/10.1126/science.1258996\">10.1126/science.1258996</a>.","ista":"William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629.","chicago":"William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1258996\">https://doi.org/10.1126/science.1258996</a>."},"type":"journal_article","date_published":"2014-10-31T00:00:00Z","status":"public","publisher":"American Association for the Advancement of Science","volume":346,"quality_controlled":"1","page":"626 - 629","department":[{"_id":"SiHi"}],"month":"10","abstract":[{"lang":"eng","text":"Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","day":"31","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/"}],"publication_status":"published","author":[{"first_name":"Joo","full_name":"William, Joo","last_name":"William"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"}]},{"date_created":"2018-12-11T11:55:16Z","citation":{"apa":"Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">https://doi.org/10.1016/j.cell.2014.10.027</a>","ista":"Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788.","chicago":"Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” <i>Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">https://doi.org/10.1016/j.cell.2014.10.027</a>.","mla":"Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” <i>Cell</i>, vol. 159, no. 4, Cell Press, 2014, pp. 775–88, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">10.1016/j.cell.2014.10.027</a>.","ieee":"P. Gao <i>et al.</i>, “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” <i>Cell</i>, vol. 159, no. 4. Cell Press, pp. 775–788, 2014.","ama":"Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. <i>Cell</i>. 2014;159(4):775-788. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">10.1016/j.cell.2014.10.027</a>","short":"P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher, E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S. Hippenmeyer, S. Shi, Cell 159 (2014) 775–788."},"publist_id":"5050","year":"2014","ec_funded":1,"file_date_updated":"2020-07-14T12:45:25Z","_id":"2022","doi":"10.1016/j.cell.2014.10.027","publication_status":"published","abstract":[{"lang":"eng","text":"Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program."}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"SiHi"},{"_id":"Bio"}],"page":"775 - 788","volume":159,"quality_controlled":"1","publisher":"Cell Press","date_published":"2014-11-06T00:00:00Z","license":"https://creativecommons.org/licenses/by/4.0/","title":"Deterministic progenitor behavior and unitary production of neurons in the neocortex","date_updated":"2021-01-12T06:54:47Z","pubrep_id":"423","oa":1,"issue":"4","scopus_import":1,"has_accepted_license":"1","intvolume":"       159","language":[{"iso":"eng"}],"publication":"Cell","author":[{"last_name":"Gao","full_name":"Gao, Peng","first_name":"Peng"},{"full_name":"Postiglione, Maria P","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","last_name":"Postiglione"},{"first_name":"Teresa","full_name":"Krieger, Teresa","last_name":"Krieger"},{"last_name":"Hernandez","first_name":"Luisirene","full_name":"Hernandez, Luisirene"},{"full_name":"Wang, Chao","first_name":"Chao","last_name":"Wang"},{"full_name":"Han, Zhi","first_name":"Zhi","last_name":"Han"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Papusheva, Ekaterina","first_name":"Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Insolera","full_name":"Insolera, Ryan","first_name":"Ryan"},{"last_name":"Chugh","full_name":"Chugh, Kritika","first_name":"Kritika"},{"first_name":"Oren","full_name":"Kodish, Oren","last_name":"Kodish"},{"last_name":"Huang","full_name":"Huang, Kun","first_name":"Kun"},{"full_name":"Simons, Benjamin","first_name":"Benjamin","last_name":"Simons"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"last_name":"Shi","first_name":"Song","full_name":"Shi, Song"}],"oa_version":"Published Version","day":"06","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:08:47Z","date_updated":"2020-07-14T12:45:25Z","file_name":"IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf","checksum":"6c5de8329bb2ffa71cba9fda750f14ce","file_id":"4709","relation":"main_file","file_size":4435787,"content_type":"application/pdf","access_level":"open_access","creator":"system"}],"month":"11","status":"public","type":"journal_article"},{"year":"2014","citation":{"chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>.","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” <i>Ecology and Evolution</i>, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. 2014;4(24):4589-4597. doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>"},"date_created":"2018-12-11T11:55:16Z","publist_id":"5049","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1125"}]},"file_date_updated":"2020-07-14T12:45:25Z","_id":"2023","doi":"10.1002/ece3.1289","publication_status":"published","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"publisher":"Wiley-Blackwell","date_published":"2014-11-27T00:00:00Z","page":"4589 - 4597","department":[{"_id":"NiBa"}],"volume":4,"quality_controlled":"1","oa":1,"date_updated":"2023-09-07T11:55:53Z","pubrep_id":"462","issue":"24","title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","intvolume":"         4","scopus_import":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Ecology and Evolution","author":[{"full_name":"Novak, Sebastian","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","orcid":"0000-0002-2519-824X"}],"month":"11","oa_version":"Published