[{"publication":"Science Translational Medicine","page":"eaao0972","date_created":"2018-12-11T11:48:01Z","doi":"10.1126/scitranslmed.aao0972","publication_status":"published","date_published":"2017-07-19T00:00:00Z","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","scopus_import":1,"publist_id":"6993","quality_controlled":"1","citation":{"chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>.","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. 2017;9(399):eaao0972. doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” <i>Science Translational Medicine</i>, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017."},"volume":9,"intvolume":"         9","year":"2017","day":"19","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"issue":"399","date_updated":"2021-01-12T08:11:31Z","_id":"702","author":[{"full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"publication_identifier":{"issn":["19466234"]},"title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"American Association for the Advancement of Science","month":"07"},{"department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"eLife","date_created":"2018-12-11T11:48:01Z","has_accepted_license":"1","related_material":{"record":[{"id":"5564","relation":"popular_science","status":"public"},{"status":"public","relation":"dissertation_contains","id":"26"}]},"volume":6,"quality_controlled":"1","pubrep_id":"890","publist_id":"6990","file":[{"access_level":"open_access","file_id":"4975","checksum":"6b908b5db9f61f6820ebd7f8fa815571","creator":"system","date_created":"2018-12-12T10:12:54Z","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","date_updated":"2020-07-14T12:47:48Z","file_size":2092088,"content_type":"application/pdf","relation":"main_file"},{"file_size":3428681,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ca21530389b720243552678125fdba35","file_id":"4976","creator":"system","date_created":"2018-12-12T10:12:55Z","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","date_updated":"2020-07-14T12:47:48Z"}],"author":[{"last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","first_name":"Magdalena","full_name":"Steinrück, Magdalena"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"25","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"eLife Sciences Publications","date_published":"2017-07-25T00:00:00Z","oa_version":"Published Version","doi":"10.7554/eLife.25100","publication_status":"published","intvolume":"         6","citation":{"ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","apa":"Steinrück, M., &#38; Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>, vol. 6, e25100, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>."},"ddc":["576"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:48Z","_id":"704","article_number":"e25100","year":"2017","abstract":[{"text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.","lang":"eng"}],"date_updated":"2024-03-25T23:30:14Z","month":"07","oa":1,"publication_identifier":{"issn":["2050084X"]},"status":"public"},{"scopus_import":1,"publist_id":"6987","quality_controlled":"1","volume":22,"intvolume":"        22","citation":{"short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","ieee":"X. Geng <i>et al.</i>, “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” <i>Genes to Cells</i>, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. <i>Genes to Cells</i>. 2017;22(8):715-722. doi:<a href=\"https://doi.org/10.1111/gtc.12508\">10.1111/gtc.12508</a>","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722.","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. <i>Genes to Cells</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/gtc.12508\">https://doi.org/10.1111/gtc.12508</a>","mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” <i>Genes to Cells</i>, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:<a href=\"https://doi.org/10.1111/gtc.12508\">10.1111/gtc.12508</a>.","chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” <i>Genes to Cells</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/gtc.12508\">https://doi.org/10.1111/gtc.12508</a>."},"publication_status":"published","doi":"10.1111/gtc.12508","date_created":"2018-12-11T11:48:02Z","page":"715 - 722","publication":"Genes to Cells","oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2017-08-01T00:00:00Z","department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","publication_identifier":{"issn":["13569597"]},"month":"08","date_updated":"2021-01-12T08:11:37Z","issue":"8","abstract":[{"text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse.","lang":"eng"}],"day":"01","year":"2017","author":[{"first_name":"Xiaoqi","last_name":"Geng","id":"3395256A-F248-11E8-B48F-1D18A9856A87","full_name":"Geng, Xiaoqi"},{"full_name":"Maruo, Tomohiko","first_name":"Tomohiko","last_name":"Maruo"},{"last_name":"Mandai","first_name":"Kenji","full_name":"Mandai, Kenji"},{"last_name":"Supriyanto","first_name":"Irwan","full_name":"Supriyanto, Irwan"},{"full_name":"Miyata, Muneaki","first_name":"Muneaki","last_name":"Miyata"},{"full_name":"Sakakibara, Shotaro","first_name":"Shotaro","last_name":"Sakakibara"},{"full_name":"Mizoguchi, Akira","last_name":"Mizoguchi","first_name":"Akira"},{"last_name":"Takai","first_name":"Yoshimi","full_name":"Takai, Yoshimi"},{"full_name":"Mori, Masahiro","last_name":"Mori","first_name":"Masahiro"}],"_id":"706"},{"page":"690 - 693","date_created":"2018-12-11T11:48:02Z","publication":"Bulletin of the London Mathematical Society","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"6982","volume":49,"quality_controlled":"1","day":"01","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"publisher":"Wiley-Blackwell","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A tight estimate for the waist of the ball ","publication_status":"published","doi":"10.1112/blms.12062","oa_version":"Preprint","date_published":"2017-08-01T00:00:00Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.06279"}],"citation":{"mla":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” <i>Bulletin of the London Mathematical Society</i>, vol. 49, no. 4, Wiley-Blackwell, 2017, pp. 690–93, doi:<a href=\"https://doi.org/10.1112/blms.12062\">10.1112/blms.12062</a>.","apa":"Akopyan, A., &#38; Karasev, R. (2017). A tight estimate for the waist of the ball . <i>Bulletin of the London Mathematical Society</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1112/blms.12062\">https://doi.org/10.1112/blms.12062</a>","ista":"Akopyan A, Karasev R. 2017. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 49(4), 690–693.","chicago":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” <i>Bulletin of the London Mathematical Society</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1112/blms.12062\">https://doi.org/10.1112/blms.12062</a>.","short":"A. Akopyan, R. Karasev, Bulletin of the London Mathematical Society 49 (2017) 690–693.","ieee":"A. Akopyan and R. Karasev, “A tight estimate for the waist of the ball ,” <i>Bulletin of the London Mathematical Society</i>, vol. 49, no. 4. Wiley-Blackwell, pp. 690–693, 2017.","ama":"Akopyan A, Karasev R. A tight estimate for the waist of the ball . <i>Bulletin of the London Mathematical Society</i>. 2017;49(4):690-693. doi:<a href=\"https://doi.org/10.1112/blms.12062\">10.1112/blms.12062</a>"},"intvolume":"        49","date_updated":"2021-01-12T08:11:41Z","issue":"4","abstract":[{"text":"We answer a question of M. Gromov on the waist of the unit ball.","lang":"eng"}],"year":"2017","_id":"707","status":"public","publication_identifier":{"issn":["00246093"]},"oa":1,"month":"08","ec_funded":1},{"file":[{"date_created":"2018-12-12T10:15:35Z","file_name":"IST-2017-889-v1+1_journal.pbio.2001993.pdf","date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","creator":"system","checksum":"0c974f430682dc832ea7b27ab5a93124","file_id":"5156","file_size":18155365,"relation":"main_file","content_type":"application/pdf"}],"author":[{"id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","last_name":"Nagy","orcid":"0000-0002-4002-4686","first_name":"Balint","full_name":"Nagy, Balint"},{"first_name":"Anahit","last_name":"Hovhannisyan","full_name":"Hovhannisyan, Anahit"},{"full_name":"Barzan, Ruxandra","last_name":"Barzan","first_name":"Ruxandra"},{"last_name":"Chen","first_name":"Ting","full_name":"Chen, Ting"},{"last_name":"Kukley","first_name":"Maria","full_name":"Kukley, Maria"}],"day":"22","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"SaSi"}],"type":"journal_article","date_created":"2018-12-11T11:48:03Z","publication":"PLoS Biology","has_accepted_license":"1","volume":15,"quality_controlled":"1","publist_id":"6983","pubrep_id":"889","_id":"708","article_number":"e2001993","year":"2017","date_updated":"2021-01-12T08:11:45Z","issue":"8","abstract":[{"lang":"eng","text":"In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells."}],"month":"08","oa":1,"publication_identifier":{"issn":["15449173"]},"status":"public","date_published":"2017-08-22T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1371/journal.pbio.2001993","citation":{"short":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, M. Kukley, PLoS Biology 15 (2017).","ama":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. <i>PLoS Biology</i>. 2017;15(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001993\">10.1371/journal.pbio.2001993</a>","ieee":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, and M. Kukley, “Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum,” <i>PLoS Biology</i>, vol. 15, no. 8. Public Library of Science, 2017.","chicago":"Nagy, Balint, Anahit Hovhannisyan, Ruxandra Barzan, Ting Chen, and Maria Kukley. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” <i>PLoS Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001993\">https://doi.org/10.1371/journal.pbio.2001993</a>.","mla":"Nagy, Balint, et al. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” <i>PLoS Biology</i>, vol. 15, no. 8, e2001993, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001993\">10.1371/journal.pbio.2001993</a>.","apa":"Nagy, B., Hovhannisyan, A., Barzan, R., Chen, T., &#38; Kukley, M. (2017). Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001993\">https://doi.org/10.1371/journal.pbio.2001993</a>","ista":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. 2017. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 15(8), e2001993."},"intvolume":"        15","ddc":["576","610"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:49Z"},{"date_updated":"2021-01-12T08:11:47Z","issue":"8","abstract":[{"lang":"eng","text":"Adipose tissues play key roles in energy homeostasis. Brown adipocytes and beige adipocytes in white adipose tissue (WAT) share the similar characters of thermogenesis, both of them could be potential targets for obesity management. Several thermo-sensitive transient receptor potential channels (thermoTRPs) are shown to be involved in adipocyte biology. However, the expression pattern of thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue (iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed in both iBAT and sWAT, and without significant difference in the mRNA expression level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA expression levels in both iBAT and sWAT were significantly decreased in high fat diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2 mRNA expression level was significantly decreased only in sWAT from HFD-induced obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression levels in iBAT and sWAT were significantly increased in HFD-induced obese mice and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues from HFD-induced obese mice and db/db mice, suggesting a potential involvement in anti-obesity regulations."