[{"publist_id":"3589","intvolume":" 24","publication":"Plant Cell","year":"2012","status":"public","day":"01","doi":"10.1105/tpc.112.098905","page":"2497 - 2514","date_created":"2018-12-11T12:01:27Z","_id":"3110","type":"journal_article","date_published":"2012-06-01T00:00:00Z","publisher":"American Society of Plant Biologists","volume":24,"title":"A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis","month":"06","publication_status":"published","abstract":[{"lang":"eng","text":"The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation. "}],"issue":"6","author":[{"first_name":"Mingqiu","last_name":"Dai","full_name":"Dai, Mingqiu"},{"full_name":"Zhang, Chen","first_name":"Chen","last_name":"Zhang"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Urszula Kania","first_name":"Urszula","last_name":"Kania"},{"full_name":"Chen, Fang","last_name":"Chen","first_name":"Fang"},{"full_name":"Xue, Qin","first_name":"Qin","last_name":"Xue"},{"full_name":"McCray, Tyra","first_name":"Tyra","last_name":"Mccray"},{"last_name":"Li","first_name":"Gang","full_name":"Li, Gang"},{"first_name":"Genji","last_name":"Qin","full_name":"Qin, Genji"},{"full_name":"Wakeley, Michelle","first_name":"Michelle","last_name":"Wakeley"},{"full_name":"Terzaghi, William","last_name":"Terzaghi","first_name":"William"},{"full_name":"Wan, Jianmin","last_name":"Wan","first_name":"Jianmin"},{"full_name":"Zhao, Yunde","first_name":"Yunde","last_name":"Zhao"},{"first_name":"Jian","last_name":"Xu","full_name":"Xu, Jian"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"full_name":"Deng, Xing W","last_name":"Deng","first_name":"Xing"},{"first_name":"Haiyang","last_name":"Wang","full_name":"Wang, Haiyang"}],"extern":1,"quality_controlled":0,"date_updated":"2021-01-12T07:41:08Z","citation":{"short":"M. Dai, C. Zhang, U. Kania, F. Chen, Q. Xue, T. Mccray, G. Li, G. Qin, M. Wakeley, W. Terzaghi, J. Wan, Y. Zhao, J. Xu, J. Friml, X. Deng, H. Wang, Plant Cell 24 (2012) 2497–2514.","mla":"Dai, Mingqiu, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell, vol. 24, no. 6, American Society of Plant Biologists, 2012, pp. 2497–514, doi:10.1105/tpc.112.098905.","apa":"Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., … Wang, H. (2012). A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.098905","chicago":"Dai, Mingqiu, Chen Zhang, Urszula Kania, Fang Chen, Qin Xue, Tyra Mccray, Gang Li, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.098905.","ama":"Dai M, Zhang C, Kania U, et al. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 2012;24(6):2497-2514. doi:10.1105/tpc.112.098905","ista":"Dai M, Zhang C, Kania U, Chen F, Xue Q, Mccray T, Li G, Qin G, Wakeley M, Terzaghi W, Wan J, Zhao Y, Xu J, Friml J, Deng X, Wang H. 2012. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 24(6), 2497–2514.","ieee":"M. Dai et al., “A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis,” Plant Cell, vol. 24, no. 6. American Society of Plant Biologists, pp. 2497–2514, 2012."}},{"date_published":"2012-07-24T00:00:00Z","publisher":"Cell Press","title":"A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots","volume":22,"publication_status":"published","month":"07","abstract":[{"text":"PIN-FORMED (PIN) protein-mediated auxin polar transport is critically important for development, pattern formation, and morphogenesis in plants. Auxin has been implicated in the regulation of polar auxin transport by inhibiting PIN endocytosis [1, 2], but how auxin regulates this process is poorly understood. Our genetic screen identified the Arabidopsis SPIKE1 (SPK1) gene whose loss-of-function mutations increased lateral root density and retarded gravitropic responses, as do pin2 knockout mutations [3]. SPK1 belongs to the conserved DHR2-Dock family of Rho guanine nucleotide exchange factors [4-6]. The spk1 mutations induced PIN2 internalization that was not suppressed by auxin, as did the loss-of-function mutations for Rho-like GTPase from Plants 6 (ROP6)-GTPase or its effector RIC1. Furthermore, SPK1 was required for auxin induction of ROP6 activation. Our results have established a Rho GTPase-based auxin signaling pathway that maintains PIN2 polar distribution to the plasma membrane via inhibition of its internalization in Arabidopsis roots. Our findings provide new insights into signaling mechanisms that underlie the regulation of the dynamic trafficking of PINs required for long-distance auxin transport and that link auxin signaling to PIN-mediated pattern formation and morphogenesis.","lang":"eng"}],"issue":"14","author":[{"full_name":"Lin, Deshu","first_name":"Deshu","last_name":"Lin"},{"first_name":"Shingo","last_name":"Nagawa","full_name":"Nagawa, Shingo"},{"full_name":"Chen, Jisheng","first_name":"Jisheng","last_name":"Chen"},{"first_name":"Lingyan","last_name":"Cao","full_name":"Cao, Lingyan"},{"full_name":"Xu Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","last_name":"Chen"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Hongjiang Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","last_name":"Li","first_name":"Hongjiang"},{"last_name":"Dhonukshe","first_name":"Pankaj","full_name":"Dhonukshe, Pankaj"},{"full_name":"Yamamuro, Chizuko","first_name":"Chizuko","last_name":"Yamamuro"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Scheres, Ben","first_name":"Ben","last_name":"Scheres"},{"full_name":"Fu, Ying","last_name":"Fu","first_name":"Ying"},{"full_name":"Yang, Zhenbiao","last_name":"Yang","first_name":"Zhenbiao"}],"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T07:41:08Z","citation":{"short":"D. Lin, S. Nagawa, J. Chen, L. Cao, X. Chen, T. Xu, H. Li, P. Dhonukshe, C. Yamamuro, J. Friml, B. Scheres, Y. Fu, Z. Yang, Current Biology 22 (2012) 1319–1325.","mla":"Lin, Deshu, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell Press, 2012, pp. 1319–25, doi:10.1016/j.cub.2012.05.019.","apa":"Lin, D., Nagawa, S., Chen, J., Cao, L., Chen, X., Xu, T., … Yang, Z. (2012). A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.019","chicago":"Lin, Deshu, Shingo Nagawa, Jisheng Chen, Lingyan Cao, Xu Chen, Tongda Xu, Hongjiang Li, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology. Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.019.","ista":"Lin D, Nagawa S, Chen J, Cao L, Chen X, Xu T, Li H, Dhonukshe P, Yamamuro C, Friml J, Scheres B, Fu Y, Yang Z. 2012. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. 22(14), 1319–1325.","ama":"Lin D, Nagawa S, Chen J, et al. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. 