[{"_id":"3113","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T07:41:09Z","citation":{"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.","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.","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.","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","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","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."},"title":"Cell wall constrains lateral diffusion of plant plasma membrane proteins","publist_id":"3586","author":[{"last_name":"Martinière","full_name":"Martinière, Alexandre","first_name":"Alexandre"},{"full_name":"Lavagi, Irene","last_name":"Lavagi","first_name":"Irene"},{"first_name":"Gayathri","last_name":"Nageswaran","full_name":"Nageswaran, Gayathri"},{"first_name":"Daniel","last_name":"Rolfe","full_name":"Rolfe, Daniel J"},{"last_name":"Maneta Peyret","full_name":"Maneta-Peyret, Lilly","first_name":"Lilly"},{"first_name":"Doan","last_name":"Luu","full_name":"Luu, Doan-Trung"},{"first_name":"Stanley","full_name":"Botchway, Stanley W","last_name":"Botchway"},{"full_name":"Webb, Stephen E","last_name":"Webb","first_name":"Stephen"},{"first_name":"Sebastien","full_name":"Mongrand, Sebastien","last_name":"Mongrand"},{"first_name":"Christophe","full_name":"Maurel, 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"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Moreau","full_name":"Moreau, Patrick","first_name":"Patrick"},{"first_name":"John","last_name":"Runions","full_name":"Runions, John"}],"abstract":[{"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.","lang":"eng"}],"intvolume":" 109","month":"07","publisher":"National Academy of Sciences","quality_controlled":0,"publication":"PNAS","day":"31","year":"2012","publication_status":"published","date_created":"2018-12-11T12:01:28Z","volume":109,"date_published":"2012-07-31T00:00:00Z","doi":"10.1073/pnas.1202040109","issue":"31","page":"12805 - 12810"},{"publist_id":"3585","author":[{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"},{"first_name":"Bangjun","last_name":"Wang","full_name":"Wang, Bangjun"},{"last_name":"Moreno","full_name":"Moreno, Ignacio","first_name":"Ignacio"},{"first_name":"Nikoleta","full_name":"Dupláková, Nikoleta","last_name":"Dupláková"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Sibu Simon"},{"full_name":"Carraro, Nicola","last_name":"Carraro","first_name":"Nicola"},{"last_name":"Reemmer","full_name":"Reemmer, Jesica","first_name":"Jesica"},{"full_name":"Pěnčík, Aleš","last_name":"Pěnčík","first_name":"Aleš"},{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Xu Chen"},{"full_name":"Tejos, Ricardo I","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Petr","full_name":"Skůpa, Petr","last_name":"Skůpa"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"last_name":"Mravec","full_name":"Mravec, Jozef","first_name":"Jozef"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"first_name":"David","last_name":"Honys","full_name":"Honys, David"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"full_name":"Murphy, Angus S","last_name":"Murphy","first_name":"Angus"},{"first_name":"Ariel","full_name":"Orellana, Ariel","last_name":"Orellana"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"}],"title":"ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis","date_updated":"2021-01-12T07:41:09Z","citation":{"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.","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.","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).","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","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","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.","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)."},"extern":1,"type":"journal_article","status":"public","_id":"3114","date_created":"2018-12-11T12:01:28Z","doi":"10.1038/ncomms1941","issue":"AN 941","date_published":"2012-07-03T00:00:00Z","volume":3,"year":"2012","publication_status":"published","publication":"Nature Communications","day":"03","quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 3","month":"07","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."}]},{"extern":1,"citation":{"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.","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","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","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.","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.","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."},"date_updated":"2021-01-12T07:41:08Z","title":"A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots","author":[{"first_name":"Deshu","full_name":"Lin, Deshu","last_name":"Lin"},{"full_name":"Nagawa, Shingo","last_name":"Nagawa","first_name":"Shingo"},{"first_name":"Jisheng","full_name":"Chen, Jisheng","last_name":"Chen"},{"first_name":"Lingyan","last_name":"Cao","full_name":"Cao, Lingyan"},{"full_name":"Xu Chen","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"full_name":"Hongjiang Li","orcid":"0000-0001-5039-9660","last_name":"Li","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pankaj","full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe"},{"first_name":"Chizuko","last_name":"Yamamuro","full_name":"Yamamuro, Chizuko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"},{"first_name":"Ying","last_name":"Fu","full_name":"Fu, Ying"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"}],"publist_id":"3588","_id":"3111","status":"public","type":"journal_article","publication":"Current