[{"publication_status":"published","volume":137,"month":"02","scopus_import":"1","quality_controlled":"1","year":"2015","article_type":"original","date_published":"2015-02-12T00:00:00Z","issue":"15","date_created":"2024-09-09T10:04:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Li","full_name":"Li, Haixing","first_name":"Haixing"},{"last_name":"Su","full_name":"Su, Timothy A.","first_name":"Timothy A."},{"first_name":"Vivian","full_name":"Zhang, Vivian","last_name":"Zhang"},{"last_name":"Steigerwald","first_name":"Michael L.","full_name":"Steigerwald, Michael L."},{"full_name":"Nuckolls, Colin","first_name":"Colin","last_name":"Nuckolls"},{"first_name":"Latha","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman"}],"OA_type":"closed access","type":"journal_article","doi":"10.1021/ja512523r","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"page":"5028-5033","article_processing_charge":"No","citation":{"ista":"Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. 2015. Electric field breakdown in single molecule junctions. Journal of the American Chemical Society. 137(15), 5028–5033.","apa":"Li, H., Su, T. A., Zhang, V., Steigerwald, M. L., Nuckolls, C., &#38; Venkataraman, L. (2015). Electric field breakdown in single molecule junctions. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja512523r\">https://doi.org/10.1021/ja512523r</a>","ama":"Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. Electric field breakdown in single molecule junctions. <i>Journal of the American Chemical Society</i>. 2015;137(15):5028-5033. doi:<a href=\"https://doi.org/10.1021/ja512523r\">10.1021/ja512523r</a>","ieee":"H. Li, T. A. Su, V. Zhang, M. L. Steigerwald, C. Nuckolls, and L. Venkataraman, “Electric field breakdown in single molecule junctions,” <i>Journal of the American Chemical Society</i>, vol. 137, no. 15. American Chemical Society, pp. 5028–5033, 2015.","mla":"Li, Haixing, et al. “Electric Field Breakdown in Single Molecule Junctions.” <i>Journal of the American Chemical Society</i>, vol. 137, no. 15, American Chemical Society, 2015, pp. 5028–33, doi:<a href=\"https://doi.org/10.1021/ja512523r\">10.1021/ja512523r</a>.","short":"H. Li, T.A. Su, V. Zhang, M.L. Steigerwald, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 137 (2015) 5028–5033.","chicago":"Li, Haixing, Timothy A. Su, Vivian Zhang, Michael L. Steigerwald, Colin Nuckolls, and Latha Venkataraman. “Electric Field Breakdown in Single Molecule Junctions.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/ja512523r\">https://doi.org/10.1021/ja512523r</a>."},"_id":"17973","pmid":1,"date_updated":"2024-12-18T12:10:06Z","extern":"1","external_id":{"pmid":["25675085"]},"oa_version":"None","language":[{"iso":"eng"}],"title":"Electric field breakdown in single molecule junctions","publication":"Journal of the American Chemical Society","publisher":"American Chemical Society","status":"public","intvolume":"       137","day":"12","abstract":[{"text":"Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S–Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor–acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si–Si and Ge–Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si–Si, Si–C, and Si–O bonds and find that Si–C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level.","lang":"eng"}]},{"day":"30","status":"public","intvolume":"        44","abstract":[{"lang":"eng","text":"Guest editors Dirk M. Guldi, Hiroshi Nishihara and Latha Venkataraman introduce the Molecular Wires issue of \"Chemical Society Reviews\"."}],"language":[{"iso":"eng"}],"oa_version":"None","publisher":"Royal Society of Chemistry","publication":"Chemical Society Reviews","title":"Molecular wires","pmid":1,"_id":"17974","citation":{"ista":"Guldi DM, Nishihara H, Venkataraman L. 2015. Molecular wires. Chemical Society Reviews. 44(4), 842–844.","ama":"Guldi DM, Nishihara H, Venkataraman L. Molecular wires. <i>Chemical Society Reviews</i>. 2015;44(4):842-844. doi:<a href=\"https://doi.org/10.1039/c5cs90010g\">10.1039/c5cs90010g</a>","apa":"Guldi, D. M., Nishihara, H., &#38; Venkataraman, L. (2015). Molecular wires. <i>Chemical Society Reviews</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c5cs90010g\">https://doi.org/10.1039/c5cs90010g</a>","ieee":"D. M. Guldi, H. Nishihara, and L. Venkataraman, “Molecular wires,” <i>Chemical Society Reviews</i>, vol. 44, no. 4. Royal Society of Chemistry, pp. 842–844, 2015.","mla":"Guldi, Dirk M., et al. “Molecular Wires.” <i>Chemical Society Reviews</i>, vol. 44, no. 4, Royal Society of Chemistry, 2015, pp. 842–44, doi:<a href=\"https://doi.org/10.1039/c5cs90010g\">10.1039/c5cs90010g</a>.","short":"D.M. Guldi, H. Nishihara, L. Venkataraman, Chemical Society Reviews 44 (2015) 842–844.","chicago":"Guldi, Dirk M., Hiroshi Nishihara, and Latha Venkataraman. “Molecular Wires.” <i>Chemical Society Reviews</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c5cs90010g\">https://doi.org/10.1039/c5cs90010g</a>."