2012;22(14):1319-1325. doi:10.1016/j.cub.2012.05.019","ieee":"D. Lin et al., “A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell Press, pp. 1319–1325, 2012."},"publist_id":"3588","intvolume":" 22","publication":"Current Biology","status":"public","day":"24","year":"2012","doi":"10.1016/j.cub.2012.05.019","page":"1319 - 1325","date_created":"2018-12-11T12:01:27Z","_id":"3111","type":"journal_article"},{"publication":"Current Biology","publist_id":"3587","intvolume":" 22","day":"24","doi":"10.1016/j.cub.2012.05.020","year":"2012","status":"public","page":"1326 - 1332","type":"journal_article","_id":"3112","date_created":"2018-12-11T12:01:27Z","volume":22,"title":"ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots","publisher":"Cell Press","date_published":"2012-07-24T00:00:00Z","issue":"14","publication_status":"published","month":"07","abstract":[{"lang":"eng","text":"The dynamic spatial and temporal distribution of the crucial plant signaling molecule auxin is achieved by feedback coordination of auxin signaling and intercellular auxin transport pathways [1, 2]. Developmental roles of auxin have been attributed predominantly to its effect on transcription; however, an alternative pathway involving AUXIN BINDING PROTEIN1 (ABP1) has been proposed to regulate clathrin-mediated endocytosis in roots and Rho-like GTPase (ROP)-dependent pavement cell interdigitation in leaves [3, 4]. In this study, we show that ROP6 and its downstream effector RIC1 regulate clathrin association with the plasma membrane for clathrin-mediated endocytosis, as well as for its feedback regulation by auxin. Genetic analysis revealed that ROP6/RIC1 acts downstream of ABP1 to regulate endocytosis. This signaling circuit is also involved in the feedback regulation of PIN-FORMED 1 (PIN1) and PIN2 auxin transporters activity (via its constitutive endocytosis) and corresponding auxin transport-mediated processes, including root gravitropism and leave vascular tissue patterning. Our findings suggest that the signaling module auxin-ABP1-ROP6/RIC1-clathrin-PIN1/PIN2 is a shared component of the feedback regulation of auxin transport during both root and aerial development."}],"author":[{"first_name":"Xu","last_name":"Chen","full_name":"Xu Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"last_name":"Löfke","first_name":"Christian","full_name":"Löfke, Christian"},{"last_name":"Lin","first_name":"Deshu","full_name":"Lin, Deshu"},{"last_name":"Yang","first_name":"Zhenbiao","full_name":"Yang, Zhenbiao"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"}],"citation":{"ama":"Chen X, Naramoto S, Robert S, et al. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 2012;22(14):1326-1332. doi:10.1016/j.cub.2012.05.020","ista":"Chen X, Naramoto S, Robert S, Tejos R, Löfke C, Lin D, Yang Z, Friml J. 2012. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 22(14), 1326–1332.","chicago":"Chen, Xu, Satoshi Naramoto, Stéphanie Robert, Ricardo Tejos, Christian Löfke, Deshu Lin, Zhenbiao Yang, and Jiří Friml. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology. Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.020.","apa":"Chen, X., Naramoto, S., Robert, S., Tejos, R., Löfke, C., Lin, D., … Friml, J. (2012). ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.020","ieee":"X. Chen et al., “ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell Press, pp. 1326–1332, 2012.","short":"X. Chen, S. Naramoto, S. Robert, R. Tejos, C. Löfke, D. Lin, Z. Yang, J. Friml, Current Biology 22 (2012) 1326–1332.","mla":"Chen, Xu, et al. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell Press, 2012, pp. 1326–32, doi:10.1016/j.cub.2012.05.020."},"extern":1,"quality_controlled":0,"date_updated":"2021-01-12T07:41:08Z"},{"author":[{"full_name":"Martinière, Alexandre","last_name":"Martinière","first_name":"Alexandre"},{"last_name":"Lavagi","first_name":"Irene","full_name":"Lavagi, Irene"},{"full_name":"Nageswaran, Gayathri","last_name":"Nageswaran","first_name":"Gayathri"},{"first_name":"Daniel","last_name":"Rolfe","full_name":"Rolfe, Daniel J"},{"last_name":"Maneta Peyret","first_name":"Lilly","full_name":"Maneta-Peyret, Lilly"},{"last_name":"Luu","first_name":"Doan","full_name":"Luu, Doan-Trung"},{"full_name":"Botchway, Stanley W","last_name":"Botchway","first_name":"Stanley"},{"full_name":"Webb, Stephen E","last_name":"Webb","first_name":"Stephen"},{"first_name":"Sebastien","last_name":"Mongrand","full_name":"Mongrand, Sebastien"},{"full_name":"Maurel, Christophe","first_name":"Christophe","last_name":"Maurel"},{"first_name":"Marisa","last_name":"Martin Fernandez","full_name":"Martin-Fernandez, Marisa L"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Moreau, Patrick","last_name":"Moreau","first_name":"Patrick"},{"first_name":"John","last_name":"Runions","full_name":"Runions, John"}],"extern":1,"quality_controlled":0,"date_updated":"2021-01-12T07:41:09Z","citation":{"short":"A. Martinière, I. Lavagi, G. Nageswaran, D. Rolfe, L. Maneta Peyret, D. Luu, S. Botchway, S. Webb, S. Mongrand, C. Maurel, M. Martin Fernandez, J. Kleine Vehn, J. Friml, P. Moreau, J. Runions, PNAS 109 (2012) 12805–12810.","mla":"Martinière, Alexandre, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS, vol. 109, no. 31, National Academy of Sciences, 2012, pp. 12805–10, doi:10.1073/pnas.1202040109.","ista":"Martinière A, Lavagi I, Nageswaran G, Rolfe D, Maneta Peyret L, Luu D, Botchway S, Webb S, Mongrand S, Maurel C, Martin Fernandez M, Kleine Vehn J, Friml J, Moreau P, Runions J. 2012. Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. 109(31), 12805–12810.","chicago":"Martinière, Alexandre, Irene Lavagi, Gayathri Nageswaran, Daniel Rolfe, Lilly Maneta Peyret, Doan Luu, Stanley Botchway, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1202040109.","ama":"Martinière A, Lavagi I, Nageswaran G, et al. Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. 2012;109(31):12805-12810. doi:10.1073/pnas.1202040109","apa":"Martinière, A., Lavagi, I., Nageswaran, G., Rolfe, D., Maneta Peyret, L., Luu, D., … Runions, J. (2012). Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1202040109","ieee":"A. Martinière et al., “Cell wall constrains lateral diffusion of plant plasma membrane proteins,” PNAS, vol. 109, no. 31. National Academy of Sciences, pp. 12805–12810, 2012."