@article{2952, abstract = {Body axis elongation represents a common and fundamental morphogenetic process in development. A key mechanism triggering body axis elongation without additional growth is convergent extension (CE), whereby a tissue undergoes simultaneous narrowing and extension. Both collective cell migration and cell intercalation are thought to drive CE and are used to different degrees in various species as they elongate their body axis. Here, we provide an overview of CE as a general strategy for body axis elongation and discuss conserved and divergent mechanisms underlying CE among different species.}, author = {Tada, Masazumi and Heisenberg, Carl-Philipp J}, journal = {Development}, number = {21}, pages = {3897 -- 3904}, publisher = {Company of Biologists}, title = {{Convergent extension Using collective cell migration and cell intercalation to shape embryos}}, doi = {10.1242/dev.073007}, volume = {139}, year = {2012}, } @article{2953, author = {Heisenberg, Carl-Philipp J and Fässler, Reinhard}, journal = {Current Opinion in Cell Biology}, number = {5}, pages = {559 -- 561}, publisher = {Elsevier}, title = {{Cell-cell adhesion and extracellular matrix diversity counts}}, doi = {10.1016/j.ceb.2012.09.002}, volume = {24}, year = {2012}, } @article{2958, abstract = {The activity of hippocampal pyramidal cells reflects both the current position of the animal and information related to its current behavior. Here we investigated whether single hippocampal neurons can encode several independent features defining trials during a memory task. We also tested whether task-related information is represented by partial remapping of the place cell population or, instead, via firing rate modulation of spatially stable place cells. To address these two questions, the activity of hippocampal neurons was recorded in rats performing a conditional discrimination task on a modified T-maze in which the identity of a food reward guided behavior. When the rat was on the central arm of the maze, the firing rate of pyramidal cells changed depending on two independent factors: (1) the identity of the food reward given to the animal and (2) the previous location of the animal on the maze. Importantly, some pyramidal cells encoded information relative to both factors. This trial-type specific and retrospective coding did not interfere with the spatial representation of the maze: hippocampal cells had stable place fields and their theta-phase precession profiles were unaltered during the task, indicating that trial-related information was encoded via rate remapping. During error trials, encoding of both trial-related information and spatial location was impaired. Finally, we found that pyramidal cells also encode trial-related information via rate remapping during the continuous version of the rewarded alternation task without delays. These results suggest that hippocampal neurons can encode several task-related cognitive aspects via rate remapping.}, author = {Allen, Kevin and Rawlins, J Nick and Bannerman, David and Csicsvari, Jozsef L}, journal = {Journal of Neuroscience}, number = {42}, pages = {14752 -- 14766}, publisher = {Society for Neuroscience}, title = {{Hippocampal place cells can encode multiple trial-dependent features through rate remapping}}, doi = {10.1523/JNEUROSCI.6175-11.2012}, volume = {32}, year = {2012}, } @article{2959, abstract = {We study maximum likelihood estimation in Gaussian graphical models from a geometric point of view. An algebraic elimination criterion allows us to find exact lower bounds on the number of observations needed to ensure that the maximum likelihood estimator (MLE) exists with probability one. This is applied to bipartite graphs, grids and colored graphs. We also study the ML degree, and we present the first instance of a graph for which the MLE exists with probability one, even when the number of observations equals the treewidth.