},"page":"842-844","article_processing_charge":"No","doi":"10.1039/c5cs90010g","publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"external_id":{"pmid":["25636152"]},"extern":"1","date_updated":"2025-01-02T13:26:36Z","type":"journal_article","OA_type":"closed access","author":[{"first_name":"Dirk M.","full_name":"Guldi, Dirk M.","last_name":"Guldi"},{"full_name":"Nishihara, Hiroshi","first_name":"Hiroshi","last_name":"Nishihara"},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","first_name":"Latha"}],"date_created":"2024-09-09T10:53:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","quality_controlled":"1","issue":"4","date_published":"2015-01-30T00:00:00Z","article_type":"letter_note","month":"01","scopus_import":"1","volume":44,"publication_status":"published"},{"author":[{"first_name":"Timothy A.","full_name":"Su, Timothy A.","last_name":"Su"},{"full_name":"Li, Haixing","first_name":"Haixing","last_name":"Li"},{"full_name":"Steigerwald, Michael L.","first_name":"Michael L.","last_name":"Steigerwald"},{"full_name":"Venkataraman, Latha","first_name":"Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089"},{"last_name":"Nuckolls","first_name":"Colin","full_name":"Nuckolls, Colin"}],"type":"journal_article","OA_type":"closed access","date_updated":"2025-01-02T13:28:51Z","extern":"1","external_id":{"pmid":["25698330"]},"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"doi":"10.1038/nchem.2180","page":"215-220","article_processing_charge":"No","pmid":1,"_id":"17975","citation":{"short":"T.A. Su, H. Li, M.L. Steigerwald, L. Venkataraman, C. Nuckolls, Nature Chemistry 7 (2015) 215–220.","chicago":"Su, Timothy A., Haixing Li, Michael L. Steigerwald, Latha Venkataraman, and Colin Nuckolls. “Stereoelectronic Switching in Single-Molecule Junctions.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2180\">https://doi.org/10.1038/nchem.2180</a>.","mla":"Su, Timothy A., et al. “Stereoelectronic Switching in Single-Molecule Junctions.” <i>Nature Chemistry</i>, vol. 7, no. 3, Springer Nature, 2015, pp. 215–20, doi:<a href=\"https://doi.org/10.1038/nchem.2180\">10.1038/nchem.2180</a>.","ieee":"T. A. Su, H. Li, M. L. Steigerwald, L. Venkataraman, and C. Nuckolls, “Stereoelectronic switching in single-molecule junctions,” <i>Nature Chemistry</i>, vol. 7, no. 3. Springer Nature, pp. 215–220, 2015.","ama":"Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. Stereoelectronic switching in single-molecule junctions. <i>Nature Chemistry</i>. 2015;7(3):215-220. doi:<a href=\"https://doi.org/10.1038/nchem.2180\">10.1038/nchem.2180</a>","apa":"Su, T. A., Li, H., Steigerwald, M. L., Venkataraman, L., &#38; Nuckolls, C. (2015). Stereoelectronic switching in single-molecule junctions. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2180\">https://doi.org/10.1038/nchem.2180</a>","ista":"Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. 2015. Stereoelectronic switching in single-molecule junctions. Nature Chemistry. 7(3), 215–220."},"title":"Stereoelectronic switching in single-molecule junctions","publication":"Nature Chemistry","publisher":"Springer Nature","oa_version":"None","language":[{"iso":"eng"}],"abstract":[{"text":"A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong σ conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur–methylene σ bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states.","lang":"eng"}],"intvolume":"         7","status":"public","day":"16","publication_status":"published","volume":7,"scopus_import":"1","month":"02","article_type":"original","date_published":"2015-02-16T00:00:00Z","issue":"3","quality_controlled":"1","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-09-09T10:54:59Z"},{"citation":{"short":"E.J. Dell, B. Capozzi, J. Xia, L. Venkataraman, L.M. Campos, Nature Chemistry 7 (2015) 209–214.","chicago":"Dell, Emma J., Brian Capozzi, Jianlong Xia, Latha Venkataraman, and Luis M. Campos. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>.","mla":"Dell, Emma J., et al. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>, vol. 7, no. 3, Springer Nature, 2015, pp. 209–14, doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>.","ieee":"E. J. Dell, B. Capozzi, J. Xia, L. Venkataraman, and L. M. Campos, “Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes,” <i>Nature Chemistry</i>, vol. 7, no. 3. Springer Nature, pp. 209–214, 2015.","apa":"Dell, E. J., Capozzi, B., Xia, J., Venkataraman, L., &#38; Campos, L. M. (2015). Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>","ama":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. 2015;7(3):209-214. doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>","ista":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. 2015. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. Nature Chemistry. 7(3), 209–214."},"_id":"17976","pmid":1,"article_processing_charge":"No","page":"209-214","doi":"10.1038/nchem.2160","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"external_id":{"pmid":["25698329"]},"extern":"1","date_updated":"2025-01-02T13:35:46Z","OA_type":"closed access","type":"journal_article","author":[{"full_name":"Dell, Emma J.","first_name":"Emma J.","last_name":"Dell"},{"last_name":"Capozzi","full_name":"Capozzi, Brian","first_name":"Brian"},{"full_name":"Xia, Jianlong","first_name":"Jianlong","last_name":"Xia"},{"full_name":"Venkataraman, Latha","first_name":"Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089"},{"last_name":"Campos","first_name":"Luis M.","full_name":"Campos, Luis M."}],"day":"02","intvolume":"         7","status":"public","abstract":[{"lang":"eng","text":"To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials."}],"language":[{"iso":"eng"}],"oa_version":"None","publisher":"Springer Nature","publication":"Nature Chemistry","title":"Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes","month":"02","scopus_import":"1","volume":7,"publication_status":"published","date_created":"2024-09-09T10:55:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","quality_controlled":"1","issue":"3","date_published":"2015-02-02T00:00:00Z","article_type":"original"},{"volume":18,"type":"journal_article","publication_status":"published","author":[{"full_name":"Sandra Siegert","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"},{"last_name":"Seo","full_name":"Seo, Jinsoo","first_name":"Jinsoo"},{"last_name":"Kwon","full_name":"Kwon, Ester J","first_name":"Ester"},{"last_name":"Rudenko","first_name":"Andrii","full_name":"Rudenko, Andrii"},{"first_name":"Sukhee","full_name":"Cho, Sukhee","last_name":"Cho"},{"last_name":"Wang","full_name":"Wang, Wenyuan","first_name":"Wenyuan"},{"last_name":"Flood","first_name":"Zachary","full_name":"Flood, Zachary C"},{"last_name":"Martorell","first_name":"Anthony","full_name":"Martorell, Anthony J"},{"full_name":"Ericsson, Maria","first_name":"Maria","last_name":"Ericsson"},{"full_name":"Mungenast, Alison E","first_name":"Alison","last_name":"Mungenast"},{"full_name":"Tsai, Lihuei","first_name":"Lihuei","last_name":"Tsai"}],"_id":"1802","citation":{"apa":"Siegert, S., Seo, J., Kwon, E., Rudenko, A., Cho, S., Wang, W., … Tsai, L. (2015). The schizophrenia risk gene product miR-137 alters presynaptic plasticity. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.4023\">https://doi.org/10.1038/nn.4023</a>","ama":"Siegert S, Seo J, Kwon E, et al. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. <i>Nature Neuroscience</i>. 2015;18:1008-1016. doi:<a href=\"https://doi.org/10.1038/nn.4023\">10.1038/nn.4023</a>","ieee":"S. Siegert <i>et al.</i>, “The schizophrenia risk gene product miR-137 alters presynaptic plasticity,” <i>Nature Neuroscience</i>, vol. 18. Nature Publishing Group, pp. 1008–1016, 2015.","short":"S. Siegert, J. Seo, E. Kwon, A. Rudenko, S. Cho, W. Wang, Z. Flood, A. Martorell, M. Ericsson, A. Mungenast, L. Tsai, Nature Neuroscience 18 (2015) 1008–1016.","mla":"Siegert, Sandra, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” <i>Nature Neuroscience</i>, vol. 18, Nature Publishing Group, 2015, pp. 1008–16, doi:<a href=\"https://doi.org/10.1038/nn.4023\">10.1038/nn.4023</a>.","chicago":"Siegert, Sandra, Jinsoo Seo, Ester Kwon, Andrii Rudenko, Sukhee Cho, Wenyuan Wang, Zachary Flood, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nn.4023\">https://doi.org/10.1038/nn.4023</a>.","ista":"Siegert S, Seo J, Kwon E, Rudenko A, Cho S, Wang W, Flood Z, Martorell A, Ericsson M, Mungenast A, Tsai L. 2015. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. 18, 1008–1016."},"page":"1008 - 1016","doi":"10.1038/nn.4023","extern":1,"month":"07","date_updated":"2021-01-12T06:53:18Z","year":"2015","quality_controlled":0,"publisher":"Nature Publishing Group","publication":"Nature Neuroscience","date_published":"2015-07-01T00:00:00Z","title":"The schizophrenia risk gene product miR-137 alters presynaptic plasticity","day":"01","date_created":"2018-12-11T11:54:05Z","intvolume":"        18","publist_id":"5308","status":"public","acknowledgement":"S.S. was supported by a Human Frontier Science Program (HFSP) long-term postdoctoral fellowship and a Swiss National Science Foundation fellowship for prospective researchers. E.J.K. was supported by a Simons Foundation Postdoctoral Fellowship. A.R. was supported by a NARSAD Young Investigator Award. This work was supported by a Seed Grant from the Simons Center for the Social Brain and US National Institutes of Health grant RO1 MH 091115 to L.-H.T.","abstract":[{"lang":"eng","text":"Noncoding variants in the human MIR137 gene locus increase schizophrenia risk with genome-wide significance. However, the functional consequence of these risk alleles is unknown. Here we examined induced human neurons harboring the minor alleles of four disease-associated single nucleotide polymorphisms in MIR137. We observed increased MIR137 levels compared to those in major allele–carrying cells. microRNA-137 gain of function caused downregulation of the presynaptic target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic vesicle pool distribution, impaired induction of mossy fiber long-term potentiation and deficits in hippocampus-dependent learning and memory. By sequestering endogenous miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement of Syt1 expression partially restored synaptic plasticity, demonstrating the importance of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by which miR-137 dysregulation can impair synaptic plasticity in the hippocampus."}]},{"author":[{"first_name":"Damien","full_name":"Rei, Damien","last_name":"Rei"},{"last_name":"Mason","first_name":"Xenos","full_name":"Mason, Xenos"},{"last_name":"Seo","first_name":"Jinsoo","full_name":"Seo, Jinsoo"},{"last_name":"Gräff","full_name":"Gräff, Johannes","first_name":"Johannes"},{"last_name":"Rudenko","full_name":"Rudenko, Andrii","first_name":"Andrii"},{"last_name":"Wang","full_name":"Wang, Jùn","first_name":"Jùn"},{"last_name":"Rueda","first_name":"Richard","full_name":"Rueda, Richard"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Sandra Siegert","first_name":"Sandra"},{"first_name":"Sukhee","full_name":"Cho, Sukhee","last_name":"Cho"},{"full_name":"Canter, Rebecca G","first_name":"Rebecca","last_name":"Canter"},{"last_name":"Mungenast","full_name":"Mungenast, Alison E","first_name":"Alison"},{"last_name":"Deisseroth","first_name":"Karl","full_name":"Deisseroth, Karl A"},{"last_name":"Tsai","full_name":"Tsai, Lihuei","first_name":"Lihuei"}],"publication_status":"published","type":"journal_article","volume":112,"doi":"10.1073/pnas.1415845112","page":"7291 - 7296","_id":"1803","citation":{"ista":"Rei D, Mason X, Seo J, Gräff J, Rudenko A, Wang J, Rueda R, Siegert S, Cho S, Canter R, Mungenast A, Deisseroth K, Tsai L. 2015. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. 112(23), 7291–7296.","apa":"Rei, D., Mason, X., Seo, J., Gräff, J., Rudenko, A., Wang, J., … Tsai, L. (2015). Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1415845112\">https://doi.org/10.1073/pnas.1415845112</a>","ama":"Rei D, Mason X, Seo J, et al. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. <i>PNAS</i>. 2015;112(23):7291-7296. doi:<a href=\"https://doi.org/10.1073/pnas.1415845112\">10.1073/pnas.1415845112</a>","chicago":"Rei, Damien, Xenos Mason, Jinsoo Seo, Johannes Gräff, Andrii Rudenko, Jùn Wang, Richard Rueda, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1415845112\">https://doi.org/10.1073/pnas.1415845112</a>.","mla":"Rei, Damien, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” <i>PNAS</i>, vol. 112, no. 23, National Academy of Sciences, 2015, pp. 7291–96, doi:<a href=\"https://doi.org/10.1073/pnas.1415845112\">10.1073/pnas.1415845112</a>.","short":"D. Rei, X. Mason, J. Seo, J. Gräff, A. Rudenko, J. Wang, R. Rueda, S. Siegert, S. Cho, R. Canter, A. Mungenast, K. Deisseroth, L. Tsai, PNAS 112 (2015) 7291–7296.","ieee":"D. Rei <i>et al.</i>, “Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway,” <i>PNAS</i>, vol. 112, no. 23. National Academy of Sciences, pp. 7291–7296, 2015."},"date_updated":"2021-01-12T06:53:18Z","month":"06","extern":1,"quality_controlled":0,"year":"2015","title":"Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway","date_published":"2015-06-09T00:00:00Z","publication":"PNAS","issue":"23","publisher":"National Academy of Sciences","acknowledgement":"AG047661; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nNS051874; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nSNSF; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung","intvolume":"       112","publist_id":"5307","status":"public","date_created":"2018-12-11T11:54:06Z","day":"09","abstract":[{"text":"Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.","lang":"eng"}]},{"corr_author":"1","abstract":[{"lang":"eng","text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control."}],"ddc":["530"],"day":"12","intvolume":"         5","status":"public","publist_id":"5306","has_accepted_license":"1","publisher":"Nature Publishing Group","publication":"Scientific Reports","title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","article_number":"10781","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"oa_version":"Published Version","external_id":{"isi":["000356150200001"]},"date_updated":"2025-09-29T10:58:13Z","_id":"1804","citation":{"ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>.","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>, vol. 5, 10781, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781."},"article_processing_charge":"No","file":[{"file_name":"IST-2016-450-v1+1_srep10781.pdf","creator":"system","access_level":"open_access","relation":"main_file","checksum":"7716f582f8c9d82d8f2bf80bf896b440","date_created":"2018-12-12T10:17:26Z","file_id":"5280","date_updated":"2020-07-14T12:45:16Z","file_size":2449723,"content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:45:16Z","doi":"10.1038/srep10781","type":"journal_article","author":[{"orcid":"0000-0001-5964-0203","last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Altmeyer, Sebastian"},{"last_name":"Do","full_name":"Do, Younghae","first_name":"Younghae"},{"first_name":"Ying","full_name":"Lai, Ying","last_name":"Lai"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:06Z","date_published":"2015-06-12T00:00:00Z","year":"2015","quality_controlled":"1","month":"06","scopus_import":"1","oa":1,"isi":1,"pubrep_id":"450","volume":5,"publication_status":"published","department":[{"_id":"BjHo"}],"license":"https://creativecommons.org/licenses/by/4.0/"},{"date_created":"2018-12-11T11:54:06Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.comgeo.2014.08.010"}],"quality_controlled":"1","date_published":"2015-06-03T00:00:00Z","article_type":"original","issue":"8","oa":1,"scopus_import":"1","month":"06","department":[{"_id":"HeEd"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2812"}]},"isi":1,"volume":48,"publist_id":"5305","status":"public","intvolume":"        48","day":"03","ec_funded":1,"corr_author":"1","abstract":[{"lang":"eng","text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard."}],"oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"Computational Geometry: Theory and Applications","title":"Homological reconstruction and simplification in R3","publisher":"Elsevier","doi":"10.1016/j.comgeo.2014.08.010","citation":{"apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2015). Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. 2015;48(8):606-621. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>.","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8, Elsevier, 2015, pp. 606–21, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>.","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 48(8), 606–621."},"_id":"1805","page":"606 - 621","article_processing_charge":"No","OA_place":"publisher","date_updated":"2025-09-23T09:18:30Z","external_id":{"isi":["000357353200006"]},"OA_type":"free access","type":"journal_article","author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"full_name":"Bauer, Ulrich","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","orcid":"0000-0002-9683-0724"},{"last_name":"Devillers","full_name":"Devillers, Olivier","first_name":"Olivier"},{"last_name":"Glisse","full_name":"Glisse, Marc","first_name":"Marc"},{"last_name":"Lieutier","first_name":"André","full_name":"Lieutier, André"}],"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7"}]},{"author":[{"full_name":"Goldman, Michael","first_name":"Michael","last_name":"Goldman"},{"last_name":"Royo-Letelier","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","first_name":"Jimena","full_name":"Royo-Letelier, Jimena"}],"type":"journal_article","doi":"10.1051/cocv/2014040","article_processing_charge":"No","page":"603 - 624","citation":{"short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences, 2015. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>.","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>.","ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","apa":"Goldman, M., &#38; Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. 2015;21(3):603-624. doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>","ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624."},"_id":"1807","date_updated":"2025-09-23T10:45:09Z","external_id":{"arxiv":["1401.1727"],"isi":["000356012000001"]},"oa_version":"Preprint","language":[{"iso":"eng"}],"title":"Sharp interface limit for two components Bose-Einstein condensates","publication":"ESAIM - Control, Optimisation and Calculus of Variations","publisher":"EDP Sciences","publist_id":"5303","status":"public","intvolume":"        21","day":"01","arxiv":1,"corr_author":"1","abstract":[{"lang":"eng","text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential."}],"department":[{"_id":"RoSe"}],"publication_status":"published","volume":21,"isi":1,"oa":1,"month":"05","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.1727"}],"quality_controlled":"1","year":"2015","date_published":"2015-05-01T00:00:00Z","issue":"3","date_created":"2018-12-11T11:54:07Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"language":[{"iso":"eng"}],"oa_version":"None","year":"2015","quality_controlled":"1","issue":"2","publisher":"ACM","publication":"ACM Transactions on Modeling and Computer Simulation","article_number":"7","title":"Guest editors' introduction to special issue on computational methods in systems biology","date_published":"2015-05-01T00:00:00Z","day":"01","date_created":"2018-12-11T11:54:07Z","intvolume":"        25","publist_id":"5302","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ToHe"}],"isi":1,"volume":25,"type":"journal_article","publication_status":"published","author":[{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh","first_name":"Ashutosh"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724"}],"citation":{"ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 7, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>.","apa":"Gupta, A., &#38; Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7."},"_id":"1808","article_processing_charge":"No","doi":"10.1145/2745799","external_id":{"isi":["000354789200001"]},"scopus_import":"1","month":"05","date_updated":"2025-09-23T09:11:51Z"},{"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9715"},{"relation":"research_data","status":"public","id":"9772"}]},"pubrep_id":"453","volume":10,"isi":1,"department":[{"_id":"NiBa"}],"month":"05","scopus_import":"1","oa":1,"date_published":"2015-05-18T00:00:00Z","issue":"5","quality_controlled":"1","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:07Z","author":[{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","first_name":"Barbora"},{"first_name":"Sebastian","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"type":"journal_article","date_updated":"2025-09-23T09:21:54Z","external_id":{"isi":["000354917300064"]},"doi":"10.1371/journal.pone.0126907","file":[{"date_created":"2018-12-12T10:09:07Z","file_id":"4730","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","relation":"main_file","content_type":"application/pdf","file_size":2748982,"date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","creator":"system","access_level":"open_access"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:45:17Z","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015)."},"_id":"1809","title":"Indirect genetic effects and the dynamics of social interactions","publication":"PLoS One","publisher":"Public Library of Science","has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570","576"],"abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"corr_author":"1","publist_id":"5299","status":"public","intvolume":"        10","day":"18"},{"external_id":{"isi":["000365065400003"]},"date_updated":"2025-09-23T07:55:38Z","file":[{"creator":"system","access_level":"open_access","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","content_type":"application/pdf","file_size":1047255,"date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:17:23Z","file_id":"5277","checksum":"1683bb0f42ef892a5b3b71a050d65d25","relation":"main_file"}],"article_processing_charge":"No","page":"1 - 9","file_date_updated":"2020-07-14T12:45:17Z","_id":"1810","citation":{"ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” <i>Current Opinion in Microbiology</i>, vol. 27. Elsevier, pp. 1–9, 2015.","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>.","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>, vol. 27, Elsevier, 2015, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>.","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. 