Biology","day":"24","year":"2012","publication_status":"published","date_created":"2018-12-11T12:01:27Z","doi":"10.1016/j.cub.2012.05.019","date_published":"2012-07-24T00:00:00Z","volume":22,"issue":"14","page":"1319 - 1325","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"}],"intvolume":" 22","month":"07","quality_controlled":0,"publisher":"Cell Press"},{"citation":{"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.","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.","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.","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.","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","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"},"date_updated":"2021-01-12T07:41:08Z","extern":1,"publist_id":"3587","author":[{"last_name":"Chen","full_name":"Xu Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Christian","last_name":"Löfke","full_name":"Löfke, Christian"},{"first_name":"Deshu","last_name":"Lin","full_name":"Lin, Deshu"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"}],"title":"ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots","_id":"3112","type":"journal_article","status":"public","publication_status":"published","year":"2012","publication":"Current Biology","day":"24","page":"1326 - 1332","date_created":"2018-12-11T12:01:27Z","doi":"10.1016/j.cub.2012.05.020","volume":22,"date_published":"2012-07-24T00:00:00Z","issue":"14","abstract":[{"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.","lang":"eng"}],"publisher":"Cell Press","quality_controlled":0,"intvolume":" 22","month":"07"},{"oa_version":"Submitted Version","abstract":[{"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). ","lang":"eng"}],"month":"10","intvolume":" 43","scopus_import":1,"file":[{"file_id":"4882","checksum":"dd3d590f383bb2ac6cfda1489ac1c42a","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:11:27Z","file_name":"IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf","date_updated":"2020-07-14T12:46:00Z","file_size":163983,"creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":43,"issue":"2","ec_funded":1,"_id":"3128","status":"public","pubrep_id":"303","type":"journal_article","ddc":["005"],"date_updated":"2021-01-12T07:41:15Z","file_date_updated":"2020-07-14T12:46:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"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).","quality_controlled":"1","publisher":"Springer","oa":1,"day":"01","publication":"Formal Methods in System Design","has_accepted_license":"1","year":"2012","date_published":"2012-10-01T00:00:00Z","doi":"10.1007/s10703-012-0164-2","date_created":"2018-12-11T12:01:33Z","page":"268 - 284","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 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","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."},"title":"A survey of partial-observation stochastic parity games","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"publist_id":"3570"},{"has_accepted_license":"1","year":"2012","day":"01","page":"242 - 255","doi":"10.1007/978-3-642-33715-4_18","date_published":"2012-10-01T00:00:00Z","date_created":"2018-12-11T12:01:32Z","publisher":"Springer","quality_controlled":"1","oa":1,"citation":{"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.","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.","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.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3574","author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","last_name":"Sharmanska","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"article_processing_charge":"No","title":"Augmented attribute representations","publication_status":"published","file":[{"date_updated":"2020-07-14T12:46:00Z","file_size":6073897,"creator":"dernst","date_created":"2020-05-15T12:29:04Z","file_name":"2012_ECCV_Sharmanska.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"bccdbe0663780d25a1e0524002b2d896","file_id":"7861"}],"language":[{"iso":"eng"}],"issue":"PART 5","volume":7576,"abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"month":"10","intvolume":" 7576","date_updated":"2023-02-23T11:13:25Z","ddc":["000"],"file_date_updated":"2020-07-14T12:46:00Z","department":[{"_id":"ChLa"}],"_id":"3125","type":"conference","conference":{"name":"ECCV: European Conference on Computer Vision","end_date":"2012-10-13","location":"Florence, Italy","start_date":"2012-10-07"},"status":"public"},{"volume":7357,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 7357","month":"06","main_file_link":[{"url":"http://arxiv.org/abs/1107.3793","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"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","lang":"eng"}],"department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:41:15Z","status":"public","conference":{"start_date":"2012-07-04","location":"Helsinki, Finland","end_date":"2012-07-06","name":"SWAT: Symposium and Workshops on Algorithm Theory"},"type":"conference","_id":"3129","date_created":"2018-12-11T12:01:33Z","date_published":"2012-06-19T00:00:00Z","doi":"10.1007/978-3-642-31155-0_17","page":"189 - 200","day":"19","year":"2012","oa":1,"quality_controlled":"1","publisher":"Springer","title":"Annotating simplices with a homology basis and its applications","external_id":{"arxiv":["1107.3793"]},"publist_id":"3569","author":[{"full_name":"Busaryev, Oleksiy","last_name":"Busaryev","first_name":"Oleksiy"},{"full_name":"Cabello, Sergio","last_name":"Cabello","first_name":"Sergio"},{"last_name":"Chen","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"full_name":"Dey, Tamal","last_name":"Dey","first_name":"Tamal"},{"first_name":"Yusu","full_name":"Wang, Yusu","last_name":"Wang"}],"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.","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.","short":"O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200.","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.","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","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","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."