}, author = {Uhler, Caroline}, journal = {Annals of Statistics}, number = {1}, pages = {238 -- 261}, publisher = {Institute of Mathematical Statistics}, title = {{Geometry of maximum likelihood estimation in Gaussian graphical models}}, doi = {10.1214/11-AOS957}, volume = {40}, year = {2012}, } @article{2966, abstract = {Background: The outcome of male-male competition can be predicted from the relative fighting qualities of the opponents, which often depend on their age. In insects, freshly emerged and still sexually inactive males are morphologically indistinct from older, sexually active males. These young inactive males may thus be easy targets for older males if they cannot conceal themselves from their attacks. The ant Cardiocondyla obscurior is characterised by lethal fighting between wingless (" ergatoid" ) males. Here, we analyse for how long young males are defenceless after eclosion, and how early adult males can detect the presence of rival males.Results: We found that old ergatoid males consistently won fights against ergatoid males younger than two days. Old males did not differentiate between different types of unpigmented pupae several days before emergence, but had more frequent contact to ready-to-eclose pupae of female sexuals and winged males than of workers and ergatoid males. In rare cases, old ergatoid males displayed alleviated biting of pigmented ergatoid male pupae shortly before adult eclosion, as well as copulation attempts to dark pupae of female sexuals and winged males. Ergatoid male behaviour may be promoted by a closer similarity of the chemical profile of ready-to-eclose pupae to the profile of adults than that of young pupae several days prior to emergence.Conclusion: Young ergatoid males of C. obscurior would benefit greatly by hiding their identity from older, resident males, as they are highly vulnerable during the first two days of their adult lives. In contrast to the winged males of the same species, which are able to prevent ergatoid male attacks by chemical female mimicry, young ergatoids do not seem to be able to produce a protective chemical profile. Conflicts in male-male competition between ergatoid males of different age thus seem to be resolved in favour of the older males. This might represent selection at the colony level rather than the individual level. © 2012 Cremer et al.; licensee BioMed Central Ltd.}, author = {Cremer, Sylvia and Suefuji, Masaki and Schrempf, Alexandra and Heinze, Jürgen}, journal = {BMC Ecology}, publisher = {BioMed Central}, title = {{The dynamics of male-male competition in Cardiocondyla obscurior ants}}, doi = {10.1186/1472-6785-12-7}, volume = {12}, year = {2012}, } @article{2962, abstract = {The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates.}, author = {Aeschbacher, Simon and Beaumont, Mark and Futschik, Andreas}, journal = {Genetics}, number = {3}, pages = {1027 -- 1047}, publisher = {Genetics Society of America}, title = {{A novel approach for choosing summary statistics in approximate Bayesian computation}}, doi = {10.1534/genetics.112.143164}, volume = {192}, year = {2012}, } @article{2965, abstract = {Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).}, author = {Danowski, Patrick}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare}, number = {2}, pages = {200 -- 212}, publisher = {VÖB}, title = {{Kontext Open Access: Creative Commons}}, volume = {65}, year = {2012}, } @article{2963, abstract = {Zebra finches are an ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 hours. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication. }, author = {Jesse, Fabienne and Riebel, Katharina}, journal = {Behavioural Processes}, number = {3}, pages = {262 -- 266}, publisher = {Elsevier}, title = {{Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata}}, doi = {10.1016/j.beproc.2012.09.006}, volume = {91}, year = {2012}, } @inproceedings{2974, abstract = {We construct a perfectly binding string commitment scheme whose security is based on the learning parity with noise (LPN) assumption, or equivalently, the hardness of decoding random linear codes. Our scheme not only allows for a simple and efficient zero-knowledge proof of knowledge for committed values (essentially a Σ-protocol), but also for such proofs showing any kind of relation amongst committed values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u) for any circuit C. To get soundness which is exponentially small in a security parameter t, and when the zero-knowledge property relies on the LPN problem with secrets of length l, our 3 round protocol has communication complexity O(t|C|l log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants are small, and the computation consists mostly of computing inner products of bit-vectors.