},"date_published":"2012-07-31T00:00:00Z","publisher":"National Academy of Sciences","volume":109,"title":"Cell wall constrains lateral diffusion of plant plasma membrane proteins","publication_status":"published","month":"07","abstract":[{"lang":"eng","text":"A cell membrane can be considered a liquid-phase plane in which lipids and proteins theoretically are free to diffuse. Numerous reports,however, describe retarded diffusion ofmembrane proteins in animal cells. This anomalous diffusion results from a combination of structuring factors including protein-protein interactions, cytoskeleton corralling, and lipid organization into microdomains. In plant cells, plasma-membrane (PM) proteins have been described as relatively immobile, but the control mechanisms that structure the PM have not been studied. Here, we use fluorescence recovery after photobleaching to estimate mobility of a set of minimal PM proteins. These proteins consist only of a PM-anchoring domain fused to a fluorescent protein, but their mobilities remained limited, as is the case for many full-length proteins. Neither the cytoskeleton nor membrane microdomain structure was involved in constraining the diffusion of these proteins. The cell wall, however, was shown to have a crucial role in immobilizing PM proteins. In addition, by single-molecule fluorescence imaging we confirmed that the pattern of cellulose deposition in the cell wall affects the trajectory and speed ofPMprotein diffusion. Regulation ofPMprotein dynamics by the plant cell wall can be interpreted as a mechanism for regulating protein interactions in processes such as trafficking and signal transduction."}],"issue":"31","page":"12805 - 12810","status":"public","doi":"10.1073/pnas.1202040109","year":"2012","day":"31","date_created":"2018-12-11T12:01:28Z","_id":"3113","type":"journal_article","publist_id":"3586","intvolume":" 109","publication":"PNAS"},{"date_created":"2018-12-11T12:01:28Z","_id":"3114","type":"journal_article","doi":"10.1038/ncomms1941","day":"03","year":"2012","status":"public","intvolume":" 3","publist_id":"3585","publication":"Nature Communications","date_updated":"2021-01-12T07:41:09Z","extern":1,"quality_controlled":0,"citation":{"short":"Z. Ding, B. Wang, I. Moreno, N. Dupláková, S. Simon, N. Carraro, J. Reemmer, A. Pěnčík, X. Chen, R. Tejos, P. Skůpa, S. Pollmann, J. Mravec, J. Petrášek, E. Zažímalová, D. Honys, J. Rolčík, A. Murphy, A. Orellana, M. Geisler, J. Friml, Nature Communications 3 (2012).","mla":"Ding, Zhaojun, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications, vol. 3, no. AN 941, Nature Publishing Group, 2012, doi:10.1038/ncomms1941.","apa":"Ding, Z., Wang, B., Moreno, I., Dupláková, N., Simon, S., Carraro, N., … Friml, J. (2012). ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms1941","ista":"Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík A, Chen X, Tejos R, Skůpa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J. 2012. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. 3(AN 941).","ama":"Ding Z, Wang B, Moreno I, et al. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. 2012;3(AN 941). doi:10.1038/ncomms1941","chicago":"Ding, Zhaojun, Bangjun Wang, Ignacio Moreno, Nikoleta Dupláková, Sibu Simon, Nicola Carraro, Jesica Reemmer, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications. Nature Publishing Group, 2012. https://doi.org/10.1038/ncomms1941.","ieee":"Z. Ding et al., “ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis,” Nature Communications, vol. 3, no. AN 941. Nature Publishing Group, 2012."},"author":[{"full_name":"Ding, Zhaojun","first_name":"Zhaojun","last_name":"Ding"},{"first_name":"Bangjun","last_name":"Wang","full_name":"Wang, Bangjun"},{"last_name":"Moreno","first_name":"Ignacio","full_name":"Moreno, Ignacio"},{"full_name":"Dupláková, Nikoleta","last_name":"Dupláková","first_name":"Nikoleta"},{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Sibu Simon"},{"first_name":"Nicola","last_name":"Carraro","full_name":"Carraro, Nicola"},{"full_name":"Reemmer, Jesica","last_name":"Reemmer","first_name":"Jesica"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"last_name":"Chen","first_name":"Xu","full_name":"Xu Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo I"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"full_name":"Pollmann, Stephan","last_name":"Pollmann","first_name":"Stephan"},{"first_name":"Jozef","last_name":"Mravec","full_name":"Mravec, Jozef"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"first_name":"David","last_name":"Honys","full_name":"Honys, David"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"full_name":"Murphy, Angus S","first_name":"Angus","last_name":"Murphy"},{"last_name":"Orellana","first_name":"Ariel","full_name":"Orellana, Ariel"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"abstract":[{"lang":"eng","text":"Auxin is a key coordinative signal required for many aspects of plant development and its levels are controlled by auxin metabolism and intercellular auxin transport. Here we find that a member of PIN auxin transporter family, PIN8 is expressed in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development and functionality. Ectopic expression in sporophytic tissues establishes a role of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter. Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation of intracellular auxin homoeostasis and gametophyte as well as sporophyte development. Our results reveal a role of the auxin transport in male gametophyte development in which the distinct actions of ER-localized PIN transporters regulate cellular auxin homoeostasis and maintain the auxin levels optimal for pollen development and pollen tube growth."}],"month":"07","publication_status":"published","issue":"AN 941","publisher":"Nature Publishing Group","date_published":"2012-07-03T00:00:00Z","volume":3,"title":"ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis"},{"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.2158"}],"date_created":"2018-12-11T12:01:28Z","type":"journal_article","_id":"3115","author":[{"full_name":"Berberich, Eric","last_name":"Berberich","first_name":"Eric"},{"last_name":"Halperin","first_name":"Dan","full_name":"Halperin, Dan"},{"orcid":"0000-0002-8030-9299","first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pogalnikova, Roza","last_name":"Pogalnikova","first_name":"Roza"}],"quality_controlled":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":48,"month":"12","issue":"4","acknowledgement":"We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting the digital-pen offset-deconstruction problem. This work has been supported in part by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation (grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational Geometry Learning).