}},{"oa_version":"None","abstract":[{"lang":"eng","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"}],"intvolume":" 7476","month":"08","quality_controlled":"1","alternative_title":["LNCS"],"publisher":"Springer","scopus_import":1,"language":[{"iso":"eng"}],"day":"14","year":"2012","publication_status":"published","date_created":"2018-12-11T12:01:32Z","doi":"10.1007/978-3-642-32717-9_21","volume":7476,"date_published":"2012-08-14T00:00:00Z","page":"205 - 215","_id":"3126","status":"public","conference":{"location":"Graz, Austria","end_date":"2012-08-31","start_date":"2012-08-28","name":"DAGM: German Association For Pattern Recognition"},"type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","short":"A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 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."},"date_updated":"2021-01-12T07:41:14Z","department":[{"_id":"ChLa"}],"title":"Information theoretic clustering using minimal spanning trees","publist_id":"3573","author":[{"full_name":"Müller, Andreas","last_name":"Müller","first_name":"Andreas"},{"first_name":"Sebastian","last_name":"Nowozin","full_name":"Nowozin, Sebastian"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}]},{"volume":7273,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:11:25Z","file_name":"IST-2012-88-v1+1_Synchronous_interface_theories_and_time_triggered_scheduling.pdf","date_updated":"2020-07-14T12:46:01Z","file_size":493198,"creator":"system","file_id":"4879","checksum":"feae2e07f2d9a59843f8ddabf25d179f","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":" 7273","month":"06","alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"We propose synchronous interfaces, a new interface theory for discrete-time systems. We use an application to time-triggered scheduling to drive the design choices for our formalism; in particular, additionally to deriving useful mathematical properties, we focus on providing a syntax which is adapted to natural high-level system modeling. As a result, we develop an interface model that relies on a guarded-command based language and is equipped with shared variables and explicit discrete-time clocks. We define all standard interface operations: compatibility checking, composition, refinement, and shared refinement. Apart from the synchronous interface model, the contribution of this paper is the establishment of a formal relation between interface theories and real-time scheduling, where we demonstrate a fully automatic framework for the incremental computation of time-triggered schedules.","lang":"eng"}],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:01Z","ddc":["004"],"date_updated":"2021-01-12T07:41:26Z","pubrep_id":"88","status":"public","conference":{"name":"FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems ","end_date":"2012-06-16","location":"Stockholm, Sweden","start_date":"2012-06-13"},"type":"conference","_id":"3155","date_created":"2018-12-11T12:01:43Z","doi":"10.1007/978-3-642-30793-5_13","date_published":"2012-06-01T00:00:00Z","page":"203 - 218","day":"01","year":"2012","has_accepted_license":"1","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"Research partially supported by the Danish-Chinese Center for Cyber Physical Systems (Grant No.61061130541) and VKR Center of Excellence MT-LAB.","title":"Synchronous interface theories and time triggered scheduling","author":[{"full_name":"Delahaye, Benoît","last_name":"Delahaye","first_name":"Benoît"},{"full_name":"Fahrenberg, Uli","last_name":"Fahrenberg","first_name":"Uli"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3539","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Delahaye, Benoît, et al. Synchronous Interface Theories and Time Triggered Scheduling. Vol. 7273, Springer, 2012, pp. 203–18, doi:10.1007/978-3-642-30793-5_13.","short":"B. Delahaye, U. Fahrenberg, T.A. Henzinger, A. Legay, D. Nickovic, in:, Springer, 2012, pp. 203–218.","ieee":"B. Delahaye, U. Fahrenberg, T. A. Henzinger, A. Legay, and D. Nickovic, “Synchronous interface theories and time triggered scheduling,” presented at the FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden, 2012, vol. 7273, pp. 203–218.","ama":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. Synchronous interface theories and time triggered scheduling. In: Vol 7273. Springer; 2012:203-218. doi:10.1007/978-3-642-30793-5_13","apa":"Delahaye, B., Fahrenberg, U., Henzinger, T. A., Legay, A., & Nickovic, D. (2012). Synchronous interface theories and time triggered scheduling (Vol. 7273, pp. 203–218). Presented at the FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden: Springer. https://doi.org/10.1007/978-3-642-30793-5_13","chicago":"Delahaye, Benoît, Uli Fahrenberg, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Synchronous Interface Theories and Time Triggered Scheduling,” 7273:203–18. Springer, 2012. https://doi.org/10.1007/978-3-642-30793-5_13.","ista":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. 2012. Synchronous interface theories and time triggered scheduling. FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , LNCS, vol. 7273, 203–218."