}, author = {Jain, Abhishek and Krenn, Stephan and Pietrzak, Krzysztof Z and Tentes, Aris}, editor = {Wang, Xiaoyun and Sako, Kazue}, location = {Beijing, China}, pages = {663 -- 680}, publisher = {Springer}, title = {{Commitments and efficient zero knowledge proofs from learning parity with noise}}, doi = {10.1007/978-3-642-34961-4_40}, volume = {7658}, year = {2012}, } @article{2969, abstract = {The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of exocytosis is a key determinant of synaptic transmission. Evoked release from parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing interneurons is generated by microdomain coupling of N-type channels. Nanodomain coupling has several functional advantages, including speed and efficacy of transmission. One potential disadvantage is that stochastic opening of presynaptic Ca^(2+) channels may trigger spontaneous transmitter release. We addressed this possibility in rat hippocampal granule cells, which receive converging inputs from different inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic Ca^(2+) channels contributes to spontaneous release. Application of the selective P/Q-type Ca^(2+) channel blocker ω-agatoxin IVa had no detectable effects, whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine reduced mIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM and the slow chelator EGTA-AM reduced the mIPSC frequency, suggesting that Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than nanodomain coupling. The CB_(1) receptor agonist WIN 55212-2 also decreased spontaneous release; this effect was occluded by prior application of ω-conotoxin GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release was generated at the terminals of CCK-expressing interneurons. Tonic inhibition generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels may be important for hippocampal information processing. }, author = {Goswami, Sarit and Bucurenciu, Iancu and Jonas, Peter M}, journal = {Journal of Neuroscience}, number = {41}, pages = {14294 -- 14304}, publisher = {Society for Neuroscience}, title = {{Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling}}, doi = {10.1523/JNEUROSCI.6104-11.2012}, volume = {32}, year = {2012}, } @article{2970, abstract = {Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms.}, author = {Kicheva, Anna and Bollenbach, Mark Tobias and Wartlick, Ortrud and Julicher, Frank and Gonzalez Gaitan, Marcos}, journal = {Current Opinion in Genetics & Development}, number = {6}, pages = {527 -- 532}, publisher = {Elsevier}, title = {{Investigating the principles of morphogen gradient formation: from tissues to cells}}, doi = {10.1016/j.gde.2012.08.004}, volume = {22}, year = {2012}, } @inproceedings{2971, abstract = {We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. }, author = {Zankl, Georg and Haxhimusa, Yll and Ion, Adrian}, location = {Graz, Austria}, pages = {11 -- 20}, publisher = {Springer}, title = {{Interactive labeling of image segmentation hierarchies}}, doi = {10.1007/978-3-642-32717-9_2}, volume = {7476}, year = {2012}, } @article{3105, abstract = {Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli.}, author = {Whitford, Ryan and Fernandez, Ana and Tejos, Ricardo and Pérez, Amparo Cuéllar and Kleine-Vehn, Jürgen and Vanneste, Steffen and Drozdzecki, Andrzej and Leitner, Johannes and Abas, Lindy and Aerts, Maarten and Hoogewijs, Kurt and Pawel Baster and De Groodt, Ruth and Lin, Yao-Cheng and Storme, Véronique and Van de Peer, Yves and Beeckman, Tom and Madder, Annemieke and Devreese, Bart and Luschnig, Christian and Jirí Friml and Hilson, Pierre}, journal = {Developmental Cell}, number = {3}, pages = {678 -- 685}, publisher = {Cell Press}, title = {{GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses}}, doi = {10.1016/j.devcel.2012.02.002}, volume = {22}, year = {2012}, } @article{3109, abstract = {Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane.}, author = {Irani, Niloufer G and Di Rubbo, Simone and Mylle, Evelien and Van Den Begin, Jos and Schneider-Pizoń, Joanna and Hniliková, Jaroslava and Šíša, Miroslav and Buyst, Dieter and Vilarrasa-Blasi, Josep and Szatmári, Anna-Maria and Van Damme, Daniël and Mishev, Kiril and Codreanu, Mirela-Corina and Kohout, Ladislav and Strnad, Miroslav and Caño-Delgado, Ana I and Jirí Friml and Madder, Annemieke and Russinova, Eugenia}, journal = {Nature Chemical Biology}, number = {6}, pages = {583 -- 589}, publisher = {Nature Publishing Group}, title = {{Fluorescent castasterone reveals BRI1 signaling from the plasma membrane}}, doi = {10.1038/nchembio.958}, volume = {8}, year = {2012}, } @article{3104, abstract = { Gradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.