}],"day":"01","year":"2017","author":[{"full_name":"Sun, Wuping","first_name":"Wuping","last_name":"Sun"},{"full_name":"Li, Chen","last_name":"Li","first_name":"Chen"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"full_name":"Jiang, Changyu","first_name":"Changyu","last_name":"Jiang"},{"id":"34009CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Zhai","first_name":"Ming-Zhu","full_name":"Zhai, Ming-Zhu"},{"last_name":"Zhou","first_name":"Qian","full_name":"Zhou, Qian"},{"last_name":"Xiao","first_name":"Lizu","full_name":"Xiao, Lizu"},{"full_name":"Deng, Qiwen","last_name":"Deng","first_name":"Qiwen"}],"_id":"709","publisher":"Wiley-Blackwell","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Gene expression changes of thermo sensitive transient receptor potential channels in obese mice","publication_identifier":{"issn":["10656995"]},"month":"08","publication_status":"published","doi":"10.1002/cbin.10783","page":"908 - 913","date_created":"2018-12-11T11:48:04Z","publication":"Cell Biology International","type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"date_published":"2017-08-01T00:00:00Z","department":[{"_id":"RySh"}],"scopus_import":1,"publist_id":"6981","volume":41,"quality_controlled":"1","intvolume":"        41","citation":{"short":"W. Sun, C. Li, Y. Zhang, C. Jiang, M.-Z. Zhai, Q. Zhou, L. Xiao, Q. Deng, Cell Biology International 41 (2017) 908–913.","ieee":"W. Sun <i>et al.</i>, “Gene expression changes of thermo sensitive transient receptor potential channels in obese mice,” <i>Cell Biology International</i>, vol. 41, no. 8. Wiley-Blackwell, pp. 908–913, 2017.","ama":"Sun W, Li C, Zhang Y, et al. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. <i>Cell Biology International</i>. 2017;41(8):908-913. doi:<a href=\"https://doi.org/10.1002/cbin.10783\">10.1002/cbin.10783</a>","apa":"Sun, W., Li, C., Zhang, Y., Jiang, C., Zhai, M.-Z., Zhou, Q., … Deng, Q. (2017). Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. <i>Cell Biology International</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cbin.10783\">https://doi.org/10.1002/cbin.10783</a>","mla":"Sun, Wuping, et al. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” <i>Cell Biology International</i>, vol. 41, no. 8, Wiley-Blackwell, 2017, pp. 908–13, doi:<a href=\"https://doi.org/10.1002/cbin.10783\">10.1002/cbin.10783</a>.","ista":"Sun W, Li C, Zhang Y, Jiang C, Zhai M-Z, Zhou Q, Xiao L, Deng Q. 2017. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 41(8), 908–913.","chicago":"Sun, Wuping, Chen Li, Yonghong Zhang, Changyu Jiang, Ming-Zhu Zhai, Qian Zhou, Lizu Xiao, and Qiwen Deng. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” <i>Cell Biology International</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1002/cbin.10783\">https://doi.org/10.1002/cbin.10783</a>."}},{"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"author":[{"first_name":"Maciej","last_name":"Obremski","full_name":"Obremski, Maciej"},{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej"}],"file":[{"date_created":"2018-12-12T10:13:10Z","file_name":"IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf","date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","file_id":"4991","checksum":"89225c7dcec2c93838458c9102858985","creator":"system","file_size":604813,"relation":"main_file","content_type":"application/pdf"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Renyi entropy estimation revisited","alternative_title":["LIPIcs"],"has_accepted_license":"1","date_created":"2018-12-11T11:48:04Z","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"publist_id":"6979","pubrep_id":"888","volume":81,"quality_controlled":"1","date_updated":"2021-01-12T08:11:50Z","abstract":[{"text":"We revisit the problem of estimating entropy of discrete distributions from independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA 2015), improving their upper and lower bounds on the necessary sample size n. For estimating Renyi entropy of order alpha, up to constant accuracy and error probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha} for integer alpha&gt;1, as the worst case over distributions with Renyi entropy equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha&gt;1, with the constant being an inverse polynomial of the accuracy, as the worst case over all distributions on K elements. Our upper bounds essentially replace the alphabet size by a factor exponential in the entropy, which offers improvements especially in low or medium entropy regimes (interesting for example in anomaly detection). As for the lower bounds, our proof explicitly shows how the complexity depends on both alphabet and accuracy, partially solving the open problem posted in previous works. The argument for upper bounds derives a clean identity for the variance of falling-power sum of a multinomial distribution. Our approach for lower bounds utilizes convex optimization to find a distribution with possibly worse estimation performance, and may be of independent interest as a tool to work with Le Cam’s two point method. ","lang":"eng"}],"year":"2017","article_number":"20","_id":"710","status":"public","publication_identifier":{"issn":["18688969"]},"oa":1,"month":"08","ec_funded":1,"publication_status":"published","conference":{"end_date":"2017-08-18","location":"Berkeley, USA","start_date":"2017-08-18","name":"20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX"},"doi":"10.4230/LIPIcs.APPROX-RANDOM.2017.20","oa_version":"Published Version","date_published":"2017-08-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:49Z","scopus_import":1,"ddc":["005","600"],"citation":{"chicago":"Obremski, Maciej, and Maciej Skórski. “Renyi Entropy Estimation Revisited,” Vol. 