}},{"article_number":"e36715","title":"Hierarchical ordering of reticular networks","author":[{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Charles","full_name":"Price, Charles","last_name":"Price"},{"first_name":"Joshua","last_name":"Weitz","full_name":"Weitz, Joshua"}],"publist_id":"3530","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering of reticular networks,” PLoS One, vol. 7, no. 6. Public Library of Science, 2012.","short":"Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).","ama":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular networks. PLoS One. 2012;7(6). doi:10.1371/journal.pone.0036715","apa":"Mileyko, Y., Edelsbrunner, H., Price, C., & Weitz, J. (2012). Hierarchical ordering of reticular networks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036715","mla":"Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” PLoS One, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:10.1371/journal.pone.0036715.","ista":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of reticular networks. PLoS One. 7(6), e36715.","chicago":"Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz. “Hierarchical Ordering of Reticular Networks.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036715."},"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"his work was supported by the National Science Foundation Plant Genome Research Program (grant 0820624 to H.E. and J.S.W.), the Defense Advanced Projects Research Agency (grant HR0011-09-1-0055 to H.E. and J.S.W.), and the European Science Foundation (under the Research Networking Programme on “Applied and Computational Algebraic Topology” run by H.E.). Joshua S. Weitz, Ph.D., holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.\r\n\r\n\r\n\r\nDuring preparation of this manuscript the authors became aware of a related work by Katifori and Magnasco (arXiv:1110.1412v1), concurrently submitted and accepted for publication in PLoS ONE.","date_created":"2018-12-11T12:01:44Z","doi":"10.1371/journal.pone.0036715","date_published":"2012-06-06T00:00:00Z","publication":"PLoS One","day":"06","year":"2012","has_accepted_license":"1","pubrep_id":"385","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"3159","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:01Z","ddc":["510"],"date_updated":"2021-01-12T07:41:28Z","intvolume":" 7","month":"06","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"The structure of hierarchical networks in biological and physical systems has long been characterized using the Horton-Strahler ordering scheme. The scheme assigns an integer order to each edge in the network based on the topology of branching such that the order increases from distal parts of the network (e.g., mountain streams or capillaries) to the "root" of the network (e.g., the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied to networks with loops because they they create a contradiction in the edge ordering in terms of which edge precedes another in the hierarchy. Here, we present a generalization of the Horton-Strahler order to weighted planar reticular networks, where weights are assumed to correlate with the importance of network edges, e.g., weights estimated from edge widths may correlate to flow capacity. Our method assigns hierarchical levels not only to edges of the network, but also to its loops, and classifies the edges into reticular edges, which are responsible for loop formation, and tree edges. In addition, we perform a detailed and rigorous theoretical analysis of the sensitivity of the hierarchical levels to weight perturbations. In doing so, we show that the ordering of the reticular edges is more robust to noise in weight estimation than is the ordering of the tree edges. We discuss applications of this generalized Horton-Strahler ordering to the study of leaf venation and other biological networks.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","issue":"6","volume":7,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-05T12:38:43Z","file_name":"2012_PLoS_Mileyko.PDF","date_updated":"2020-07-14T12:46:01Z","file_size":541583,"creator":"kschuh","file_id":"5922","checksum":"515a98ad72e470752f03f13663dcaff8","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published"},{"status":"public","type":"journal_article","_id":"3156","department":[{"_id":"SyCr"}],"title":"Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion","author":[{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883"},{"first_name":"Anne","full_name":"Andersen, Anne","last_name":"Andersen"},{"last_name":"Boomsma","full_name":"Boomsma, Jacobus","first_name":"Jacobus"},{"last_name":"Nash","full_name":"Nash, David","first_name":"David"}],"publist_id":"3538","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Ugelvig, L. V., Andersen, A., Boomsma, J., & Nash, D. (2012). Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05592.x","ama":"Ugelvig LV, Andersen A, Boomsma J, Nash D. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 2012;21(13):3224-3236. doi:10.1111/j.1365-294X.2012.05592.x","ieee":"L. V. Ugelvig, A. Andersen, J. Boomsma, and D. Nash, “Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion,” Molecular Ecology, vol. 21, no. 13. Wiley-Blackwell, pp. 3224–3236, 2012.","short":"L.V. Ugelvig, A. Andersen, J. Boomsma, D. Nash, Molecular Ecology 21 (2012) 3224–3236.","mla":"Ugelvig, Line V., et al. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology, vol. 21, no. 13, Wiley-Blackwell, 2012, pp. 3224–36, doi:10.1111/j.1365-294X.2012.05592.x.","ista":"Ugelvig LV, Andersen A, Boomsma J, Nash D. 2012. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 21(13), 3224–3236.","chicago":"Ugelvig, Line V, Anne Andersen, Jacobus Boomsma, and David Nash. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05592.x."