}, author = {Grunewald, Wim and De Smet, Ive and Lewis, Daniel R and Löfke, Christian and Jansen, Leentje and Goeminne, Geert and Vanden Bossche, Robin and Karimi, Mansour and De Rybel, Bert and Vanholme, Bartel and Teichmann, Thomas and Boerjan, Wout and Van Montagu, Marc C and Gheysen, Godelieve and Muday, Gloria K and Jirí Friml and Beeckman, Tom}, journal = {PNAS}, number = {5}, pages = {1554 -- 1559}, publisher = {National Academy of Sciences}, title = {{Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis}}, doi = {10.1073/pnas.1121134109}, volume = {109}, year = {2012}, } @article{3108, abstract = {The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes.}, author = {Barbez, Elke and Kubeš, Martin and Rolčík, Jakub and Béziat, Chloe and Pěnčík, Aleš and Wang, Bangjun and Rosquete, Michel Ruiz and Zhu, Jinsheng and Dobrev, Petre I and Lee, Yuree and Zašímalová, Eva and Petrášek, Jan and Geisler, Markus and Jirí Friml and Kleine-Vehn, Jürgen}, journal = {Nature}, number = {7396}, pages = {119 -- 122}, publisher = {Nature Publishing Group}, title = {{A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants}}, doi = {10.1038/nature11001}, volume = {485}, year = {2012}, } @article{3106, abstract = {Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis.}, author = {Nagawa, Shingo and Xu, Tongda and Lin, Deshu and Dhonukshe, Pankaj and Zhang, Xingxing and Jirí Friml and Scheres, Ben and Fu, Ying and Yang, Zhenbiao}, journal = {PLoS Biology}, number = {4}, publisher = {Public Library of Science}, title = {{ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis}}, doi = {10.1371/journal.pbio.1001299}, volume = {10}, year = {2012}, } @misc{3107, author = {Vanneste, Steffen and Friml, Jirí}, booktitle = {Nature Chemical Biology}, number = {5}, pages = {415 -- 416}, publisher = {Nature Publishing Group}, title = {{Plant signaling: Deconstructing auxin sensing}}, doi = {10.1038/nchembio.943}, volume = {8}, year = {2012}, } @inproceedings{3119, abstract = {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. }, author = {Raveendran, Karthik and Thuerey, Nils and Wojtan, Christopher J and Turk, Greg}, booktitle = {Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation}, location = {Aire-la-Ville, Switzerland}, pages = {255 -- 264}, publisher = {ACM}, title = {{Controlling liquids using meshes}}, year = {2012}, } @article{3118, abstract = {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.}, author = {Bojsen-Hansen, Morten and Li, Hao and Wojtan, Christopher J}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Tracking surfaces with evolving topology}}, doi = {10.1145/2185520.2185549}, volume = {31}, year = {2012}, } @article{3122, abstract = {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. }, author = {Field, David and Barrett, Spencer}, journal = {Molecular Ecology}, number = {15}, pages = {3640 -- 3643}, publisher = {Wiley-Blackwell}, title = {{Disassortative mating and the maintenance of sexual polymorphism in painted maple}}, doi = {10.1111/j.1365-294X.2012.05643.x}, volume = {21}, year = {2012}, } @article{3121, abstract = {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.}, author = {Williams, Courtney and Chen, Wenyan and Lee, Chia and Yaeger, Daniel and Vyleta, Nicholas and Smith, Stephen}, journal = {Nature Neuroscience}, number = {9}, pages = {1195 -- 1197}, publisher = {Nature Publishing Group}, title = {{Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA}}, doi = {10.1038/nn.3162}, volume = {15}, year = {2012}, } @article{3120, abstract = {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.}, author = {Brown, Gavin and Kerber, Michael and Reid, Miles}, journal = {Compositio Mathematica}, number = {4}, pages = {1171 -- 1194}, publisher = {Cambridge University Press}, title = {{Fano 3 folds in codimension 4 Tom and Jerry Part I}}, doi = {10.1112/S0010437X11007226}, volume = {148}, year = {2012}, } @article{3117, abstract = {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.}, author = {Kolmogorov, Vladimir}, journal = {Discrete Applied Mathematics}, number = {15}, pages = {2246 -- 2258}, publisher = {Elsevier}, title = {{Minimizing a sum of submodular functions}}, doi = {10.1016/j.dam.2012.05.025}, volume = {160}, year = {2012}, } @article{3131, abstract = {In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.}, author = {Weissman, Daniel and Barton, Nicholas H}, journal = {PLoS Genetics}, number = {6}, publisher = {Public Library of Science}, title = {{Limits to the rate of adaptive substitution in sexual populations}}, doi = {10.1371/journal.pgen.1002740}, volume = {8}, year = {2012}, } @article{3130, abstract = {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.