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20\">https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20</a>.","mla":"Obremski, Maciej, and Maciej Skórski. <i>Renyi Entropy Estimation Revisited</i>. Vol. 81, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20\">10.4230/LIPIcs.APPROX-RANDOM.2017.20</a>.","apa":"Obremski, M., &#38; Skórski, M. (2017). Renyi entropy estimation revisited (Vol. 81). Presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20\">https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20</a>","ista":"Obremski M, Skórski M. 2017. Renyi entropy estimation revisited. 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, LIPIcs, vol. 81, 20.","ama":"Obremski M, Skórski M. Renyi entropy estimation revisited. In: Vol 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20\">10.4230/LIPIcs.APPROX-RANDOM.2017.20</a>","ieee":"M. Obremski and M. Skórski, “Renyi entropy estimation revisited,” presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA, 2017, vol. 81.","short":"M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"intvolume":"        81"},{"oa_version":"Published Version","date_published":"2017-08-01T00:00:00Z","publication_status":"published","conference":{"name":"28th International Conference on Concurrency Theory, CONCUR","start_date":"2017-09-05","location":"Berlin, Germany","end_date":"2017-09-08"},"doi":"10.4230/LIPIcs.CONCUR.2017.5","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.5\">https://doi.org/10.4230/LIPIcs.CONCUR.2017.5</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Bidirectional Nested Weighted Automata</i>. Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.5\">10.4230/LIPIcs.CONCUR.2017.5</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2017). Bidirectional nested weighted automata (Vol. 85). Presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.5\">https://doi.org/10.4230/LIPIcs.CONCUR.2017.5</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ama":"Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2017.5\">10.4230/LIPIcs.CONCUR.2017.5</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted automata,” presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany, 2017, vol. 85."},"intvolume":"        85","scopus_import":1,"file_date_updated":"2020-07-14T12:47:49Z","ddc":["004","005"],"article_number":"5","_id":"711","date_updated":"2021-01-12T08:11:53Z","abstract":[{"text":"Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts.","lang":"eng"}],"year":"2017","month":"08","status":"public","publication_identifier":{"issn":["18688969"]},"oa":1,"type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"has_accepted_license":"1","date_created":"2018-12-11T11:48:04Z","quality_controlled":"1","volume":85,"publist_id":"6976","pubrep_id":"886","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan"}],"file":[{"date_created":"2018-12-12T10:08:02Z","date_updated":"2020-07-14T12:47:49Z","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf","access_level":"open_access","checksum":"d2bda4783821a6358333fe27f11f4737","file_id":"4661","creator":"system","file_size":570294,"content_type":"application/pdf","relation":"main_file"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Bidirectional nested weighted automata"},{"scopus_import":1,"publist_id":"6975","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00730"}],"citation":{"chicago":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” <i>Nonlinear Analysis: Theory, Methods and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.na.2017.03.001\">https://doi.org/10.1016/j.na.2017.03.001</a>.","apa":"Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. <i>Nonlinear Analysis: Theory, Methods and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.na.2017.03.001\">https://doi.org/10.1016/j.na.2017.03.001</a>","ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.","mla":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” <i>Nonlinear Analysis: Theory, Methods and Applications</i>, vol. 159, Elsevier, 2017, pp. 181–207, doi:<a href=\"https://doi.org/10.1016/j.na.2017.03.001\">10.1016/j.na.2017.03.001</a>.","ieee":"J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations,” <i>Nonlinear Analysis: Theory, Methods and Applications</i>, vol. 159. Elsevier, pp. 181–207, 2017.","ama":"Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. <i>Nonlinear Analysis: Theory, Methods and Applications</i>. 2017;159:181-207. doi:<a href=\"https://doi.org/10.1016/j.na.2017.03.001\">10.1016/j.na.2017.03.001</a>","short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207."},"quality_controlled":"1","intvolume":"       159","volume":159,"page":"181 - 207","date_created":"2018-12-11T11:48:05Z","publication":"Nonlinear Analysis: Theory, Methods and Applications","publication_status":"published","doi":"10.1016/j.na.2017.03.001","language":[{"iso":"eng"}],"department":[{"_id":"JuFi"}],"date_published":"2017-08-01T00:00:00Z","oa_version":"Submitted Version","type":"journal_article","title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations","oa":1,"publication_identifier":{"issn":["0362546X"]},"status":"public","publisher":"Elsevier","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"08","day":"01","year":"2017","date_updated":"2021-01-12T08:11:55Z","abstract":[{"lang":"eng","text":"We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions."}],"_id":"712","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer"}]},{"publisher":"eLife Sciences Publications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"}],"author":[{"full_name":"Andergassen, Daniel","first_name":"Daniel","last_name":"Andergassen"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph"},{"last_name":"Wenzel","first_name":"Dyniel","full_name":"Wenzel, Dyniel"},{"full_name":"Sigl, Verena","last_name":"Sigl","first_name":"Verena"},{"full_name":"Bammer, Philipp","first_name":"Philipp","last_name":"Bammer"},{"full_name":"Muckenhuber, Markus","first_name":"Markus","last_name":"Muckenhuber"},{"full_name":"Mayer, Daniela","first_name":"Daniela","last_name":"Mayer"},{"last_name":"Kulinski","first_name":"Tomasz","full_name":"Kulinski, Tomasz"},{"first_name":"Hans","last_name":"Theussl","full_name":"Theussl, Hans"},{"first_name":"Josef","last_name":"Penninger","full_name":"Penninger, Josef"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"},{"full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Hudson, Quanah","first_name":"Quanah","last_name":"Hudson"}],"file":[{"file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","date_updated":"2020-07-14T12:47:50Z","date_created":"2018-12-12T10:13:36Z","creator":"system","file_id":"5020","checksum":"1ace3462e64a971b9ead896091829549","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":6399510},{"access_level":"open_access","file_id":"5021","checksum":"6241dc31eeb87b03facadec3a53a6827","creator":"system","date_created":"2018-12-12T10:13:36Z","date_updated":"2020-07-14T12:47:50Z","file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","file_size":4264398,"content_type":"application/pdf","relation":"main_file"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"14","volume":6,"quality_controlled":"1","publist_id":"6971","pubrep_id":"885","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"},{"_id":"SiHi"}],"has_accepted_license":"1","date_created":"2018-12-11T11:48:05Z","publication":"eLife","month":"08","status":"public","oa":1,"publication_identifier":{"issn":["2050084X"]},"article_number":"e25125","_id":"713","date_updated":"2021-01-12T08:11:57Z","abstract":[{"lang":"eng","text":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta."}],"year":"2017","intvolume":"         6","citation":{"short":"D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017).","ieee":"D. Andergassen <i>et al.</i>, “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","ama":"Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25125\">10.7554/eLife.25125</a>","chicago":"Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25125\">https://doi.org/10.7554/eLife.25125</a>.","apa":"Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25125\">https://doi.org/10.7554/eLife.25125</a>","ista":"Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125.","mla":"Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” <i>ELife</i>, vol. 6, e25125, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25125\">10.7554/eLife.25125</a>."},"file_date_updated":"2020-07-14T12:47:50Z","scopus_import":1,"ddc":["576"],"oa_version":"Published Version","date_published":"2017-08-14T00:00:00Z","publication_status":"published","doi":"10.7554/eLife.25125"},{"abstract":[{"text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients.","lang":"eng"}],"date_updated":"2021-01-12T08:12:00Z","year":"2017","_id":"714","status":"public","publication_identifier":{"issn":["03768716"]},"oa":1,"month":"09","doi":"10.1016/j.drugalcdep.2017.04.015","publication_status":"published","oa_version":"Submitted Version","date_published":"2017-09-01T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705","open_access":"1"}],"scopus_import":1,"intvolume":"       178","citation":{"ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. <i>Drug and Alcohol Dependence</i>. 2017;178:7-14. doi:<a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">10.1016/j.drugalcdep.2017.04.015</a>","ieee":"G. Brailoiu <i>et al.</i>, “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” <i>Drug and Alcohol Dependence</i>, vol. 178. Elsevier, pp. 7–14, 2017.","short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” <i>Drug and Alcohol Dependence</i>, vol. 178, Elsevier, 2017, pp. 7–14, doi:<a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">10.1016/j.drugalcdep.2017.04.015</a>.","ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14.","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. <i>Drug and Alcohol Dependence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">https://doi.org/10.1016/j.drugalcdep.2017.04.015</a>","chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” <i>Drug and Alcohol Dependence</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">https://doi.org/10.1016/j.drugalcdep.2017.04.015</a>."},"pmid":1,"acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","day":"01","author":[{"first_name":"Gabriela","last_name":"Brailoiu","full_name":"Brailoiu, Gabriela"},{"last_name":"Deliu","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena"},{"full_name":"Barr, Jeffrey","last_name":"Barr","first_name":"Jeffrey"},{"full_name":"Console Bram, Linda","first_name":"Linda","last_name":"Console Bram"},{"last_name":"Ciuciu","first_name":"Alexandra","full_name":"Ciuciu, Alexandra"},{"full_name":"Abood, Mary","first_name":"Mary","last_name":"Abood"},{"last_name":"Unterwald","first_name":"Ellen","full_name":"Unterwald, Ellen"},{"first_name":"Eugen","last_name":"Brǎiloiu","full_name":"Brǎiloiu, Eugen"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","publication":"Drug and Alcohol Dependence","date_created":"2018-12-11T11:48:05Z","page":"7 - 14","type":"journal_article","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","publist_id":"6967","volume":178,"quality_controlled":"1","external_id":{"pmid":["28623807"]}},{"_id":"715","author":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"article_number":"aao4218","year":"2017","day":"30","abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"issue":"405","date_updated":"2021-01-12T08:12:04Z","month":"08","publication_identifier":{"issn":["19466234"]},"title":"More excitation for Rett syndrome","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","status":"public","department":[{"_id":"GaNo"}],"date_published":"2017-08-30T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publication":"Science Translational Medicine","date_created":"2018-12-11T11:48:06Z","doi":"10.1126/scitranslmed.aao4218","publication_status":"published","intvolume":"         9","citation":{"ama":"Novarino G. More excitation for Rett syndrome. <i>Science Translational Medicine</i>. 