Version","day":"27","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:12:28Z","date_updated":"2020-07-14T12:45:25Z","file_id":"4946","file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf","checksum":"9ab43db1b0fede7bfe560ed77e177b76","relation":"main_file","file_size":118813,"content_type":"application/pdf","access_level":"open_access","creator":"system"}],"type":"journal_article","status":"public"},{"title":"Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole","date_updated":"2021-01-12T06:54:48Z","oa":1,"pubrep_id":"616","intvolume":"         5","scopus_import":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Nature Communications","author":[{"last_name":"Toshima","full_name":"Toshima, Junko","first_name":"Junko"},{"full_name":"Nishinoaki, Show","first_name":"Show","last_name":"Nishinoaki"},{"full_name":"Sato, Yoshifumi","first_name":"Yoshifumi","last_name":"Sato"},{"full_name":"Yamamoto, Wataru","first_name":"Wataru","last_name":"Yamamoto"},{"full_name":"Furukawa, Daiki","first_name":"Daiki","last_name":"Furukawa"},{"first_name":"Daria E","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"},{"last_name":"Sawaguchi","full_name":"Sawaguchi, Akira","first_name":"Akira"},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"oa_version":"Submitted Version","day":"25","file":[{"file_name":"IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf","checksum":"614fb6579c86d1f95bdd95eeb9ab01b0","file_id":"4864","date_created":"2018-12-12T10:11:11Z","date_updated":"2020-07-14T12:45:25Z","creator":"system","file_size":4803515,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"03","status":"public","type":"journal_article","date_created":"2018-12-11T11:55:16Z","citation":{"apa":"Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms4498\">https://doi.org/10.1038/ncomms4498</a>","ama":"Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. <i>Nature Communications</i>. 2014;5. doi:<a href=\"https://doi.org/10.1038/ncomms4498\">10.1038/ncomms4498</a>","ieee":"J. Toshima <i>et al.</i>, “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” <i>Nature Communications</i>, vol. 5. Nature Publishing Group, 2014.","short":"J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014).","mla":"Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” <i>Nature Communications</i>, vol. 5, 3498, Nature Publishing Group, 2014, doi:<a href=\"https://doi.org/10.1038/ncomms4498\">10.1038/ncomms4498</a>.","chicago":"Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” <i>Nature Communications</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncomms4498\">https://doi.org/10.1038/ncomms4498</a>.","ista":"Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498."},"publist_id":"5048","year":"2014","article_number":"3498","file_date_updated":"2020-07-14T12:45:25Z","_id":"2024","doi":"10.1038/ncomms4498","publication_status":"published","abstract":[{"lang":"eng","text":"The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and in the endocytic pathway from the plasma membrane to the vacuole. However, the intracellular location at which these two pathways converge remains unclear. In addition, the endocytic pathway is not completely blocked in yeast cells lacking all Rab5 genes, suggesting the existence of an unidentified route that bypasses the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic and VPS pathways occurs upstream of the requirement for Vps21p in these pathways. We also identify a previously unidentified endocytic pathway mediated by the AP-3 complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted cells, and thus works as an alternative route to the vacuole/lysosome. We propose that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent VPS pathway and a Rab5-independent AP-3-mediated pathway."}],"ddc":["570"],"department":[{"_id":"DaSi"}],"quality_controlled":"1","volume":5,"publisher":"Nature Publishing Group","date_published":"2014-03-25T00:00:00Z"},{"language":[{"iso":"eng"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","date_updated":"2021-01-12T06:54:49Z","intvolume":"      8837","editor":[{"full_name":"Cassez, Franck","first_name":"Franck","last_name":"Cassez"},{"last_name":"Raskin","full_name":"Raskin, Jean-François","first_name":"Jean-François"}],"alternative_title":["LNCS"],"status":"public","type":"conference","author":[{"first_name":"Zuzana","full_name":"Komárková, Zuzana","last_name":"Komárková"},{"orcid":"0000-0002-8122-2881","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","first_name":"Jan"}],"day":"01","oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2014-11-07","location":"Sydney, Australia","start_date":"2014-11-03","name":"ATVA: Automated Technology for Verification and Analysis"},"month":"01","_id":"2026","doi":"10.1007/978-3-319-11936-6_17","citation":{"apa":"Komárková, Z., &#38; Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez &#38; J.-F. Raskin (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>","short":"Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.","ieee":"Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Sydney, Australia, 2014, vol. 8837, pp. 235–241.","ama":"Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8837. Springer; 2014:235-241. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>","chicago":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>.","mla":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>.","ista":"Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241."