}, author = {Bergmiller, Tobias and Ackermann, Martin and Silander, Olin}, journal = {PLoS Genetics}, number = {6}, publisher = {Public Library of Science}, title = {{Patterns of evolutionary conservation of essential genes correlate with their compensability}}, doi = {10.1371/journal.pgen.1002803}, volume = {8}, year = {2012}, } @inproceedings{3136, abstract = {Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event's initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag.}, author = {Guet, Calin C and Gupta, Ashutosh and Henzinger, Thomas A and Mateescu, Maria and Sezgin, Ali}, location = {Berkeley, CA, USA}, pages = {294 -- 309}, publisher = {Springer}, title = {{Delayed continuous time Markov chains for genetic regulatory circuits}}, doi = {10.1007/978-3-642-31424-7_24}, volume = {7358 }, year = {2012}, } @inproceedings{3135, abstract = {We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. }, author = {Brázdil, Brázdil and Chatterjee, Krishnendu and Kučera, Antonín and Novotny, Petr}, location = {Berkeley, CA, USA}, pages = {23 -- 38}, publisher = {Springer}, title = {{Efficient controller synthesis for consumption games with multiple resource types}}, doi = {10.1007/978-3-642-31424-7_8}, volume = {7358}, year = {2012}, } @inproceedings{3133, abstract = {This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. }, author = {Edelsbrunner, Herbert and Kerber, Michael}, booktitle = {Proceedings of the twenty-eighth annual symposium on Computational geometry }, location = {Chapel Hill, NC, USA}, pages = {249 -- 258}, publisher = {ACM}, title = {{Alexander duality for functions: The persistent behavior of land and water and shore}}, doi = {10.1145/2261250.2261287}, year = {2012}, } @inproceedings{3134, abstract = {It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. }, author = {Edelsbrunner, Herbert and Fasy, Brittany and Rote, Günter}, booktitle = {Proceedings of the twenty-eighth annual symposium on Computational geometry }, location = {Chapel Hill, NC, USA}, pages = {91 -- 100}, publisher = {ACM}, title = {{Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions}}, doi = {10.1145/2261250.2261265}, year = {2012}, } @article{3132, abstract = {Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony.}, author = {Konrad, Matthias and Pamminger, Tobias and Foitzik, Susanne}, journal = {Naturwissenschaften}, number = {8}, pages = {627 -- 636}, publisher = {Springer}, title = {{Two pathways ensuring social harmony}}, doi = {10.1007/s00114-012-0943-z}, volume = {99}, year = {2012}, } @article{3161, abstract = {Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined.}, author = {Vyleta, Meghan and Wong, John and Magun, Bruce}, journal = {PLoS One}, number = {5}, publisher = {Public Library of Science}, title = {{Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome}}, doi = {10.1371/journal.pone.0036044}, volume = {7}, year = {2012}, } @inproceedings{3162, abstract = {Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space.}, author = {Asarin, Eugene and Donzé, Alexandre and Maler, Oded and Nickovic, Dejan}, location = {San Francisco, CA, United States}, pages = {147 -- 160}, publisher = {Springer}, title = {{Parametric identification of temporal properties}}, doi = {10.1007/978-3-642-29860-8_12}, volume = {7186}, year = {2012}, } @article{3160, abstract = {There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation.}, author = {Pantazis, Periklis and Bollenbach, Tobias}, journal = {Cell Cycle}, number = {11}, pages = {2055 -- 2058}, publisher = {Taylor and Francis}, title = {{Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo}}, doi = {10.4161/cc.20118}, volume = {11}, year = {2012}, } @article{3164, abstract = {Overview of the Special Issue on structured prediction and inference.}, author = {Blaschko, Matthew and Lampert, Christoph}, journal = {International Journal of Computer Vision}, number = {3}, pages = {257 -- 258}, publisher = {Springer}, title = {{Guest editorial: Special issue on structured prediction and inference}}, doi = {10.1007/s11263-012-0530-y}, volume = {99}, year = {2012}, } @article{3166, abstract = {There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)}, author = {Vladar, Harold}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Amino acid fermentation at the origin of the genetic code}}, doi = {10.1186/1745-6150-7-6}, volume = {7}, year = {2012}, } @article{3167, author = {Weber, Michele}, journal = {Science}, number = {6077}, pages = {32--34}, publisher = {American Association