\r\n","day":"01","doi":"10.1007/s00454-012-9441-5","page":"964 - 989","year":"2012","oa":1,"intvolume":" 48","publist_id":"3584","arxiv":1,"publication":"Discrete & Computational Geometry","related_material":{"record":[{"status":"public","id":"3329","relation":"earlier_version"}]},"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1109.2158"]},"date_updated":"2023-02-23T11:22:30Z","department":[{"_id":"HeEd"}],"citation":{"ieee":"E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” Discrete & Computational Geometry, vol. 48, no. 4. Springer, pp. 964–989, 2012.","apa":"Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2012). Deconstructing approximate offsets. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-012-9441-5","ista":"Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate offsets. Discrete & Computational Geometry. 48(4), 964–989.","ama":"Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. Discrete & Computational Geometry. 2012;48(4):964-989. doi:10.1007/s00454-012-9441-5","chicago":"Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-012-9441-5.","short":"E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete & Computational Geometry 48 (2012) 964–989.","mla":"Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:10.1007/s00454-012-9441-5."},"publisher":"Springer","date_published":"2012-12-01T00:00:00Z","title":"Deconstructing approximate offsets","abstract":[{"lang":"eng","text":"We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one."}],"publication_status":"published"},{"oa":1,"date_created":"2018-12-11T12:01:29Z","_id":"3117","type":"journal_article","day":"01","year":"2012","page":"2246 - 2258","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.1990"}],"doi":"10.1016/j.dam.2012.05.025","scopus_import":1,"publist_id":"3582","intvolume":" 160","publication":"Discrete Applied Mathematics","quality_controlled":"1","department":[{"_id":"VlKo"}],"date_updated":"2021-01-12T07:41:11Z","citation":{"ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025","ama":"Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025","ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258.","chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.","mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258."},"oa_version":"Preprint","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","publication_status":"published","abstract":[{"lang":"eng","text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms."}],"issue":"15","date_published":"2012-10-01T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Elsevier","title":"Minimizing a sum of submodular functions","volume":160},{"oa_version":"Submitted Version","quality_controlled":"1","author":[{"first_name":"Morten","last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten"},{"first_name":"Hao","last_name":"Li","full_name":"Li, Hao"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546"}],"issue":"4","article_number":"53","file":[{"relation":"main_file","checksum":"1e219c5bf4e5552c1290c62eefa5cd60","file_id":"5359","creator":"system","access_level":"open_access","file_size":44538518,"content_type":"application/pdf","date_created":"2018-12-12T10:18:37Z","date_updated":"2020-07-14T12:46:00Z","file_name":"IST-2016-602-v1+1_topoReg.pdf"}],"has_accepted_license":"1","month":"07","article_processing_charge":"No","volume":31,"language":[{"iso":"eng"}],"_id":"3118","type":"journal_article","article_type":"original","date_created":"2018-12-11T12:01:29Z","status":"public","pubrep_id":"602","citation":{"ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53.","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549","chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549.","apa":"Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.","short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).","mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549."},"date_updated":"2022-05-24T08:21:11Z","department":[{"_id":"ChWo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["SIGGRAPH"],"ddc":["000"],"abstract":[{"text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.","lang":"eng"}],"publication_status":"published","title":"Tracking surfaces with evolving topology","publisher":"ACM","file_date_updated":"2020-07-14T12:46:00Z","date_published":"2012-07-01T00:00:00Z","oa":1,"day":"01","year":"2012","doi":"10.1145/2185520.2185549","acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","scopus_import":"1","publication":"ACM Transactions on Graphics","intvolume":" 31","publist_id":"3581"},{"status":"public","date_created":"2018-12-11T12:01:30Z","_id":"3119","type":"conference","conference":{"location":"Aire-la-Ville, Switzerland","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2012-07-29","end_date":"2012-07-31"},"pubrep_id":"600","author":[{"full_name":"Raveendran, Karthik","first_name":"Karthik","last_name":"Raveendran"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"},{"first_name":"Greg","last_name":"Turk","full_name":"Turk, Greg"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"07","file":[{"file_name":"IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:11:23Z","creator":"system","file_id":"4877","checksum":"babda64c24cf90a4d05ae86d712bed08","file_size":4939370,"access_level":"open_access","relation":"main_file"}],"acknowledgement":"This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.","page":"255 - 264","year":"2012","day":"29","oa":1,"publist_id":"3580","publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","scopus_import":1,"related_material":{"link":[{"relation":"table_of_contents","url":"http://dl.acm.org/citation.cfm?id=2422393"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChWo"}],"date_updated":"2023-02-23T11:13:07Z","citation":{"mla":"Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–64.","short":"K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264.","apa":"Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM.","chicago":"Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 255–64. ACM, 2012.","ama":"Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM; 2012:255-264.","ista":"Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.","ieee":"K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264."