},"publist_id":"5045","date_created":"2018-12-11T11:55:17Z","acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","year":"2014","ec_funded":1,"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"page":"235 - 241","department":[{"_id":"ToHe"}],"quality_controlled":"1","volume":8837,"publisher":"Springer","date_published":"2014-01-01T00:00:00Z","publication_status":"published","abstract":[{"text":"We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata.","lang":"eng"}]},{"publication_status":"published","abstract":[{"text":"We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples.","lang":"eng"}],"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"26241A12-B435-11E9-9278-68D0E5697425","grant_number":"24696","name":"LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publisher":"Society of Industrial and Applied Mathematics","date_published":"2014-11-01T00:00:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"page":"98 - 114","quality_controlled":"1","volume":8837,"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1.","year":"2014","citation":{"apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska, M., … Ujma, M. (2014). Verification of markov decision processes using learning algorithms. In F. Cassez &#38; J.-F. Raskin (Eds.), <i> Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8837, pp. 98–114). Sydney, Australia: Society of Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">https://doi.org/10.1007/978-3-319-11936-6_8</a>","short":"T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.),  Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114.","ama":"Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision processes using learning algorithms. In: Cassez F, Raskin J-F, eds. <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8837. Society of Industrial and Applied Mathematics; 2014:98-114. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">10.1007/978-3-319-11936-6_8</a>","ieee":"T. Brázdil <i>et al.</i>, “Verification of markov decision processes using learning algorithms,” in <i> Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Sydney, Australia, 2014, vol. 8837, pp. 98–114.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt, Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification of Markov Decision Processes Using Learning Algorithms.” In <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">https://doi.org/10.1007/978-3-319-11936-6_8</a>.","mla":"Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">10.1007/978-3-319-11936-6_8</a>.","ista":"Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M, Parker D, Ujma M. 2014. Verification of markov decision processes using learning algorithms.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm Engineering and Experiments, LNCS, vol. 8837, 98–114."},"publist_id":"5046","date_created":"2018-12-11T11:55:17Z","ec_funded":1,"_id":"2027","doi":"10.1007/978-3-319-11936-6_8","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin","first_name":"Martin"},{"first_name":"Vojtěch","full_name":"Forejt, Vojtěch","last_name":"Forejt"},{"last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","full_name":"Kretinsky, Jan"},{"last_name":"Kwiatkowska","full_name":"Kwiatkowska, Marta","first_name":"Marta"},{"full_name":"Parker, David","first_name":"David","last_name":"Parker"},{"last_name":"Ujma","first_name":"Mateusz","full_name":"Ujma, Mateusz"}],"conference":{"location":"Sydney, Australia","end_date":"2014-11-07","name":"ALENEX: Algorithm Engineering and Experiments","start_date":"2014-11-03"},"month":"11","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.2967"}],"day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"type":"conference","status":"public","date_updated":"2021-01-12T06:54:49Z","oa":1,"title":"Verification of markov decision processes using learning algorithms","editor":[{"full_name":"Cassez, Franck","first_name":"Franck","last_name":"Cassez"},{"last_name":"Raskin","first_name":"Jean-François","full_name":"Raskin, Jean-François"}],"intvolume":"      8837","language":[{"iso":"eng"}],"publication":" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)"},{"abstract":[{"lang":"eng","text":"Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"],"publication_status":"published","volume":365,"quality_controlled":"1","page":"40 - 54","department":[{"_id":"GaTk"}],"date_published":"2014-10-12T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"Academic Press","related_material":{"link":[{"url":"https://doi.org/10.1016/j.jtbi.2015.03.013","relation":"erratum"}]},"citation":{"ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” <i> Journal of Theoretical Biology</i>, vol. 365. Academic Press, pp. 40–54, 2014.","ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. <i> Journal of Theoretical Biology</i>. 2014;365:40-54. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">10.1016/j.jtbi.2014.09.041</a>","short":"K. Bodova, D. Paydarfar, D. Forger,  Journal of Theoretical Biology 365 (2014) 40–54.","chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” <i> Journal of Theoretical Biology</i>. Academic Press, 2014. <a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">https://doi.org/10.1016/j.jtbi.2014.09.041</a>.","mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” <i> Journal of Theoretical Biology</i>, vol. 365, Academic Press, 2014, pp. 40–54, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">10.1016/j.jtbi.2014.09.041</a>.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons.  Journal of Theoretical Biology. 