for the Advancement of Science}, title = {{NextGen speaks 13 }}, doi = {10.1126/science.336.6077.32}, volume = {336}, year = {2012}, } @article{3241, abstract = {We prove a negative result concerning error reduction by parallel repetition for computationally sound protocols, e.g., interactive arguments. Our main result is a complete and computationally sound eight round interactive argument for which k-fold parallel repetition does not reduce the error below a constant for any polynomial k. The starting point for our construction is the work of Bellare, Impagliazzo and Naor (FOCS'97). For any fixed k, they construct a four round protocol for which k-fold parallel repetition does not lower the soundness error. The communication complexity of this protocol is linear in k. By using universal arguments due to Barak and Goldreich (CCC 2002), we turn this protocol into an eight-round protocol whose complexity is basically independent of k. }, author = {Krzysztof Pietrzak and Wikström, Douglas}, journal = {Journal of Cryptology}, number = {1}, pages = {116 -- 135}, publisher = {Springer}, title = {{Parallel repetition of computationally sound protocols revisited}}, doi = {10.1007/s00145-010-9090-x}, volume = {25}, year = {2012}, } @inproceedings{3252, abstract = {We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents, the trusted third party (TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove that the satisfaction of the objectives of the agents and the TTP imply satisfaction of the protocol objectives. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail in synthesizing these protocols, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee synthesis is attack-free; no subset of participants can violate the objectives of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner (ASW) certified mail protocol that has known vulnerabilities is not a solution of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can generate correct protocols and automatically discover vulnerabilities. The solution to assume-guarantee synthesis can be computed efficiently as the secure equilibrium solution of three-player graph games. © 2012 Springer-Verlag.}, author = {Chatterjee, Krishnendu and Raman, Vishwanath}, location = {Philadelphia, PA, USA}, pages = {152 -- 168}, publisher = {Springer}, title = {{Synthesizing protocols for digital contract signing}}, doi = {10.1007/978-3-642-27940-9_11}, volume = {7148}, year = {2012}, } @inproceedings{3255, abstract = {In this paper we survey results of two-player games on graphs and Markov decision processes with parity, mean-payoff and energy objectives, and the combination of mean-payoff and energy objectives with parity objectives. These problems have applications in verification and synthesis of reactive systems in resource-constrained environments.}, author = {Chatterjee, Krishnendu and Doyen, Laurent}, location = {Lednice, Czech Republic}, pages = {37 -- 46}, publisher = {Springer}, title = {{Games and Markov decision processes with mean payoff parity and energy parity objectives}}, doi = {10.1007/978-3-642-25929-6_3}, volume = {7119}, year = {2012}, } @inproceedings{3250, abstract = {The Learning Parity with Noise (LPN) problem has recently found many applications in cryptography as the hardness assumption underlying the constructions of "provably secure" cryptographic schemes like encryption or authentication protocols. Being provably secure means that the scheme comes with a proof showing that the existence of an efficient adversary against the scheme implies that the underlying hardness assumption is wrong. LPN based schemes are appealing for theoretical and practical reasons. On the theoretical side, LPN based schemes offer a very strong security guarantee. The LPN problem is equivalent to the problem of decoding random linear codes, a problem that has been extensively studied in the last half century. The fastest known algorithms run in exponential time and unlike most number-theoretic problems used in cryptography, the LPN problem does not succumb to known quantum algorithms. On the practical side, LPN based schemes are often extremely simple and efficient in terms of code-size as well as time and space requirements. This makes them prime candidates for light-weight devices like RFID tags, which are too weak to implement standard cryptographic primitives like the AES block-cipher. This talk will be a gentle introduction to provable security using simple LPN based schemes as examples. Starting from pseudorandom generators and symmetric key encryption, over secret-key authentication protocols, and, if time admits, touching on recent constructions of public-key identification, commitments and zero-knowledge proofs.