},"file_date_updated":"2020-07-14T12:46:00Z","date_published":"2012-07-29T00:00:00Z","publisher":"ACM","title":"Controlling liquids using meshes","publication_status":"published","abstract":[{"text":"We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n","lang":"eng"}],"ddc":["000"]},{"language":[{"iso":"eng"}],"volume":148,"month":"07","issue":"4","author":[{"full_name":"Brown, Gavin","last_name":"Brown","first_name":"Gavin"},{"orcid":"0000-0002-8030-9299","first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reid, Miles","first_name":"Miles","last_name":"Reid"}],"quality_controlled":"1","oa_version":"Preprint","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1009.4313"}],"date_created":"2018-12-11T12:01:30Z","_id":"3120","type":"journal_article","publisher":"Cambridge University Press","date_published":"2012-07-01T00:00:00Z","title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","publication_status":"published","abstract":[{"text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:41:12Z","citation":{"ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","apa":"Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X11007226","ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press, 2012. https://doi.org/10.1112/S0010437X11007226.","ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:10.1112/S0010437X11007226.","short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194."},"publist_id":"3579","intvolume":" 148","publication":"Compositio Mathematica","scopus_import":1,"acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","doi":"10.1112/S0010437X11007226","day":"01","page":"1171 - 1194","year":"2012","oa":1},{"issue":"9","month":"09","volume":15,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","author":[{"last_name":"Williams","first_name":"Courtney","full_name":"Williams, Courtney"},{"full_name":"Chen, Wenyan","last_name":"Chen","first_name":"Wenyan"},{"first_name":"Chia","last_name":"Lee","full_name":"Lee, Chia"},{"first_name":"Daniel","last_name":"Yaeger","full_name":"Yaeger, Daniel"},{"first_name":"Nicholas","last_name":"Vyleta","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Nicholas"},{"last_name":"Smith","first_name":"Stephen","full_name":"Smith, Stephen"}],"_id":"3121","type":"journal_article","date_created":"2018-12-11T12:01:30Z","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/"}],"abstract":[{"lang":"eng","text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type."}],"publication_status":"published","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA","date_published":"2012-09-01T00:00:00Z","publisher":"Nature Publishing Group","pmid":1,"citation":{"mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162.","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197.","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197.","chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3162.","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162"},"date_updated":"2021-01-12T07:41:12Z","department":[{"_id":"PeJo"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["22842148"]},"scopus_import":1,"publication":"Nature Neuroscience","intvolume":" 15","publist_id":"3578","oa":1,"doi":"10.1038/nn.3162","day":"01","page":"1195 - 1197","year":"2012","acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. "},{"scopus_import":1,"intvolume":" 21","publist_id":"3577","publication":"Molecular Ecology","date_created":"2018-12-11T12:01:31Z","type":"journal_article","_id":"3122","page":"3640 - 3643","doi":"10.1111/j.1365-294X.2012.05643.x","status":"public","year":"2012","day":"01","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"publication_status":"published","month":"08","issue":"15","language":[{"iso":"eng"}],"date_published":"2012-08-01T00:00:00Z","publisher":"Wiley-Blackwell","volume":21,"title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","date_updated":"2021-01-12T07:41:13Z","quality_controlled":"1","department":[{"_id":"NiBa"}],"oa_version":"None","citation":{"apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643."},"author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"status":"public","_id":"3123","type":"conference","date_created":"2018-12-11T12:01:31Z","conference":{"end_date":"2012-05-18","start_date":"2012-05-13","name":"EUROGRAPHICS: Conference on European Association for Computer Graphics","location":"Cagliari, Sardinia, Italy"},"pubrep_id":"601","author":[{"last_name":"Yu","first_name":"Jihun","full_name":"Yu, Jihun"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J"},{"full_name":"Turk, Greg","last_name":"Turk","first_name":"Greg"},{"first_name":"Chee","last_name":"Yap","full_name":"Yap, Chee"}],"oa_version":"Submitted Version","quality_controlled":"1","article_processing_charge":"No","volume":31,"language":[{"iso":"eng"}],"issue":"2","file":[{"file_size":5740527,"access_level":"open_access","creator":"system","file_id":"5092","checksum":"acb325dd1e31859bedd30e013f61d0b9","relation":"main_file","file_name":"IST-2016-601-v1+1_meshSPH.pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:14:39Z","content_type":"application/pdf"}],"has_accepted_license":"1","month":"05","year":"2012","doi":"10.1111/j.1467-8659.2012.03062.x","page":"815 - 824","day":"01","acknowledgement":"This work was funded by NSF grant IIS-1017014 and CCF- 0917093.","oa":1,"publication":"Computer Graphics Forum","intvolume":" 31","publist_id":"3576","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Eurographics"],"citation":{"mla":"Yu, Jihun, et al. “Explicit Mesh Surfaces for Particle Based Fluids.” Computer Graphics Forum, vol. 31, no. 2, Wiley, 2012, pp. 815–24, doi:10.1111/j.1467-8659.2012.03062.x.","short":"J. Yu, C. Wojtan, G. Turk, C. Yap, in:, Computer Graphics Forum, Wiley, 2012, pp. 815–824.","ista":"Yu J, Wojtan C, Turk G, Yap C. 2012. Explicit mesh surfaces for particle based fluids. Computer Graphics Forum. EUROGRAPHICS: Conference on European Association for Computer Graphics, Eurographics, vol. 31, 815–824.","chicago":"Yu, Jihun, Chris Wojtan, Greg Turk, and Chee Yap. “Explicit Mesh Surfaces for Particle Based Fluids.” In Computer Graphics Forum, 31:815–24. Wiley, 2012. https://doi.org/10.1111/j.1467-8659.2012.03062.x.","ama":"Yu J, Wojtan C, Turk G, Yap C. Explicit mesh surfaces for particle based fluids. In: Computer Graphics Forum. Vol 31. Wiley; 2012:815-824. doi:10.1111/j.1467-8659.2012.03062.x","apa":"Yu, J., Wojtan, C., Turk, G., & Yap, C. (2012). Explicit mesh surfaces for particle based fluids. In Computer Graphics Forum (Vol. 31, pp. 815–824). Cagliari, Sardinia, Italy: Wiley. https://doi.org/10.1111/j.1467-8659.2012.03062.x","ieee":"J. Yu, C. Wojtan, G. Turk, and C. Yap, “Explicit mesh surfaces for particle based fluids,” in Computer Graphics Forum, Cagliari, Sardinia, Italy, 2012, vol. 31, no. 2, pp. 815–824."