2015;27:1-9. doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>"},"doi":"10.1016/j.mib.2015.05.008","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"author":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias"}],"type":"journal_article","ddc":["570"],"corr_author":"1","abstract":[{"text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.","lang":"eng"}],"ec_funded":1,"day":"01","status":"public","publist_id":"5298","intvolume":"        27","publisher":"Elsevier","has_accepted_license":"1","title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","publication":"Current Opinion in Microbiology","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"06","scopus_import":"1","oa":1,"pubrep_id":"493","isi":1,"volume":27,"publication_status":"published","department":[{"_id":"ToBo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:08Z","date_published":"2015-06-01T00:00:00Z","quality_controlled":"1","year":"2015"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","date_created":"2018-12-11T11:54:08Z","date_published":"2015-05-20T00:00:00Z","issue":"5","main_file_link":[{"url":"http://arxiv.org/abs/1409.0110","open_access":"1"}],"year":"2015","month":"05","scopus_import":"1","oa":1,"publication_status":"published","volume":56,"isi":1,"department":[{"_id":"MiLe"}],"arxiv":1,"abstract":[{"text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.","lang":"eng"}],"corr_author":"1","intvolume":"        56","status":"public","publist_id":"5295","day":"20","ec_funded":1,"article_number":"052105","title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","publication":"Journal of Mathematical Physics","publisher":"American Institute of Physics","oa_version":"Preprint","language":[{"iso":"eng"}],"date_updated":"2025-09-23T07:53:00Z","external_id":{"isi":["000355920800016"],"arxiv":["1409.0110"]},"doi":"10.1063/1.4921227","article_processing_charge":"No","_id":"1811","citation":{"mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>.","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5. American Institute of Physics, 2015.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., &#38; Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. 2015;56(5). doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105."},"author":[{"last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","full_name":"Safari, Laleh"},{"last_name":"Santos","first_name":"José","full_name":"Santos, José"},{"first_name":"Pedro","full_name":"Amaro, Pedro","last_name":"Amaro"},{"first_name":"Kari","full_name":"Jänkälä, Kari","last_name":"Jänkälä"},{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"}],"type":"journal_article","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"date_created":"2018-12-11T11:54:09Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","year":"2015","date_published":"2015-04-01T00:00:00Z","issue":"4","oa":1,"scopus_import":"1","month":"04","department":[{"_id":"MiLe"}],"publication_status":"published","isi":1,"pubrep_id":"446","volume":17,"intvolume":"        17","status":"public","publist_id":"5294","day":"01","ddc":["530"],"abstract":[{"lang":"eng","text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"article_number":"045005","title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","publication":"New Journal of Physics","has_accepted_license":"1","publisher":"IOP Publishing","doi":"10.1088/1367-2630/17/4/045005","file_date_updated":"2020-07-14T12:45:17Z","file":[{"relation":"main_file","checksum":"551f751a75b39b89a1db2f7f498f9a49","date_created":"2018-12-12T10:15:59Z","file_id":"5184","date_updated":"2020-07-14T12:45:17Z","file_size":1900925,"content_type":"application/pdf","file_name":"IST-2016-446-v1+1_document.pdf","access_level":"open_access","creator":"system"}],"article_processing_charge":"No","citation":{"apa":"Lahrz, M., Lemeshko, M., &#38; Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. 2015;17(4). doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” <i>New Journal of Physics</i>, vol. 17, no. 4. IOP Publishing, 2015.","mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>, vol. 17, no. 4, 045005, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>.","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>.","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005."