}, author = {Pietrzak, Krzysztof Z}, location = {Špindlerův Mlýn, Czech Republic}, pages = {99 -- 114}, publisher = {Springer}, title = {{Cryptography from learning parity with noise}}, doi = {10.1007/978-3-642-27660-6_9}, volume = {7147}, year = {2012}, } @article{3256, abstract = {We use a distortion to define the dual complex of a cubical subdivision of ℝ n as an n-dimensional subcomplex of the nerve of the set of n-cubes. Motivated by the topological analysis of high-dimensional digital image data, we consider such subdivisions defined by generalizations of quad- and oct-trees to n dimensions. Assuming the subdivision is balanced, we show that mapping each vertex to the center of the corresponding n-cube gives a geometric realization of the dual complex in ℝ n.}, author = {Edelsbrunner, Herbert and Kerber, Michael}, journal = {Discrete & Computational Geometry}, number = {2}, pages = {393 -- 414}, publisher = {Springer}, title = {{Dual complexes of cubical subdivisions of ℝn}}, doi = {10.1007/s00454-011-9382-4}, volume = {47}, year = {2012}, } @article{3254, abstract = {The theory of graph games with ω-regular winning conditions is the foundation for modeling and synthesizing reactive processes. In the case of stochastic reactive processes, the corresponding stochastic graph games have three players, two of them (System and Environment) behaving adversarially, and the third (Uncertainty) behaving probabilistically. We consider two problems for stochastic graph games: the qualitative problem asks for the set of states from which a player can win with probability 1 (almost-sure winning); and the quantitative problem asks for the maximal probability of winning (optimal winning) from each state. We consider ω-regular winning conditions formalized as Müller winning conditions. We present optimal memory bounds for pure (deterministic) almost-sure winning and optimal winning strategies in stochastic graph games with Müller winning conditions. We also study the complexity of stochastic Müller games and show that both the qualitative and quantitative analysis problems are PSPACE-complete. Our results are relevant in synthesis of stochastic reactive processes.}, author = {Chatterjee, Krishnendu}, journal = {Information and Computation}, pages = {29 -- 48}, publisher = {Elsevier}, title = {{The complexity of stochastic Müller games}}, doi = {10.1016/j.ic.2011.11.004}, volume = {211}, year = {2012}, } @inproceedings{3253, abstract = {We describe a framework for reasoning about programs with lists carrying integer numerical data. We use abstract domains to describe and manipulate complex constraints on configurations of these programs mixing constraints on the shape of the heap, sizes of the lists, on the multisets of data stored in these lists, and on the data at their different positions. Moreover, we provide powerful techniques for automatic validation of Hoare-triples and invariant checking, as well as for automatic synthesis of invariants and procedure summaries using modular inter-procedural analysis. The approach has been implemented in a tool called Celia and experimented successfully on a large benchmark of programs.}, author = {Bouajjani, Ahmed and Dragoi, Cezara and Enea, Constantin and Sighireanu, Mihaela}, location = {Philadelphia, PA, USA}, pages = {1 -- 22}, publisher = {Springer}, title = {{Abstract domains for automated reasoning about list manipulating programs with infinite data}}, doi = {10.1007/978-3-642-27940-9_1}, volume = {7148}, year = {2012}, } @inproceedings{3265, abstract = {We propose a mid-level statistical model for image segmentation that composes multiple figure-ground hypotheses (FG) obtained by applying constraints at different locations and scales, into larger interpretations (tilings) of the entire image. Inference is cast as optimization over sets of maximal cliques sampled from a graph connecting all non-overlapping figure-ground segment hypotheses. Potential functions over cliques combine unary, Gestalt-based figure qualities, and pairwise compatibilities among spatially neighboring segments, constrained by T-junctions and the boundary interface statistics of real scenes. Learning the model parameters is based on maximum likelihood, alternating between sampling image tilings and optimizing their potential function parameters. State of the art results are reported on the Berkeley and Stanford segmentation datasets, as well as VOC2009, where a 28% improvement was achieved.