},"date_updated":"2023-10-16T09:54:40Z","department":[{"_id":"ChWo"}],"title":"Explicit mesh surfaces for particle based fluids","publisher":"Wiley","file_date_updated":"2020-07-14T12:46:00Z","date_published":"2012-05-01T00:00:00Z","ddc":["000"],"abstract":[{"lang":"eng","text":"We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time-steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent surface mesh allows us to simulate high-resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation."}],"publication_status":"published"},{"year":"2012","status":"public","day":"30","type":"conference","_id":"3124","date_created":"2018-12-11T12:01:31Z","oa":1,"conference":{"name":"ICML: International Conference on Machine Learning","location":"Edinburgh, Scotland","start_date":"2012-06-26","end_date":"2012-07-01"},"publist_id":"3575","pubrep_id":"565","related_material":{"record":[{"relation":"later_version","id":"5396","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","alternative_title":["Inferning 2012"],"author":[{"full_name":"Korc, Filip","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Filip","last_name":"Korc"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"citation":{"ieee":"F. Korc, V. Kolmogorov, and C. Lampert, “Approximating marginals using discrete energy minimization,” presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland, 2012.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization. ICML: International Conference on Machine Learning, Inferning 2012, .","ama":"Korc F, Kolmogorov V, Lampert C. Approximating marginals using discrete energy minimization. In: ICML; 2012.","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. “Approximating Marginals Using Discrete Energy Minimization.” ICML, 2012.","apa":"Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals using discrete energy minimization. Presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland: ICML.","short":"F. Korc, V. Kolmogorov, C. Lampert, in:, ICML, 2012.","mla":"Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. ICML, 2012."},"oa_version":"Submitted Version","date_updated":"2023-02-23T12:24:24Z","quality_controlled":"1","department":[{"_id":"ChLa"},{"_id":"VlKo"}],"title":"Approximating marginals using discrete energy minimization","date_published":"2012-06-30T00:00:00Z","file_date_updated":"2020-07-14T12:46:00Z","publisher":"ICML","language":[{"iso":"eng"}],"ddc":["000"],"file":[{"file_name":"IST-2016-565-v1+1_DM-inferning2012.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:11:34Z","date_updated":"2020-07-14T12:46:00Z","file_id":"4889","checksum":"3d0d4246548c736857302aadb2ff5d15","creator":"system","access_level":"open_access","file_size":305836,"relation":"main_file"}],"abstract":[{"lang":"eng","text":"We consider the problem of inference in a graphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pairwise terms over a discretized domain. This allows the use of techniques originally developed for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can outperform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.\r\n"}],"month":"06","has_accepted_license":"1","publication_status":"published"},{"issue":"PART 5","file":[{"content_type":"application/pdf","date_created":"2020-05-15T12:29:04Z","date_updated":"2020-07-14T12:46:00Z","file_name":"2012_ECCV_Sharmanska.pdf","relation":"main_file","file_id":"7861","checksum":"bccdbe0663780d25a1e0524002b2d896","creator":"dernst","access_level":"open_access","file_size":6073897}],"has_accepted_license":"1","month":"10","article_processing_charge":"No","volume":7576,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia","last_name":"Sharmanska","orcid":"0000-0003-0192-9308"},{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"conference":{"end_date":"2012-10-13","start_date":"2012-10-07","name":"ECCV: European Conference on Computer Vision","location":"Florence, Italy"},"_id":"3125","type":"conference","date_created":"2018-12-11T12:01:32Z","status":"public","ddc":["000"],"abstract":[{"text":"We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone.","lang":"eng"}],"publication_status":"published","title":"Augmented attribute representations","file_date_updated":"2020-07-14T12:46:00Z","date_published":"2012-10-01T00:00:00Z","publisher":"Springer","citation":{"ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Augmented attribute representations,” presented at the ECCV: European Conference on Computer Vision, Florence, Italy, 2012, vol. 7576, no. PART 5, pp. 242–255.","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Augmented Attribute Representations,” 7576:242–55. Springer, 2012. https://doi.org/10.1007/978-3-642-33715-4_18.","ista":"Sharmanska V, Quadrianto N, Lampert C. 2012. Augmented attribute representations. ECCV: European Conference on Computer Vision, LNCS, vol. 7576, 242–255.","ama":"Sharmanska V, Quadrianto N, Lampert C. Augmented attribute representations. In: Vol 7576. Springer; 2012:242-255. doi:10.1007/978-3-642-33715-4_18","apa":"Sharmanska, V., Quadrianto, N., & Lampert, C. (2012). Augmented attribute representations (Vol. 7576, pp. 242–255). Presented at the ECCV: European Conference on Computer Vision, Florence, Italy: Springer. https://doi.org/10.1007/978-3-642-33715-4_18","mla":"Sharmanska, Viktoriia, et al. Augmented Attribute Representations. Vol. 7576, no. PART 5, Springer, 2012, pp. 242–55, doi:10.1007/978-3-642-33715-4_18.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 242–255."},"date_updated":"2023-02-23T11:13:25Z","department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 7576","publist_id":"3574","oa":1,"page":"242 - 255","day":"01","year":"2012","doi":"10.1007/978-3-642-33715-4_18"},{"intvolume":" 7476","conference":{"location":"Graz, Austria","name":"DAGM: German Association For Pattern Recognition","start_date":"2012-08-28","end_date":"2012-08-31"},"publist_id":"3573","scopus_import":1,"doi":"10.1007/978-3-642-32717-9_21","status":"public","day":"14","year":"2012","page":"205 - 215","date_created":"2018-12-11T12:01:32Z","type":"conference","_id":"3126","language":[{"iso":"eng"}],"publisher":"Springer","date_published":"2012-08-14T00:00:00Z","volume":7476,"title":"Information theoretic clustering using minimal spanning trees","abstract":[{"text":"In this work we propose a new information-theoretic clustering algorithm that infers cluster memberships by direct optimization of a non-parametric mutual information estimate between data distribution and cluster assignment. Although the optimization objective has a solid theoretical foundation it is hard to optimize. We propose an approximate optimization formulation that leads to an efficient algorithm with low runtime complexity. The algorithm has a single free parameter, the number of clusters to find. We demonstrate superior performance on several synthetic and real datasets.