},"_id":"1812","date_updated":"2025-09-23T08:45:19Z","external_id":{"isi":["000354022400001"]},"author":[{"last_name":"Lahrz","first_name":"Martin","full_name":"Lahrz, Martin"},{"orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"last_name":"Mathey","full_name":"Mathey, Ludwig","first_name":"Ludwig"}],"type":"journal_article"},{"scopus_import":"1","month":"05","oa":1,"publication_status":"published","volume":114,"isi":1,"department":[{"_id":"MiLe"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:09Z","date_published":"2015-05-18T00:00:00Z","issue":"20","main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"quality_controlled":"1","year":"2015","date_updated":"2025-09-23T10:40:28Z","external_id":{"isi":["000354969900003"],"arxiv":["1502.03447"]},"doi":"10.1103/PhysRevLett.114.203001","article_processing_charge":"No","citation":{"ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>.","short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>.","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” <i>Physical Review Letters</i>, vol. 114, no. 20. American Physical Society, 2015.","apa":"Schmidt, R., &#38; Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>","ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. 2015;114(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>"},"_id":"1813","author":[{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"}],"type":"journal_article","arxiv":1,"abstract":[{"text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.","lang":"eng"}],"corr_author":"1","status":"public","publist_id":"5293","intvolume":"       114","day":"18","article_number":"203001","title":"Rotation of quantum impurities in the presence of a many-body environment","publication":"Physical Review Letters","publisher":"American Physical Society","oa_version":"Preprint","language":[{"iso":"eng"}]},{"date_published":"2015-04-01T00:00:00Z","issue":"3","quality_controlled":"1","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:09Z","publication_status":"published","volume":34,"pubrep_id":"575","isi":1,"department":[{"_id":"ChWo"}],"scopus_import":"1","month":"04","oa":1,"title":"Water wave animation via wavefront parameter interpolation","article_number":"27","publication":"ACM Transactions on Graphics","has_accepted_license":"1","publisher":"ACM","oa_version":"Submitted Version","language":[{"iso":"eng"}],"ddc":["000"],"corr_author":"1","abstract":[{"text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.","lang":"eng"}],"status":"public","intvolume":"        34","publist_id":"5292","day":"01","ec_funded":1,"author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","full_name":"Jeschke, Stefan","first_name":"Stefan"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"type":"journal_article","project":[{"call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images","grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425"},{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"date_updated":"2025-09-29T11:05:55Z","external_id":{"isi":["000354800700004"]},"doi":"10.1145/2714572","file":[{"relation":"main_file","date_created":"2018-12-12T10:12:15Z","file_id":"4933","checksum":"67c9f4fa370def68cdf31299e48bc91f","file_size":23712153,"date_updated":"2020-07-14T12:45:17Z","content_type":"application/pdf","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","access_level":"open_access","creator":"system"}],"file_date_updated":"2020-07-14T12:45:17Z","article_processing_charge":"No","citation":{"apa":"Jeschke, S., &#38; Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. 2015;34(3). doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3. ACM, 2015.","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3, 27, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>.","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27."},"_id":"1814"},{"intvolume":"       521","publist_id":"5289","status":"public","day":"16","corr_author":"1","abstract":[{"text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ","lang":"eng"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"publication":"Nature","title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","publisher":"Nature Publishing Group","doi":"10.1038/nature14215","citation":{"ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. 2015;521(7551):217-221. doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>.","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>.","ieee":"S. Porazinski <i>et al.</i>, “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” <i>Nature</i>, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221."},"_id":"1817","pmid":1,"page":"217 - 221","article_processing_charge":"No","date_updated":"2025-09-29T11:07:11Z","external_id":{"isi":["000354377800058"],"pmid":["25778702"]},"type":"journal_article","author":[{"last_name":"Porazinski","first_name":"Sean","full_name":"Porazinski, Sean"},{"full_name":"Wang, Huijia","first_name":"Huijia","last_name":"Wang"},{"first_name":"Yoichi","full_name":"Asaoka, Yoichi","last_name":"Asaoka"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin"},{"first_name":"Tatsuo","full_name":"Miyamoto, Tatsuo","last_name":"Miyamoto"},{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","first_name":"Hitoshi","full_name":"Morita, Hitoshi"},{"first_name":"Shoji","full_name":"Hata, Shoji","last_name":"Hata"},{"last_name":"Sasaki","full_name":"Sasaki, Takashi","first_name":"Takashi"},{"orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel"},{"last_name":"Osada","first_name":"Yumi","full_name":"Osada, Yumi"},{"first_name":"Satoshi","full_name":"Asaka, Satoshi","last_name":"Asaka"},{"last_name":"Momoi","first_name":"Akihiro","full_name":"Momoi, Akihiro"},{"full_name":"Linton, Sarah","first_name":"Sarah","last_name":"Linton"},{"last_name":"Miesfeld","full_name":"Miesfeld, Joel","first_name":"Joel"},{"last_name":"Link","full_name":"Link, Brian","first_name":"Brian"},{"last_name":"Senga","full_name":"Senga, Takeshi","first_name":"Takeshi"},{"first_name":"Atahualpa","full_name":"Castillo