365, 40–54.","apa":"Bodova, K., Paydarfar, D., &#38; Forger, D. (2014). Characterizing spiking in noisy type II neurons. <i> Journal of Theoretical Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">https://doi.org/10.1016/j.jtbi.2014.09.041</a>"},"publist_id":"5043","date_created":"2018-12-11T11:55:18Z","year":"2014","acknowledgement":"This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ","doi":"10.1016/j.jtbi.2014.09.041","_id":"2028","file_date_updated":"2020-07-14T12:45:25Z","file":[{"date_created":"2018-12-12T10:17:58Z","date_updated":"2020-07-14T12:45:25Z","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf","file_id":"5316","content_type":"application/pdf","access_level":"open_access","file_size":2679222,"relation":"main_file","creator":"system"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"12","month":"10","author":[{"orcid":"0000-0002-7214-0171","last_name":"Bodova","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","full_name":"Bodova, Katarina"},{"last_name":"Paydarfar","first_name":"David","full_name":"Paydarfar, David"},{"last_name":"Forger","first_name":"Daniel","full_name":"Forger, Daniel"}],"status":"public","type":"journal_article","has_accepted_license":"1","scopus_import":"1","intvolume":"       365","title":"Characterizing spiking in noisy type II neurons","article_processing_charge":"No","oa":1,"date_updated":"2022-08-25T14:00:47Z","pubrep_id":"444","publication":" Journal of Theoretical Biology","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication":"EPL","title":"Validity of spin-wave theory for the quantum Heisenberg model","oa":1,"date_updated":"2021-01-12T06:54:50Z","issue":"2","scopus_import":1,"intvolume":"       108","status":"public","type":"journal_article","author":[{"full_name":"Correggi, Michele","first_name":"Michele","last_name":"Correggi"},{"last_name":"Giuliani","full_name":"Giuliani, Alessandro","first_name":"Alessandro"},{"first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.4717"}],"day":"13","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"10","_id":"2029","doi":"10.1209/0295-5075/108/20003","publist_id":"5044","date_created":"2018-12-11T11:55:18Z","citation":{"ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory for the quantum Heisenberg model,” <i>EPL</i>, vol. 108, no. 2. IOP Publishing Ltd., 2014.","ama":"Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. <i>EPL</i>. 2014;108(2). doi:<a href=\"https://doi.org/10.1209/0295-5075/108/20003\">10.1209/0295-5075/108/20003</a>","short":"M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014).","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” <i>EPL</i>. IOP Publishing Ltd., 2014. <a href=\"https://doi.org/10.1209/0295-5075/108/20003\">https://doi.org/10.1209/0295-5075/108/20003</a>.","ista":"Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003.","mla":"Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” <i>EPL</i>, vol. 108, no. 2, 20003, IOP Publishing Ltd., 2014, doi:<a href=\"https://doi.org/10.1209/0295-5075/108/20003\">10.1209/0295-5075/108/20003</a>.","apa":"Correggi, M., Giuliani, A., &#38; Seiringer, R. (2014). Validity of spin-wave theory for the quantum Heisenberg model. <i>EPL</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1209/0295-5075/108/20003\">https://doi.org/10.1209/0295-5075/108/20003</a>"},"acknowledgement":"239694; ERC; European Research Council","year":"2014","article_number":"20003","department":[{"_id":"RoSe"}],"quality_controlled":"1","volume":108,"publisher":"IOP Publishing Ltd.","date_published":"2014-10-13T00:00:00Z","publication_status":"published","abstract":[{"text":"Spin-wave theory is a key ingredient in our comprehension of quantum spin systems, and is used successfully for understanding a wide range of magnetic phenomena, including magnon condensation and stability of patterns in dipolar systems. Nevertheless, several decades of research failed to establish the validity of spin-wave theory rigorously, even for the simplest models of quantum spins. A rigorous justification of the method for the three-dimensional quantum Heisenberg ferromagnet at low temperatures is presented here. We derive sharp bounds on its free energy by combining a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic estimates and operator inequalities.","lang":"eng"}]},{"oa":1,"pubrep_id":"421","date_updated":"2021-01-12T06:54:51Z","title":"Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse","has_accepted_license":"1","scopus_import":1,"intvolume":"         3","language":[{"iso":"eng"}],"publication":"eLife","author":[{"first_name":"Itaru","full_name":"Arai, Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"month":"12","day":"09","oa_version":"Submitted Version","file":[{"relation":"main_file","file_size":2239563,"content_type":"application/pdf","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:45:26Z","date_created":"2018-12-12T10:14:41Z","file_id":"5094","file_name":"IST-2016-421-v1+1_e04057.full.pdf","checksum":"c240f915450d4ebe8f95043a2a8c7b1a"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","year":"2014","publist_id":"5041","date_created":"2018-12-11T11:55:19Z","citation":{"apa":"Arai,  itaru, &#38; Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.04057\">https://doi.org/10.7554/eLife.04057</a>","mla":"Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” <i>ELife</i>, vol. 3, eLife Sciences Publications, 2014, doi:<a href=\"https://doi.org/10.7554/eLife.04057\">10.7554/eLife.04057</a>.","ista":"Arai  itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3.","chicago":"Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” <i>ELife</i>. eLife Sciences Publications, 2014. <a href=\"https://doi.org/10.7554/eLife.04057\">https://doi.org/10.7554/eLife.04057</a>.","ama":"Arai  itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. <i>eLife</i>. 