},"date_updated":"2021-01-12T07:41:27Z","intvolume":" 21","month":"07","scopus_import":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","acknowledgement":"The work was financed by the Danish National Science Research Foundation via a grant to the Centre for Social Evolution.\r\nWe thank four anonymous reviewers for useful comments on the manuscript, J. Bergsten, P. Bina, B. Carlsson, M. Johannesson and A.E. Lomborg for providing additional wingtip samples, A. Illum for assistance in the field, and in particular P.S. Nielsen for mediating the contact to the collectors and the Swedish authorities. Collection was made possible through a permit by the Åtgärdsprogrammet, supported by the Swedish Environmental Protection Agency.","oa_version":"None","abstract":[{"text":"Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km.","lang":"eng"}],"date_created":"2018-12-11T12:01:43Z","volume":21,"date_published":"2012-07-01T00:00:00Z","issue":"13","doi":"10.1111/j.1365-294X.2012.05592.x","page":"3224 - 3236","language":[{"iso":"eng"}],"publication":"Molecular Ecology","day":"01","publication_status":"published","year":"2012"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S., … Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2012.04.002","ama":"Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 2012;91(11-12):923-929. doi:10.1016/j.ejcb.2012.04.002","ieee":"H. Schachtner et al., “Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo,” European Journal of Cell Biology, vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.","short":"H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K. Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell Biology 91 (2012) 923–929.","mla":"Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology, vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:10.1016/j.ejcb.2012.04.002.","ista":"Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK, Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 91(11–12), 923–929.","chicago":"Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas, Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ejcb.2012.04.002."},"title":"Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo","external_id":{"pmid":["22658956"]},"publist_id":"3534","author":[{"first_name":"Hannah","last_name":"Schachtner","full_name":"Schachtner, Hannah"},{"first_name":"Ang","full_name":"Li, Ang","last_name":"Li"},{"last_name":"Stevenson","full_name":"Stevenson, David","first_name":"David"},{"first_name":"Simon","last_name":"Calaminus","full_name":"Calaminus, Simon"},{"full_name":"Thomas, Steven","last_name":"Thomas","first_name":"Steven"},{"last_name":"Watson","full_name":"Watson, Steve","first_name":"Steve"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"Roland","full_name":"Wedlich Söldner, Roland","last_name":"Wedlich Söldner"},{"first_name":"Douglas","full_name":"Strathdee, Douglas","last_name":"Strathdee"},{"last_name":"Machesky","full_name":"Machesky, Laura","first_name":"Laura"}],"publication":"European Journal of Cell Biology","day":"01","year":"2012","date_created":"2018-12-11T12:01:44Z","date_published":"2012-11-01T00:00:00Z","doi":"10.1016/j.ejcb.2012.04.002","page":"923 - 929","oa":1,"quality_controlled":"1","publisher":"Elsevier","date_updated":"2021-01-12T07:41:27Z","department":[{"_id":"MiSi"}],"_id":"3158","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"11-12","volume":91,"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment.","lang":"eng"}],"intvolume":" 91","month":"11","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/"}],"scopus_import":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 7(1), 31–41.","chicago":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing. Springer, 2012. https://doi.org/10.1007/s11554-010-0168-3.","ieee":"C. Lampert and J. Peters, “Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components,” Journal of Real-Time Image Processing, vol. 7, no. 1. Springer, pp. 31–41, 2012.","short":"C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.","apa":"Lampert, C., & Peters, J. (2012). Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. Springer. https://doi.org/10.1007/s11554-010-0168-3","ama":"Lampert C, Peters J. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 2012;7(1):31-41. doi:10.1007/s11554-010-0168-3","mla":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:10.1007/s11554-010-0168-3."},"title":"Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components","author":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peters, Jan","last_name":"Peters","first_name":"Jan"}],"publist_id":"3417","article_processing_charge":"No","publisher":"Springer","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Real-Time Image Processing","has_accepted_license":"1","year":"2012","date_published":"2012-03-01T00:00:00Z","doi":"10.1007/s11554-010-0168-3","date_created":"2018-12-11T12:02:15Z","page":"31 - 41","_id":"3248","status":"public","type":"journal_article","article_type":"original","ddc":["000"],"date_updated":"2022-05-24T08:05:40Z","file_date_updated":"2020-07-14T12:46:04Z","department":[{"_id":"ChLa"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz."}],"month":"03","intvolume":" 7","scopus_import":"1","file":[{"file_id":"5958","checksum":"241be47ea50e81a283bcf4c45b07e8cc","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2012_Springer_Lampert.pdf","date_created":"2019-02-12T10:52:25Z","creator":"kschuh","file_size":2933187,"date_updated":"2020-07-14T12:46:04Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1861-8219"],"issn":["1861-8200"]},"publication_status":"published","issue":"1","volume":7},{"year":"2012","publication_status":"published","publication":"Conservation Genetics","language":[{"iso":"eng"}],"day":"01","page":"293 - 298","date_created":"2018-12-11T12:02:15Z","issue":"1","doi":"10.1007/s10592-011-0262-5","date_published":"2012-02-01T00:00:00Z","volume":13,"abstract":[{"lang":"eng","text":"The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species."