2017;9(405). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">10.1126/scitranslmed.aao4218</a>","ieee":"G. Novarino, “More excitation for Rett syndrome,” <i>Science Translational Medicine</i>, vol. 9, no. 405. American Association for the Advancement of Science, 2017.","short":"G. Novarino, Science Translational Medicine 9 (2017).","apa":"Novarino, G. (2017). More excitation for Rett syndrome. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">https://doi.org/10.1126/scitranslmed.aao4218</a>","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218.","mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” <i>Science Translational Medicine</i>, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">10.1126/scitranslmed.aao4218</a>.","chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">https://doi.org/10.1126/scitranslmed.aao4218</a>."},"quality_controlled":"1","volume":9,"scopus_import":1,"publist_id":"6968"},{"doi":"10.1145/3121408","publication_status":"published","date_published":"2017-09-01T00:00:00Z","oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1201.2829","open_access":"1"}],"citation":{"apa":"Chatterjee, K., &#38; Velner, Y. (2017). The complexity of mean-payoff pushdown games. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3121408\">https://doi.org/10.1145/3121408</a>","mla":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” <i>Journal of the ACM</i>, vol. 64, no. 5, ACM, 2017, p. 34, doi:<a href=\"https://doi.org/10.1145/3121408\">10.1145/3121408</a>.","ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” <i>Journal of the ACM</i>. ACM, 2017. <a href=\"https://doi.org/10.1145/3121408\">https://doi.org/10.1145/3121408</a>.","ieee":"K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” <i>Journal of the ACM</i>, vol. 64, no. 5. ACM, p. 34, 2017.","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. <i>Journal of the ACM</i>. 2017;64(5):34. doi:<a href=\"https://doi.org/10.1145/3121408\">10.1145/3121408</a>","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34."},"intvolume":"        64","year":"2017","issue":"5","arxiv":1,"abstract":[{"text":"Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.","lang":"eng"}],"date_updated":"2021-01-12T08:12:08Z","_id":"716","oa":1,"publication_identifier":{"issn":["00045411"]},"status":"public","ec_funded":1,"month":"09","publication":"Journal of the ACM","page":"34","date_created":"2018-12-11T11:48:06Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","publist_id":"6964","quality_controlled":"1","volume":64,"external_id":{"arxiv":["1201.2829"]},"day":"01","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"title":"The complexity of mean-payoff pushdown games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM"},{"date_created":"2019-12-09T23:03:03Z","has_accepted_license":"1","doi":"10.15479/AT:ISTA:7163","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2017-12-01T00:00:00Z","oa_version":"Published Version","type":"research_data","ddc":["576"],"file_date_updated":"2020-07-14T12:47:50Z","article_processing_charge":"No","related_material":{"record":[{"id":"614","relation":"research_paper","status":"public"}]},"citation":{"ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>","ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","short":"C. Fraisse, (2017).","chicago":"Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>.","ista":"Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","mla":"Fraisse, Christelle. <i>Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>"},"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","date_updated":"2024-02-21T13:47:47Z","abstract":[{"lang":"eng","text":"The de novo genome assemblies generated for this study, and the associated metadata."}],"file":[{"file_size":841375478,"content_type":"application/zip","relation":"main_file","date_created":"2019-12-10T08:46:46Z","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","file_id":"7164","creator":"cfraisse","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3"}],"_id":"7163","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"}],"title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"first_name":"Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"month":"12"},{"type":"journal_article","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publication":"Journal of Computer and System Sciences","page":"236 - 259","date_created":"2018-12-11T11:48:07Z","volume":88,"quality_controlled":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2329"}]},"publist_id":"6963","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Academic Press","title":"Hyperplane separation technique for multidimensional mean-payoff games","oa_version":"Preprint","date_published":"2017-09-01T00:00:00Z","doi":"10.1016/j.jcss.2017.04.005","publication_status":"published","citation":{"apa":"Chatterjee, K., &#38; Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. <i>Journal of Computer and System Sciences</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">https://doi.org/10.1016/j.jcss.2017.04.005</a>","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” <i>Journal of Computer and System Sciences</i>, vol. 88, Academic Press, 2017, pp. 236–59, doi:<a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">10.1016/j.jcss.2017.04.005</a>.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” <i>Journal of Computer and System Sciences</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">https://doi.org/10.1016/j.jcss.2017.04.005</a>.