2014;3. doi:<a href=\"https://doi.org/10.7554/eLife.04057\">10.7554/eLife.04057</a>","ieee":"itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse,” <i>eLife</i>, vol. 3. eLife Sciences Publications, 2014.","short":"itaru Arai, P.M. Jonas, ELife 3 (2014)."},"ec_funded":1,"file_date_updated":"2020-07-14T12:45:26Z","_id":"2031","doi":"10.7554/eLife.04057","publication_status":"published","ddc":["570"],"abstract":[{"lang":"eng","text":"A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release."}],"project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"publisher":"eLife Sciences Publications","date_published":"2014-12-09T00:00:00Z","department":[{"_id":"PeJo"}],"volume":3,"quality_controlled":"1"},{"publication":"Molecular and Cellular Oncology","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":"         1","has_accepted_license":"1","oa":1,"date_updated":"2021-01-12T06:54:51Z","issue":"4","title":"The optogenetic promise for oncology: Episode I","type":"journal_article","status":"public","month":"12","day":"31","oa_version":"Published Version","file":[{"access_level":"open_access","file_size":1765933,"content_type":"application/pdf","relation":"main_file","creator":"kschuh","date_created":"2019-05-16T13:39:11Z","date_updated":"2020-07-14T12:45:26Z","file_name":"2014_Taylor_Alvaro.pdf","file_id":"6464","checksum":"44e17ad40577ab46eb602e88a8b0b8fd"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro"},{"first_name":"Eva","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738"},{"last_name":"Schelch","full_name":"Schelch, Karin","first_name":"Karin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L"},{"first_name":"Michael","full_name":"Grusch, Michael","last_name":"Grusch"}],"doi":"10.4161/23723548.2014.964045","file_date_updated":"2020-07-14T12:45:26Z","_id":"2032","article_number":"e964045","year":"2014","citation":{"short":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014).","ieee":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and M. Grusch, “The optogenetic promise for oncology: Episode I,” <i>Molecular and Cellular Oncology</i>, vol. 1, no. 4. Taylor &#38; Francis, 2014.","ama":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. The optogenetic promise for oncology: Episode I. <i>Molecular and Cellular Oncology</i>. 2014;1(4). doi:<a href=\"https://doi.org/10.4161/23723548.2014.964045\">10.4161/23723548.2014.964045</a>","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode I.” <i>Molecular and Cellular Oncology</i>. Taylor &#38; Francis, 2014. <a href=\"https://doi.org/10.4161/23723548.2014.964045\">https://doi.org/10.4161/23723548.2014.964045</a>.","ista":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. 2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 1(4), e964045.","mla":"Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode I.” <i>Molecular and Cellular Oncology</i>, vol. 1, no. 4, e964045, Taylor &#38; Francis, 2014, doi:<a href=\"https://doi.org/10.4161/23723548.2014.964045\">10.4161/23723548.2014.964045</a>.","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L., &#38; Grusch, M. (2014). The optogenetic promise for oncology: Episode I. <i>Molecular and Cellular Oncology</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/23723548.2014.964045\">https://doi.org/10.4161/23723548.2014.964045</a>"},"date_created":"2018-12-11T11:55:19Z","publist_id":"5040","publisher":"Taylor & Francis","date_published":"2014-12-31T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","department":[{"_id":"HaJa"}],"volume":1,"quality_controlled":"1","ddc":["570"],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"abstract":[{"text":"As light-based control of fundamental signaling pathways is becoming a reality, the field of optogenetics is rapidly moving beyond neuroscience. We have recently developed receptor tyrosine kinases that are activated by light and control cell proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell behaviors central to cancer progression.","lang":"eng"}],"publication_status":"published"},{"date_updated":"2023-02-23T10:25:24Z","oa":1,"year":"2014","issue":"January","publist_id":"5038","date_created":"2018-12-11T11:55:20Z","title":"Mind the nuisance: Gaussian process classification using privileged noise","citation":{"ieee":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto, “Mind the nuisance: Gaussian process classification using privileged noise,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2014, vol. 1, no. January, pp. 837–845.","ama":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind the nuisance: Gaussian process classification using privileged noise. In: <i>Advances in Neural Information Processing Systems</i>. Vol 1. Neural Information Processing Systems; 2014:837-845.","short":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems, 2014, pp. 837–845.","mla":"Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” <i>Advances in Neural Information Processing Systems</i>, vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45.","ista":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014. Mind the nuisance: Gaussian process classification using privileged noise. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 1, 837–845.","chicago":"Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” In <i>Advances in Neural Information Processing Systems</i>, 1:837–45. Neural Information Processing Systems, 2014.","apa":"Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., &#38; Quadrianto, N. (2014). Mind the nuisance: Gaussian process classification using privileged noise. In <i>Advances in Neural Information Processing Systems</i> (Vol. 1, pp. 837–845). Montreal, Canada: Neural Information Processing Systems."},"intvolume":"         1","scopus_import":1,"language":[{"iso":"eng"}],"_id":"2033","publication":"Advances in Neural Information Processing Systems","author":[{"last_name":"Hernandez Lobato","first_name":"Daniel","full_name":"Hernandez Lobato, Daniel"},{"first_name":"Viktoriia","full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","last_name":"Sharmanska","orcid":"0000-0003-0192-9308"},{"first_name":"Kristian","full_name":"Kersting, Kristian","last_name":"Kersting"},{"first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"},{"first_name":"Novi","full_name":"Quadrianto, Novi","last_name":"Quadrianto"}],"publication_status":"published","conference":{"location":"Montreal, Canada","end_date":"2014-12-13","name":"NIPS: Neural Information Processing Systems","start_date":"2014-12-08"},"month":"12","oa_version":"Submitted Version","day":"08","main_file_link":[{"url":"https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise","open_access":"1"}],"abstract":[{"lang":"eng","text":"The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems","date_published":"2014-12-08T00:00:00Z","type":"conference","status":"public","page":"837-845","department":[{"_id":"ChLa"}],"volume":1,"quality_controlled":"1"},{"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato"},{"last_name":"Colegrave","first_name":"Nick","full_name":"Colegrave, Nick"},{"last_name":"Neve","full_name":"Neve, Paul","first_name":"Paul"}],"month":"09","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/","open_access":"1"}],"oa_version":"Submitted Version","day":"17","status":"public","type":"journal_article","issue":"1794","oa":1,"date_updated":"2023-02-23T14:06:44Z","title":"Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","intvolume":"       281","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","publication_status":"published","abstract":[{"text":" In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. ","lang":"eng"}],"date_published":"2014-09-17T00:00:00Z","publisher":"Royal Society, The","quality_controlled":"1","volume":281,"department":[{"_id":"CaGu"}],"year":"2014","acknowledgement":"The project was supported by Leverhulme Trust.","date_created":"2018-12-11T11:55:21Z","citation":{"apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2014.1679\">https://doi.org/10.1098/rspb.2014.1679</a>","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794. Royal Society, The, 2014.","ama":"Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2014;281(1794). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1679\">10.1098/rspb.2014.1679</a>","short":"M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","mla":"Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794, 20141679, Royal Society, The, 2014, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1679\">10.1098/rspb.2014.1679</a>.","ista":"Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2014. <a href=\"https://doi.org/10.1098/rspb.2014.1679\">https://doi.org/10.1098/rspb.2014.1679</a>."},"publist_id":"5019","article_number":"20141679","related_material":{"record":[{"status":"public","id":"9741","relation":"research_data"}]},"_id":"2036","doi":"10.1098/rspb.2014.1679"},{"doi":"10.1145/2629686","file_date_updated":"2020-07-14T12:45:26Z","_id":"2038","article_type":"original","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3356"},{"status":"public","relation":"earlier_version","id":"5385"}]},"article_number":"27","acknowledgement":"The research was supported in part by ERC Starting grant 278410 (QUALITY).","year":"2014","date_created":"2018-12-11T11:55:21Z","citation":{"chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. “Temporal Specifications with Accumulative Values.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2014. <a href=\"https://doi.org/10.1145/2629686\">https://doi.org/10.1145/2629686</a>.","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 15(4), 27.","mla":"Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 15, no. 4, 27, ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2629686\">10.1145/2629686</a>.","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications with accumulative values,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 15, no. 4. ACM, 2014.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with accumulative values. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2014;15(4). doi:<a href=\"https://doi.org/10.1145/2629686\">10.1145/2629686</a>","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 15 (2014).","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., &#38; Kupferman, O. (2014). Temporal specifications with accumulative values. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/2629686\">https://doi.org/10.1145/2629686</a>"},"publist_id":"5013","publisher":"ACM","date_published":"2014-09-16T00:00:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"quality_controlled":"1","volume":15,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"ddc":["000","004"],"abstract":[{"lang":"eng","text":"Recently, there has been an effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions. At the heart of quantitative objectives lies the accumulation of values along a computation. It is often the accumulated sum, as with energy objectives, or the accumulated average, as with mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point in time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire infinite computation. We study the border of decidability for such quantitative extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with both prefix-accumulation assertions, or extending LTL with both path-accumulation assertions, results in temporal logics whose model-checking problem is decidable. Moreover, the prefix-accumulation assertions may be generalized with &quot;controlled accumulation,&quot; allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that this branching-time logic is, in a sense, the maximal logic with one or both of the prefix-accumulation assertions that permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL, makes the problem undecidable."}],"publication_status":"published","publication":"ACM Transactions on Computational Logic (TOCL)","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":"        15","has_accepted_license":"1","oa":1,"date_updated":"2023-02-23T12:23:54Z","pubrep_id":"192","issue":"4","article_processing_charge":"No","title":"Temporal specifications with accumulative values","type":"journal_article","status":"public","month":"09","oa_version":"Submitted Version","day":"16","file":[{"file_id":"4851","checksum":"354c41d37500b56320afce94cf9a99c2","file_name":"IST-2014-192-v1+1_AccumulativeValues.pdf","date_created":"2018-12-12T10:10:59Z","date_updated":"2020-07-14T12:45:26Z","creator":"system","file_size":346184,"relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Udi","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}]},{"publication":"PLoS Computational Biology","language":[{"iso":"eng"}],"intvolume":"        10","scopus_import":1,"has_accepted_license":"1","title":"The time scale of evolutionary innovation","date_updated":"2023-02-23T14:06:36Z","oa":1,"pubrep_id":"440","issue":"9","status":"public","type":"journal_article","day":"11","oa_version":"Published Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","content_type":"application/pdf","access_level":"open_access","file_size":1399093,"relation":"main_file","checksum":"712d4c5787ddf97809cfc962507f0738","file_id":"4890","file_name":"IST-2016-440-v1+1_journal.pcbi.1003818.pdf","date_created":"2018-12-12T10:11:35Z","date_updated":"2020-07-14T12:45:26Z"}],"month":"09","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas"},{"last_name":"Adlam","first_name":"Ben","full_name":"Adlam, Ben"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"doi":"10.1371/journal.pcbi.1003818","file_date_updated":"2020-07-14T12:45:26Z","_id":"2039","ec_funded":1,"article_number":"7p","related_material":{"record":[{"status":"public","id":"9739","relation":"research_data"}]},"citation":{"ama":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. <i>PLoS Computational Biology</i>. 2014;10(9). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">10.1371/journal.pcbi.1003818</a>","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” <i>PLoS Computational Biology</i>, vol. 10, no. 9. Public Library of Science, 2014.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014).","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” <i>PLoS Computational Biology</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">https://doi.org/10.1371/journal.pcbi.1003818</a>.","mla":"Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” <i>PLoS Computational Biology</i>, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">10.1371/journal.pcbi.1003818</a>.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Nowak, M. (2014). The time scale of evolutionary innovation. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">https://doi.org/10.1371/journal.pcbi.1003818</a>"},"publist_id":"5012","date_created":"2018-12-11T11:55:22Z","year":"2014","department":[{"_id":"KrCh"}],"quality_controlled":"1","volume":10,"publisher":"Public Library of Science","date_published":"2014-09-11T00:00:00Z","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time."}],"ddc":["510"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published"},{"publication":"Science","doi":"10.1126/science.1254927","_id":"2040","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":"       345","article_number":"1254927","date_updated":"2021-01-12T06:54:55Z","oa":1,"issue":"6204","year":"2014","title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","date_created":"2018-12-11T11:55:22Z","citation":{"ieee":"A. Kicheva <i>et al.</i>, “Coordination of progenitor specification and growth in mouse and chick spinal cord,” <i>Science</i>, vol. 345, no. 6204. American Association for the Advancement of Science, 2014.","ama":"Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. <i>Science</i>. 