\r\n","lang":"eng"}],"month":"08","publication_status":"published","author":[{"full_name":"Müller, Andreas","first_name":"Andreas","last_name":"Müller"},{"last_name":"Nowozin","first_name":"Sebastian","full_name":"Nowozin, Sebastian"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_updated":"2021-01-12T07:41:14Z","quality_controlled":"1","department":[{"_id":"ChLa"}],"oa_version":"None","citation":{"apa":"Müller, A., Nowozin, S., & Lampert, C. (2012). Information theoretic clustering using minimal spanning trees (Vol. 7476, pp. 205–215). Presented at the DAGM: German Association For Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_21","chicago":"Müller, Andreas, Sebastian Nowozin, and Christoph Lampert. “Information Theoretic Clustering Using Minimal Spanning Trees,” 7476:205–15. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_21.","ama":"Müller A, Nowozin S, Lampert C. Information theoretic clustering using minimal spanning trees. In: Vol 7476. Springer; 2012:205-215. doi:10.1007/978-3-642-32717-9_21","ista":"Müller A, Nowozin S, Lampert C. 2012. Information theoretic clustering using minimal spanning trees. DAGM: German Association For Pattern Recognition, LNCS, vol. 7476, 205–215.","ieee":"A. Müller, S. Nowozin, and C. Lampert, “Information theoretic clustering using minimal spanning trees,” presented at the DAGM: German Association For Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 205–215.","short":"A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 205–215.","mla":"Müller, Andreas, et al. Information Theoretic Clustering Using Minimal Spanning Trees. Vol. 7476, Springer, 2012, pp. 205–15, doi:10.1007/978-3-642-32717-9_21."}},{"date_created":"2018-12-11T12:01:33Z","oa":1,"type":"conference","_id":"3127","day":"01","year":"2012","status":"public","page":"211-218","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1206.4652"}],"scopus_import":"1","conference":{"location":"Edinburgh, United Kingdom","name":"ICML: International Conference on Machine Learning","start_date":"2012-06-26","end_date":"2012-07-01"},"publist_id":"3572","publication":"Proceedings of the 29th International Conference on Machine Learning","department":[{"_id":"ChLa"},{"_id":"HeEd"}],"quality_controlled":"1","date_updated":"2023-10-17T11:55:06Z","citation":{"short":"N. Quadrianto, C. Lampert, C. Chen, in:, Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–218.","mla":"Quadrianto, Novi, et al. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–18.","ieee":"N. Quadrianto, C. Lampert, and C. Chen, “The most persistent soft-clique in a set of sampled graphs,” in Proceedings of the 29th International Conference on Machine Learning, Edinburgh, United Kingdom, 2012, pp. 211–218.","apa":"Quadrianto, N., Lampert, C., & Chen, C. (2012). The most persistent soft-clique in a set of sampled graphs. In Proceedings of the 29th International Conference on Machine Learning (pp. 211–218). Edinburgh, United Kingdom: ML Research Press.","ama":"Quadrianto N, Lampert C, Chen C. The most persistent soft-clique in a set of sampled graphs. In: Proceedings of the 29th International Conference on Machine Learning. ML Research Press; 2012:211-218.","ista":"Quadrianto N, Lampert C, Chen C. 2012. The most persistent soft-clique in a set of sampled graphs. Proceedings of the 29th International Conference on Machine Learning. ICML: International Conference on Machine Learning, 211–218.","chicago":"Quadrianto, Novi, Christoph Lampert, and Chao Chen. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” In Proceedings of the 29th International Conference on Machine Learning, 211–18. ML Research Press, 2012."},"oa_version":"Preprint","author":[{"full_name":"Quadrianto, Novi","last_name":"Quadrianto","first_name":"Novi"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","publication_status":"published","abstract":[{"text":"When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques.\r\n We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations.","lang":"eng"}],"publisher":"ML Research Press","date_published":"2012-06-01T00:00:00Z","language":[{"iso":"eng"}],"title":"The most persistent soft-clique in a set of sampled graphs","article_processing_charge":"No"},{"oa":1,"day":"01","page":"268 - 284","year":"2012","doi":"10.1007/s10703-012-0164-2","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No. S11407-N23(RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, ERC Advanced grant QUAREM, and FWF Grant No. S11403-N23 (RiSE).","scopus_import":1,"publication":"Formal Methods in System Design","intvolume":" 43","publist_id":"3570","citation":{"short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284.","mla":"Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design, vol. 43, no. 2, Springer, 2012, pp. 268–84, doi:10.1007/s10703-012-0164-2.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design. Springer, 2012. https://doi.org/10.1007/s10703-012-0164-2.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2012. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 43(2), 268–284.","ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 2012;43(2):268-284. doi:10.1007/s10703-012-0164-2","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2012). A survey of partial-observation stochastic parity games. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0164-2","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation stochastic parity games,” Formal Methods in System Design, vol. 43, no. 2. Springer, pp. 268–284, 2012."},"date_updated":"2021-01-12T07:41:15Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["005"],"abstract":[{"lang":"eng","text":"We consider two-player zero-sum stochastic games on graphs with ω-regular winning conditions specified as parity objectives. These games have applications in the design and control of reactive systems. We survey the complexity results for the problem of deciding the winner in such games, and in classes of interest obtained as special cases, based on the information and the power of randomization available to the players, on the class of objectives and on the winning mode. On the basis of information, these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have complete view of the game). The one-sided partial-observation games have two important subclasses: the one-player games, known as partial-observation Markov decision processes (POMDPs), and the blind one-player games, known as probabilistic automata. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Finally, various classes of games are obtained by restricting the parity objective to a reachability, safety, Büchi, or coBüchi condition. We also consider several winning modes, such as sure-winning (i.e., all outcomes of a strategy have to satisfy the winning condition), almost-sure winning (i.e., winning with probability 1), limit-sure winning (i.e., winning with probability arbitrarily close to 1), and value-threshold winning (i.e., winning with probability at least ν, where ν is a given rational). "}],"publication_status":"published","title":"A survey of partial-observation stochastic parity games","publisher":"Springer","date_published":"2012-10-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:00Z","type":"journal_article","_id":"3128","date_created":"2018-12-11T12:01:33Z","status":"public","pubrep_id":"303","ec_funded":1,"oa_version":"Submitted Version","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"issue":"2","file":[{"relation":"main_file","creator":"system","file_id":"4882","checksum":"dd3d590f383bb2ac6cfda1489ac1c42a","file_size":163983,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:11:27Z","file_name":"IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf"}],"month":"10","has_accepted_license":"1","volume":43,"language":[{"iso":"eng"}]},{"status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1107.3793","open_access":"1"}],"type":"conference","_id":"3129","date_created":"2018-12-11T12:01:33Z","conference":{"end_date":"2012-07-06","start_date":"2012-07-04","location":"Helsinki, Finland","name":"SWAT: Symposium and Workshops on Algorithm Theory"},"author":[{"first_name":"Oleksiy","last_name":"Busaryev","full_name":"Busaryev, Oleksiy"},{"full_name":"Cabello, Sergio","first_name":"Sergio","last_name":"Cabello"},{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen"},{"first_name":"Tamal","last_name":"Dey","full_name":"Dey, Tamal"},{"full_name":"Wang, Yusu","last_name":"Wang","first_name":"Yusu"}],"oa_version":"Preprint","quality_controlled":"1","volume":7357,"language":[{"iso":"eng"}],"month":"06","year":"2012","day":"19","page":"189 - 200","doi":"10.1007/978-3-642-31155-0_17","oa":1,"arxiv":1,"publist_id":"3569","intvolume":" 7357","scopus_import":1,"alternative_title":["LNCS"],"external_id":{"arxiv":["1107.3793"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. 2012. Annotating simplices with a homology basis and its applications. SWAT: Symposium and Workshops on Algorithm Theory, LNCS, vol. 7357, 189–200.","ama":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. Annotating simplices with a homology basis and its applications. In: Vol 7357. Springer; 2012:189-200. doi:10.1007/978-3-642-31155-0_17","chicago":"Busaryev, Oleksiy, Sergio Cabello, Chao Chen, Tamal Dey, and Yusu Wang. “Annotating Simplices with a Homology Basis and Its Applications,” 7357:189–200. Springer, 2012. https://doi.org/10.1007/978-3-642-31155-0_17.","apa":"Busaryev, O., Cabello, S., Chen, C., Dey, T., & Wang, Y. (2012). Annotating simplices with a homology basis and its applications (Vol. 7357, pp. 189–200). Presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-642-31155-0_17","ieee":"O. Busaryev, S. Cabello, C. Chen, T. Dey, and Y. Wang, “Annotating simplices with a homology basis and its applications,” presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland, 2012, vol. 7357, pp. 189–200.","short":"O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200.","mla":"Busaryev, Oleksiy, et al. Annotating Simplices with a Homology Basis and Its Applications. Vol. 7357, Springer, 2012, pp. 189–200, doi:10.1007/978-3-642-31155-0_17."},"department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:41:15Z","title":"Annotating simplices with a homology basis and its applications","date_published":"2012-06-19T00:00:00Z","publisher":"Springer","publication_status":"published","abstract":[{"lang":"eng","text":"Let K be a simplicial complex and g the rank of its p-th homology group Hp(K) defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and annotate each p-simplex of K with a binary vector of length g with the following property: the annotations, summed over all p-simplices in any p-cycle z, provide the coordinate vector of the homology class [z] in the basis H. The basis and the annotations for all simplices can be computed in O(n ω ) time, where n is the size of K and ω < 2.376 is a quantity so that two n×n matrices can be multiplied in O(n ω ) time. The precomputed annotations permit answering queries about the independence or the triviality of p-cycles efficiently.\r\n\r\nUsing annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing an optimal basis of H1(K) , we improve the previously known time complexity from O(n 4) to O(n ω + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n ω ) + 2 O(g) n 2logn time using annotations.\r\n"}]},{"pubrep_id":"386","date_created":"2018-12-11T12:01:34Z","_id":"3130","type":"journal_article","status":"public","month":"06","has_accepted_license":"1","issue":"6","article_number":"e1002803","file":[{"file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:12:52Z","creator":"system","file_id":"4973","checksum":"f8506fb579eda6fc5613ba9bf421b86a","file_size":2674138,"access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":8,"quality_controlled":"1","oa_version":"Published Version","author":[{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"},{"full_name":"Silander, Olin","first_name":"Olin","last_name":"Silander"}],"scopus_import":1,"intvolume":" 8","publist_id":"3567","publication":"PLoS Genetics","oa":1,"acknowledgement":"We thank Alex Boehm for discussions and comments.","day":"28","year":"2012","doi":"10.1371/journal.pgen.1002803","abstract":[{"text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.","lang":"eng"}],"publication_status":"published","ddc":["576"],"date_published":"2012-06-28T00:00:00Z","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:46:01Z","title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","date_updated":"2021-01-12T07:41:16Z","department":[{"_id":"CaGu"}],"citation":{"ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803.","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.","apa":"Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803","short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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)"}}]