}],"acknowledgement":"The present study received grants from FAPEMIG, CNPq, Petrobras Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all ethical guidelines and legal requirements of Brazil for sampling and studying an endangered species.\r\nWe thank the Specialist Work Group for the Conservation of Brazilian Merganser for valuable discussions and opinions on this manuscript. We also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing the samples from Argentina, Bradley C. Livezey for sending copies of his papers, and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly improved this manuscript.","oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"Springer","intvolume":" 13","month":"02","citation":{"ieee":"S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics, vol. 13, no. 1. Springer, pp. 293–298, 2012.","short":"S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298.","apa":"Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5","ama":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298. doi:10.1007/s10592-011-0262-5","mla":"Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:10.1007/s10592-011-0262-5.","ista":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 13(1), 293–298.","chicago":"Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5."},"date_updated":"2021-01-12T07:42:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3420","author":[{"last_name":"Vilaça","full_name":"Vilaça, Sibelle","first_name":"Sibelle"},{"last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A"},{"last_name":"Lins","full_name":"Lins, Lívia","first_name":"Lívia"},{"first_name":"Fabrício","last_name":"Santos","full_name":"Santos, Fabrício"}],"title":"Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)","department":[{"_id":"JoBo"}],"_id":"3247","type":"journal_article","status":"public"},{"quality_controlled":"1","scopus_import":1,"publisher":"Cell Press","month":"01","intvolume":" 22","abstract":[{"text":"How cells orchestrate their behavior during collective migration is a long-standing question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated mechanosensitive response that promotes cell polarization and movement persistence during the collective mesendoderm migration in gastrulation.","lang":"eng"}],"oa_version":"None","page":"3 - 4","date_published":"2012-01-17T00:00:00Z","volume":22,"doi":"10.1016/j.devcel.2011.12.018","issue":"1","date_created":"2018-12-11T12:02:14Z","year":"2012","publication_status":"published","day":"17","language":[{"iso":"eng"}],"publication":"Developmental Cell","type":"journal_article","status":"public","_id":"3245","author":[{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"publist_id":"3426","title":"Spurred by resistance mechanosensation in collective migration","department":[{"_id":"CaHe"}],"citation":{"short":"M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 22 (2012) 3–4.","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Spurred by resistance mechanosensation in collective migration,” Developmental Cell, vol. 22, no. 1. Cell Press, pp. 3–4, 2012.","ama":"Behrndt M, Heisenberg C-PJ. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 2012;22(1):3-4. doi:10.1016/j.devcel.2011.12.018","apa":"Behrndt, M., & Heisenberg, C.-P. J. (2012). Spurred by resistance mechanosensation in collective migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.12.018","mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell, vol. 22, no. 1, Cell Press, 2012, pp. 3–4, doi:10.1016/j.devcel.2011.12.018.","ista":"Behrndt M, Heisenberg C-PJ. 2012. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 22(1), 3–4.","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2011.12.018."},"date_updated":"2021-01-12T07:42:05Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"article_number":"041903","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903","apa":"Tkačik, G., Walczak, A., & Bialek, W. (2012). Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.85.041903","short":"G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012).","ieee":"G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks. III. A self-interacting gene,” Physical Review E statistical nonlinear and soft matter physics , vol. 85, no. 4. American Institute of Physics, 2012.","mla":"Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 85, no. 4, 041903, American Institute of Physics, 2012, doi:10.1103/PhysRevE.85.041903.","ista":"Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 85(4), 041903.","chicago":"Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2012. https://doi.org/10.1103/PhysRevE.85.041903."},"title":"Optimizing information flow in small genetic networks. III. A self-interacting gene","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Walczak","full_name":"Walczak, Aleksandra","first_name":"Aleksandra"},{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"}],"publist_id":"3386","acknowledgement":"We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W. M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania.","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","publication":" Physical Review E statistical nonlinear and soft matter physics ","day":"01","year":"2012","date_created":"2018-12-11T12:02:20Z","date_published":"2012-04-01T00:00:00Z","doi":"10.1103/PhysRevE.85.041903","_id":"3262","status":"public","type":"journal_article","date_updated":"2021-01-12T07:42:14Z","department":[{"_id":"GaTk"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point."