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. <i>Journal of Computer and System Sciences</i>. 2017;88:236-259. doi:<a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">10.1016/j.jcss.2017.04.005</a>","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” <i>Journal of Computer and System Sciences</i>, vol. 88. Academic Press, pp. 236–259, 2017.","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259."},"intvolume":"        88","main_file_link":[{"url":"https://arxiv.org/abs/1210.3141","open_access":"1"}],"scopus_import":1,"_id":"717","abstract":[{"text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard.","lang":"eng"}],"date_updated":"2023-02-23T10:38:15Z","year":"2017","month":"09","ec_funded":1,"status":"public","oa":1},{"publist_id":"6962","volume":49,"quality_controlled":"1","external_id":{"arxiv":["1607.05915"]},"related_material":{"record":[{"id":"6287","relation":"dissertation_contains","status":"public"}]},"publication":"Advances in Applied Probability","date_created":"2018-12-11T11:48:07Z","page":"745 - 767","type":"journal_article","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cambridge University Press","title":"Expected sizes of poisson Delaunay mosaics and their discrete Morse functions","day":"01","author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-0659-3201","first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","full_name":"Nikitenko, Anton"},{"full_name":"Reitzner, Matthias","last_name":"Reitzner","first_name":"Matthias"}],"project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1607.05915","open_access":"1"}],"intvolume":"        49","citation":{"short":"H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767.","ama":"Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. <i>Advances in Applied Probability</i>. 2017;49(3):745-767. doi:<a href=\"https://doi.org/10.1017/apr.2017.20\">10.1017/apr.2017.20</a>","ieee":"H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” <i>Advances in Applied Probability</i>, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” <i>Advances in Applied Probability</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/apr.2017.20\">https://doi.org/10.1017/apr.2017.20</a>.","apa":"Edelsbrunner, H., Nikitenko, A., &#38; Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. <i>Advances in Applied Probability</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/apr.2017.20\">https://doi.org/10.1017/apr.2017.20</a>","ista":"Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767.","mla":"Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” <i>Advances in Applied Probability</i>, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:<a href=\"https://doi.org/10.1017/apr.2017.20\">10.1017/apr.2017.20</a>."},"doi":"10.1017/apr.2017.20","publication_status":"published","oa_version":"Preprint","date_published":"2017-09-01T00:00:00Z","status":"public","oa":1,"publication_identifier":{"issn":["00018678"]},"month":"09","ec_funded":1,"arxiv":1,"abstract":[{"lang":"eng","text":"Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4."}],"issue":"3","date_updated":"2023-09-07T12:07:12Z","year":"2017","_id":"718"},{"month":"09","status":"public","publisher":"Springer","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Special issue: Synthesis and SYNT 2014","publication_identifier":{"issn":["00015903"]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ehlers","first_name":"Rüdiger","full_name":"Ehlers, Rüdiger"}],"_id":"719","date_updated":"2021-01-12T08:12:18Z","issue":"6","abstract":[{"text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains.","lang":"eng"}],"day":"01","year":"2017","volume":54,"citation":{"chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-017-0299-0\">https://doi.org/10.1007/s00236-017-0299-0</a>.","apa":"Chatterjee, K., &#38; Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-017-0299-0\">https://doi.org/10.1007/s00236-017-0299-0</a>","mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” <i>Acta Informatica</i>, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:<a href=\"https://doi.org/10.1007/s00236-017-0299-0\">10.1007/s00236-017-0299-0</a>.","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. <i>Acta Informatica</i>. 2017;54(6):543-544. doi:<a href=\"https://doi.org/10.1007/s00236-017-0299-0\">10.1007/s00236-017-0299-0</a>","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” <i>Acta Informatica</i>, vol. 54, no. 6. Springer, pp. 543–544, 2017."},"quality_controlled":"1","intvolume":"        54","publist_id":"6961","scopus_import":1,"type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"date_published":"2017-09-01T00:00:00Z","publication_status":"published","doi":"10.1007/s00236-017-0299-0","date_created":"2018-12-11T11:48:07Z","page":"543 - 544","publication":"Acta Informatica"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","author":[{"full_name":"Humplik, Jan","first_name":"Jan","last_name":"Humplik","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"project":[{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"},{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"file":[{"file_id":"5352","checksum":"81107096c19771c36ddbe6f0282a3acb","creator":"system","access_level":"open_access","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","date_updated":"2020-07-14T12:47:53Z","date_created":"2018-12-12T10:18:30Z","relation":"main_file","content_type":"application/pdf","file_size":14167050}],"day":"19","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","volume":13,"article_processing_charge":"Yes","pubrep_id":"884","publist_id":"6960","type":"journal_article","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:48:08Z","month":"09","status":"public","oa":1,"publication_identifier":{"issn":["1553734X"]},"article_number":"e1005763","_id":"720","abstract":[{"text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.","lang":"eng"}],"issue":"9","date_updated":"2021-01-12T08:12:21Z","year":"2017","citation":{"chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>.","mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>.","apa":"Humplik, J., &#38; Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. 