2014;345(6204). doi:<a href=\"https://doi.org/10.1126/science.1254927\">10.1126/science.1254927</a>","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","mla":"Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” <i>Science</i>, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:<a href=\"https://doi.org/10.1126/science.1254927\">10.1126/science.1254927</a>.","ista":"Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927.","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1254927\">https://doi.org/10.1126/science.1254927</a>.","apa":"Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., &#38; Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1254927\">https://doi.org/10.1126/science.1254927</a>"},"publist_id":"5011","publisher":"American Association for the Advancement of Science","status":"public","date_published":"2014-09-26T00:00:00Z","type":"journal_article","department":[{"_id":"ToBo"}],"quality_controlled":"1","volume":345,"month":"09","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/"}],"day":"26","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. "}],"publication_status":"published","author":[{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva"},{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ribeiro, Ana","first_name":"Ana","last_name":"Ribeiro"},{"last_name":"Pérez Valle","full_name":"Pérez Valle, Helena","first_name":"Helena"},{"first_name":"Robin","full_name":"Lovell Badge, Robin","last_name":"Lovell Badge"},{"first_name":"Vasso","full_name":"Episkopou, Vasso","last_name":"Episkopou"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"}]},{"doi":"10.3389/fncir.2014.00107","_id":"2041","file_date_updated":"2020-07-14T12:45:26Z","article_number":"2p","year":"2014","citation":{"ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p.","mla":"Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” <i>Frontiers in Neural Circuits</i>, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fncir.2014.00107\">10.3389/fncir.2014.00107</a>.","chicago":"Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” <i>Frontiers in Neural Circuits</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fncir.2014.00107\">https://doi.org/10.3389/fncir.2014.00107</a>.","short":"P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014).","ieee":"P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” <i>Frontiers in Neural Circuits</i>, vol. 8. Frontiers Research Foundation, 2014.","ama":"Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. <i>Frontiers in Neural Circuits</i>. 2014;8. doi:<a href=\"https://doi.org/10.3389/fncir.2014.00107\">10.3389/fncir.2014.00107</a>","apa":"Jonas, P. M., &#38; Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. <i>Frontiers in Neural Circuits</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncir.2014.00107\">https://doi.org/10.3389/fncir.2014.00107</a>"},"publist_id":"5010","date_created":"2018-12-11T11:55:22Z","date_published":"2014-09-10T00:00:00Z","publisher":"Frontiers Research Foundation","quality_controlled":"1","volume":8,"department":[{"_id":"PeJo"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time.","lang":"eng"}],"publication_status":"published","publication":"Frontiers in Neural Circuits","language":[{"iso":"eng"}],"intvolume":"         8","scopus_import":1,"has_accepted_license":"1","pubrep_id":"424","oa":1,"date_updated":"2021-01-12T06:54:55Z","title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits","type":"journal_article","status":"public","month":"09","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:17:38Z","date_updated":"2020-07-14T12:45:26Z","file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf","file_id":"5294","checksum":"3ca57b164045523f876407e9f13a9fb8","relation":"main_file","content_type":"application/pdf","file_size":201110,"access_level":"open_access","creator":"system"}],"day":"10","oa_version":"Published Version","author":[{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"},{"first_name":"John","full_name":"Lisman, John","last_name":"Lisman"}]},{"author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","full_name":"Kupczok, Anne","first_name":"Anne"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"}],"month":"08","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":1489769,"file_id":"4878","file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf","checksum":"3f6d2776b90a842a28359cc957d3d04b","date_created":"2018-12-12T10:11:24Z","date_updated":"2020-07-14T12:45:26Z"}],"day":"08","oa_version":"Published Version","status":"public","type":"journal_article","issue":"1","oa":1,"date_updated":"2021-01-12T06:54:56Z","pubrep_id":"396","title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","intvolume":"        15","scopus_import":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"BMC Genomics","publication_status":"published","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"ddc":["570"],"abstract":[{"lang":"eng","text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here."}],"date_published":"2014-08-08T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","publisher":"BioMed Central","quality_controlled":"1","volume":15,"department":[{"_id":"JoBo"}],"year":"2014","date_created":"2018-12-11T11:55:23Z","citation":{"apa":"Kupczok, A., &#38; Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663.","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>. BioMed Central, 2014. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>, vol. 15, no. 1, 663, BioMed Central, 2014, doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>.","short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).","ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. 2014;15(1). doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” <i>BMC Genomics</i>, vol. 15, no. 1. BioMed Central, 2014."},"publist_id":"5009","article_number":"663","_id":"2042","file_date_updated":"2020-07-14T12:45:26Z","doi":"10.1186/1471-2164-15-663"}]