}],"intvolume":" 85","month":"04","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1112.5026"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":85},{"department":[{"_id":"VlKo"}],"date_updated":"2023-02-23T11:04:49Z","status":"public","type":"journal_article","_id":"3257","volume":160,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2934"}]},"issue":"4-5","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 160","month":"03","main_file_link":[{"url":"http://arxiv.org/abs/1005.2305","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"Consider a convex relaxation f̂ of a pseudo-Boolean function f. We say that the relaxation is totally half-integral if f̂(x) is a polyhedral function with half-integral extreme points x, and this property is preserved after adding an arbitrary combination of constraints of the form x i=x j, x i=1-x j, and x i=γ where γ∈{0,1,1/2} is a constant. A well-known example is the roof duality relaxation for quadratic pseudo-Boolean functions f. We argue that total half-integrality is a natural requirement for generalizations of roof duality to arbitrary pseudo-Boolean functions. Our contributions are as follows. First, we provide a complete characterization of totally half-integral relaxations f̂ by establishing a one-to-one correspondence with bisubmodular functions. Second, we give a new characterization of bisubmodular functions. Finally, we show some relationships between general totally half-integral relaxations and relaxations based on the roof duality. On the conceptual level, our results show that bisubmodular functions provide a natural generalization of the roof duality approach to higher-order terms. This can be viewed as a non-submodular analogue of the fact that submodular functions generalize the s-t minimum cut problem with non-negative weights to higher-order terms.","lang":"eng"}],"title":"Generalized roof duality and bisubmodular functions","external_id":{"arxiv":["1005.2305"]},"publist_id":"3397","author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics, vol. 160, no. 4–5, Elsevier, 2012, pp. 416–26, doi:10.1016/j.dam.2011.10.026.","ama":"Kolmogorov V. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 2012;160(4-5):416-426. doi:10.1016/j.dam.2011.10.026","apa":"Kolmogorov, V. (2012). Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2011.10.026","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 416–426.","ieee":"V. Kolmogorov, “Generalized roof duality and bisubmodular functions,” Discrete Applied Mathematics, vol. 160, no. 4–5. Elsevier, pp. 416–426, 2012.","chicago":"Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2011.10.026.","ista":"Kolmogorov V. 2012. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 160(4–5), 416–426."},"date_created":"2018-12-11T12:02:18Z","date_published":"2012-03-01T00:00:00Z","doi":"10.1016/j.dam.2011.10.026","page":"416 - 426","publication":"Discrete Applied Mathematics","day":"01","year":"2012","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"oa_version":"None","abstract":[{"lang":"eng","text":"The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons."}],"month":"01","intvolume":" 24","publisher":"Springer","alternative_title":["Cellular Origin, Life in Extreme Habitats and Astrobiology"],"quality_controlled":"1","day":"01","language":[{"iso":"eng"}],"publication":"Life on Earth and other planetary bodies","year":"2012","publication_status":"published","date_published":"2012-01-01T00:00:00Z","volume":24,"doi":"10.1007/978-94-007-4966-5_22","date_created":"2018-12-11T12:02:25Z","page":"387 - 405","_id":"3277","status":"public","type":"book_chapter","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22.","short":"H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, Springer, 2012, pp. 387–405.","ieee":"H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be anticipated in the exploration of the solar system?,” in Life on Earth and other planetary bodies, vol. 24, Springer, 2012, pp. 387–405.","ama":"de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and Other Planetary Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22","apa":"de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity be anticipated in the exploration of the solar system? In Life on Earth and other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22","chicago":"Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” In Life on Earth and Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22.","ista":"de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and other planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol. 24, 387–405."},"date_updated":"2021-01-12T07:42:20Z","department":[{"_id":"NiBa"}],"title":"Can the evolution of multicellularity be anticipated in the exploration of the solar system?","publist_id":"3369","author":[{"full_name":"de Vladar, Harold","orcid":"0000-0002-5985-7653","last_name":"de Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"},{"full_name":"Chela Flores, Julian","last_name":"Chela Flores","first_name":"Julian"}]},{"acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)","publisher":"Springer","quality_controlled":"1","day":"04","year":"2012","date_published":"2012-05-04T00:00:00Z","doi":"10.1007/978-3-642-28914-9_21","date_created":"2018-12-11T12:02:25Z","page":"369 - 382","project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Jain A, Pietrzak KZ, Tentes A. 2012. Hardness preserving constructions of pseudorandom functions. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 369–382.","chicago":"Jain, Abhishek, Krzysztof Z Pietrzak, and Aris Tentes. “Hardness Preserving Constructions of Pseudorandom Functions,” 7194:369–82. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_21.","ama":"Jain A, Pietrzak KZ, Tentes A. Hardness preserving constructions of pseudorandom functions. In: Vol 7194. Springer; 2012:369-382. doi:10.1007/978-3-642-28914-9_21","apa":"Jain, A., Pietrzak, K. Z., & Tentes, A. (2012). Hardness preserving constructions of pseudorandom functions (Vol. 7194, pp. 369–382). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_21","short":"A. Jain, K.Z. Pietrzak, A. Tentes, in:, Springer, 2012, pp. 369–382.","ieee":"A. Jain, K. Z. Pietrzak, and A. Tentes, “Hardness preserving constructions of pseudorandom functions,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 369–382.","mla":"Jain, Abhishek, et al. Hardness Preserving Constructions of Pseudorandom Functions. Vol. 7194, Springer, 2012, pp. 369–82, doi:10.1007/978-3-642-28914-9_21."},"title":"Hardness preserving constructions of pseudorandom functions","author":[{"first_name":"Abhishek","last_name":"Jain","full_name":"Jain, Abhishek"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"first_name":"Aris","full_name":"Tentes, Aris","last_name":"Tentes"}],"publist_id":"3367","oa_version":"None","abstract":[{"text":"We show a hardness-preserving construction of a PRF from any length doubling PRG which improves upon known constructions whenever we can put a non-trivial upper bound q on the number of queries to the PRF. Our construction requires only O(logq) invocations to the underlying PRG with each query. In comparison, the number of invocations by the best previous hardness-preserving construction (GGM using Levin's trick) is logarithmic in the hardness of the PRG. For example, starting from an exponentially secure PRG {0,1} n → {0,1} 2n, we get a PRF which is exponentially secure if queried at most q = exp(√n)times and where each invocation of the PRF requires Θ(√n) queries to the underlying PRG. This is much less than the Θ(n) required by known constructions. \r\n","lang":"eng"}],"month":"05","intvolume":" 7194","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://www.iacr.org/archive/tcc2012/tcc2012-index.html"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7194,"ec_funded":1,"_id":"3279","status":"public","type":"conference","conference":{"name":"TCC: Theory of Cryptography Conference","location":"Taormina, Sicily, Italy","end_date":"2012-03-21","start_date":"2012-03-19"},"date_updated":"2021-01-12T07:42:21Z","department":[{"_id":"KrPi"}]},{"abstract":[{"lang":"eng","text":"A boundary element model of a tunnel running through horizontally layered soil with anisotropic material properties is presented. Since there is no analytical fundamental solution for wave propagation inside a layered orthotropic medium in 3D, the fundamental displacements and stresses have to be calculated numerically. In our model this is done in the Fourier domain with respect to space and time. The assumption of a straight tunnel with infinite extension in the x direction makes it possible to decouple the system for every wave number kx, leading to a 2.5D-problem, which is suited for parallel computation. The special form of the fundamental solution, resulting from our Fourier ansatz, and the fact, that the calculation of the boundary integral equation is performed in the Fourier domain, enhances the stability and efficiency of the numerical calculations."}],"oa_version":"None","acknowledgement":"This work was supported by the Austrian Federal Ministry of Transport, Innovation and Technology under the Grant Bmvit-isb2 and the FFG under the project Pr. Nr. 809089.","quality_controlled":"1","scopus_import":1,"publisher":"Elsevier","month":"06","intvolume":" 36","year":"2012","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":" Engineering Analysis with Boundary Elements","page":"960 - 967","issue":"6","volume":36,"doi":"10.1016/j.enganabound.2011.12.014","date_published":"2012-06-01T00:00:00Z","date_created":"2018-12-11T12:02:24Z","_id":"3274","type":"journal_article","status":"public","citation":{"mla":"Rieckh, Georg, et al. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements, vol. 36, no. 6, Elsevier, 2012, pp. 960–67, doi:10.1016/j.enganabound.2011.12.014.","ieee":"G. Rieckh, W. Kreuzer, H. Waubke, and P. Balazs, “A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil,” Engineering Analysis with Boundary Elements, vol. 36, no. 6. Elsevier, pp. 960–967, 2012.","short":"G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs, Engineering Analysis with Boundary Elements 36 (2012) 960–967.","apa":"Rieckh, G., Kreuzer, W., Waubke, H., & Balazs, P. (2012). A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. Elsevier. https://doi.org/10.1016/j.enganabound.2011.12.014","ama":"Rieckh G, Kreuzer W, Waubke H, Balazs P. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 2012;36(6):960-967. doi:10.1016/j.enganabound.2011.12.014","chicago":"Rieckh, Georg, Wolfgang Kreuzer, Holger Waubke, and Peter Balazs. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements. Elsevier, 2012. https://doi.org/10.1016/j.enganabound.2011.12.014.","ista":"Rieckh G, Kreuzer W, Waubke H, Balazs P. 2012. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 36(6), 960–967."},"date_updated":"2021-01-12T07:42:19Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","last_name":"Rieckh"},{"full_name":"Kreuzer, Wolfgang","last_name":"Kreuzer","first_name":"Wolfgang"},{"full_name":"Waubke, Holger","last_name":"Waubke","first_name":"Holger"},{"first_name":"Peter","last_name":"Balazs","full_name":"Balazs, Peter"}],"publist_id":"3372","department":[{"_id":"GaTk"}],"title":"A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil"}]