2017;13(9). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” <i>PLoS Computational Biology</i>, vol. 13, no. 9. Public Library of Science, 2017."},"intvolume":"        13","file_date_updated":"2020-07-14T12:47:53Z","scopus_import":1,"ddc":["530","571"],"oa_version":"Published Version","date_published":"2017-09-19T00:00:00Z","doi":"10.1371/journal.pcbi.1005763","publication_status":"published"},{"publist_id":"6959","volume":70,"quality_controlled":"1","publication":"Communications on Pure and Applied Mathematics","date_created":"2018-12-11T11:48:08Z","page":"1672 - 1705","type":"journal_article","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","day":"01","author":[{"full_name":"Ajanki, Oskari H","last_name":"Ajanki","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H"},{"full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","orcid":"0000-0002-4821-3297","first_name":"Torben H"},{"full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603"}],"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"main_file_link":[{"url":"https://arxiv.org/abs/1512.03703","open_access":"1"}],"scopus_import":1,"intvolume":"        70","citation":{"short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. <i>Communications on Pure and Applied Mathematics</i>. 2017;70(9):1672-1705. doi:<a href=\"https://doi.org/10.1002/cpa.21639\">10.1002/cpa.21639</a>","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” <i>Communications on Pure and Applied Mathematics</i>, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","apa":"Ajanki, O. H., Krüger, T. H., &#38; Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cpa.21639\">https://doi.org/10.1002/cpa.21639</a>","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” <i>Communications on Pure and Applied Mathematics</i>, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:<a href=\"https://doi.org/10.1002/cpa.21639\">10.1002/cpa.21639</a>.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1002/cpa.21639\">https://doi.org/10.1002/cpa.21639</a>."},"doi":"10.1002/cpa.21639","publication_status":"published","oa_version":"Submitted Version","date_published":"2017-09-01T00:00:00Z","status":"public","publication_identifier":{"issn":["00103640"]},"oa":1,"month":"09","ec_funded":1,"abstract":[{"lang":"eng","text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur."}],"issue":"9","date_updated":"2021-01-12T08:12:24Z","year":"2017","_id":"721"},{"day":"11","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"pmid":1,"file":[{"date_created":"2019-04-17T07:46:40Z","date_updated":"2020-07-14T12:47:54Z","file_name":"2017_CurrentBiology_Morris.pdf","access_level":"open_access","checksum":"e45588b21097b408da6276a3e5eedb2e","creator":"dernst","file_id":"6332","file_size":1576593,"relation":"main_file","content_type":"application/pdf"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"author":[{"full_name":"Morris, Emily","first_name":"Emily","last_name":"Morris"},{"last_name":"Griffiths","first_name":"Marcus","full_name":"Griffiths, Marcus"},{"full_name":"Golebiowska, Agata","last_name":"Golebiowska","first_name":"Agata"},{"full_name":"Mairhofer, Stefan","last_name":"Mairhofer","first_name":"Stefan"},{"first_name":"Jasmine","last_name":"Burr Hersey","full_name":"Burr Hersey, Jasmine"},{"last_name":"Goh","first_name":"Tatsuaki","full_name":"Goh, Tatsuaki"},{"first_name":"Daniel","orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel"},{"full_name":"Atkinson, Brian","first_name":"Brian","last_name":"Atkinson"},{"last_name":"Sturrock","first_name":"Craig","full_name":"Sturrock, Craig"},{"last_name":"Lynch","first_name":"Jonathan","full_name":"Lynch, Jonathan"},{"full_name":"Vissenberg, Kris","first_name":"Kris","last_name":"Vissenberg"},{"full_name":"Ritz, Karl","last_name":"Ritz","first_name":"Karl"},{"full_name":"Wells, Darren","first_name":"Darren","last_name":"Wells"},{"full_name":"Mooney, Sacha","last_name":"Mooney","first_name":"Sacha"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"}],"title":"Shaping 3D root system architecture","publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"R919 - R930","date_created":"2018-12-11T11:48:08Z","publication":"Current Biology","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"type":"journal_article","publist_id":"6956","pubrep_id":"982","external_id":{"pmid":["28898665"]},"quality_controlled":"1","volume":27,"year":"2017","date_updated":"2021-01-12T08:12:29Z","issue":"17","abstract":[{"text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises.","lang":"eng"}],"_id":"722","oa":1,"publication_identifier":{"issn":["09609822"]},"status":"public","ec_funded":1,"month":"09","publication_status":"published","doi":"10.1016/j.cub.2017.06.043","date_published":"2017-09-11T00:00:00Z","oa_version":"Submitted Version","ddc":["581"],"file_date_updated":"2020-07-14T12:47:54Z","scopus_import":1,"citation":{"ieee":"E. Morris <i>et al.</i>, “Shaping 3D root system architecture,” <i>Current Biology</i>, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. <i>Current Biology</i>. 2017;27(17):R919-R930. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">10.1016/j.cub.2017.06.043</a>","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” <i>Current Biology</i>, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">10.1016/j.cub.2017.06.043</a>.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">https://doi.org/10.1016/j.cub.2017.06.043</a>","ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">https://doi.org/10.1016/j.cub.2017.06.043</a>."},"intvolume":"        27"}]