Morales, Atahualpa","last_name":"Castillo Morales"},{"full_name":"Urrutia, Araxi","first_name":"Araxi","last_name":"Urrutia"},{"full_name":"Shimizu, Nobuyoshi","first_name":"Nobuyoshi","last_name":"Shimizu"},{"first_name":"Hideaki","full_name":"Nagase, Hideaki","last_name":"Nagase"},{"first_name":"Shinya","full_name":"Matsuura, Shinya","last_name":"Matsuura"},{"last_name":"Bagby","full_name":"Bagby, Stefan","first_name":"Stefan"},{"first_name":"Hisato","full_name":"Kondoh, Hisato","last_name":"Kondoh"},{"first_name":"Hiroshi","full_name":"Nishina, Hiroshi","last_name":"Nishina"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"},{"full_name":"Furutani Seiki, Makoto","first_name":"Makoto","last_name":"Furutani Seiki"}],"date_created":"2018-12-11T11:54:10Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"date_published":"2015-03-16T00:00:00Z","issue":"7551","oa":1,"scopus_import":"1","month":"03","department":[{"_id":"CaHe"}],"publication_status":"published","isi":1,"volume":521},{"date_created":"2018-12-11T11:54:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"quality_controlled":"1","year":"2015","date_published":"2015-05-19T00:00:00Z","issue":"20","oa":1,"month":"05","scopus_import":"1","department":[{"_id":"NiBa"}],"publication_status":"published","volume":112,"isi":1,"intvolume":"       112","status":"public","publist_id":"5288","ec_funded":1,"day":"19","corr_author":"1","abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"title":"Limits to adaptation along environmental gradients","publication":"PNAS","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1421515112","article_processing_charge":"No","page":"6401 - 6406","_id":"1818","citation":{"short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406."},"pmid":1,"date_updated":"2025-09-23T09:27:16Z","external_id":{"pmid":["25941385"],"isi":["000354729500058"]},"author":[{"full_name":"Polechova, Jitka","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","orcid":"0000-0003-0951-3112"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"type":"journal_article","project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}]},{"page":"1175 - 1187","article_processing_charge":"No","citation":{"ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. 2015;8(8):1175-1187. doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., &#38; Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” <i>Molecular Plant</i>, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>.","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187."},"_id":"1819","doi":"10.1016/j.molp.2015.03.007","external_id":{"isi":["000359136100006"]},"date_updated":"2025-09-23T09:47:17Z","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"author":[{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","full_name":"Friml, Jiřĺ"}],"type":"journal_article","day":"03","ec_funded":1,"publist_id":"5287","status":"public","intvolume":"         8","corr_author":"1","abstract":[{"lang":"eng","text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity."}],"language":[{"iso":"eng"}],"oa_version":"None","publisher":"Elsevier","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","publication":"Molecular Plant","scopus_import":"1","month":"08","department":[{"_id":"JiFr"}],"volume":8,"isi":1,"publication_status":"published","date_created":"2018-12-11T11:54:11Z","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","year":"2015","issue":"8","date_published":"2015-08-03T00:00:00Z"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"quality_controlled":"1","year":"2015","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:54:11Z","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"KrCh"}],"volume":5,"isi":1,"publication_status":"published","related_material":{"record":[{"id":"1529","relation":"later_version","status":"public"}]},"oa":1,"scopus_import":"1","month":"06","language":[{"iso":"eng"}],"conference":{"location":"Austin, TX, USA","start_date":"2015-01-25","end_date":"2015-01-30","name":"IAAI: Innovative Applications of Artificial Intelligence"},"oa_version":"Preprint","publisher":"AAAI Press","alternative_title":["Artifical Intelligence"],"title":"Optimal cost almost-sure reachability in POMDPs","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","ec_funded":1,"day":"01","status":"public","publist_id":"5286","intvolume":"         5","arxiv":1,"corr_author":"1","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.","lang":"eng"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin"},{"last_name":"Gupta","first_name":"Raghav","full_name":"Gupta, Raghav"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"}],"type":"conference","article_processing_charge":"No","page":"3496-3502","_id":"1820","citation":{"short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, vol. 5, AAAI Press, 2015, pp. 3496–502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, 5:3496–3502. AAAI Press, 2015.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i> (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>. Vol 5. AAAI Press; 2015:3496-3502.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502."},"external_id":{"arxiv":["1411.3880"],"isi":["000372683700002"]},"date_updated":"2025-09-18T11:05:08Z"}]