}, author = {Ion, Adrian and Carreira, Joao and Sminchisescu, Cristian}, location = {Barcelona, Spain}, publisher = {IEEE}, title = {{Image segmentation by figure-ground composition into maximal cliques}}, doi = {10.1109/ICCV.2011.6126486}, year = {2012}, } @inproceedings{3282, abstract = {Traditionally, symmetric-key message authentication codes (MACs) are easily built from pseudorandom functions (PRFs). In this work we propose a wide variety of other approaches to building efficient MACs, without going through a PRF first. In particular, unlike deterministic PRF-based MACs, where each message has a unique valid tag, we give a number of probabilistic MAC constructions from various other primitives/assumptions. Our main results are summarized as follows: We show several new probabilistic MAC constructions from a variety of general assumptions, including CCA-secure encryption, Hash Proof Systems and key-homomorphic weak PRFs. By instantiating these frameworks under concrete number theoretic assumptions, we get several schemes which are more efficient than just using a state-of-the-art PRF instantiation under the corresponding assumption. For probabilistic MACs, unlike deterministic ones, unforgeability against a chosen message attack (uf-cma ) alone does not imply security if the adversary can additionally make verification queries (uf-cmva ). We give an efficient generic transformation from any uf-cma secure MAC which is "message-hiding" into a uf-cmva secure MAC. This resolves the main open problem of Kiltz et al. from Eurocrypt'11; By using our transformation on their constructions, we get the first efficient MACs from the LPN assumption. While all our new MAC constructions immediately give efficient actively secure, two-round symmetric-key identification schemes, we also show a very simple, three-round actively secure identification protocol from any weak PRF. In particular, the resulting protocol is much more efficient than the trivial approach of building a regular PRF from a weak PRF. © 2012 International Association for Cryptologic Research.}, author = {Dodis, Yevgeniy and Pietrzak, Krzysztof Z and Kiltz, Eike and Wichs, Daniel}, location = {Cambridge, UK}, pages = {355 -- 374}, publisher = {Springer}, title = {{Message authentication, revisited}}, doi = {10.1007/978-3-642-29011-4_22}, volume = {7237}, year = {2012}, } @inproceedings{3280, abstract = {The (decisional) learning with errors problem (LWE) asks to distinguish "noisy" inner products of a secret vector with random vectors from uniform. The learning parities with noise problem (LPN) is the special case where the elements of the vectors are bits. In recent years, the LWE and LPN problems have found many applications in cryptography. In this paper we introduce a (seemingly) much stronger adaptive assumption, called "subspace LWE" (SLWE), where the adversary can learn the inner product of the secret and random vectors after they were projected into an adaptively and adversarially chosen subspace. We prove that, surprisingly, the SLWE problem mapping into subspaces of dimension d is almost as hard as LWE using secrets of length d (the other direction is trivial.) This result immediately implies that several existing cryptosystems whose security is based on the hardness of the LWE/LPN problems are provably secure in a much stronger sense than anticipated. As an illustrative example we show that the standard way of using LPN for symmetric CPA secure encryption is even secure against a very powerful class of related key attacks. }, author = {Pietrzak, Krzysztof Z}, location = {Taormina, Sicily, Italy}, pages = {548 -- 563}, publisher = {Springer}, title = {{Subspace LWE}}, doi = {10.1007/978-3-642-28914-9_31}, volume = {7194}, year = {2012}, } @inproceedings{3281, abstract = {We consider the problem of amplifying the "lossiness" of functions. We say that an oracle circuit C*: {0,1} m → {0,1}* amplifies relative lossiness from ℓ/n to L/m if for every function f:{0,1} n → {0,1} n it holds that 1 If f is injective then so is C f. 2 If f has image size of at most 2 n-ℓ, then C f has image size at most 2 m-L. The question is whether such C* exists for L/m ≫ ℓ/n. This problem arises naturally in the context of cryptographic "lossy functions," where the relative lossiness is the key parameter. We show that for every circuit C* that makes at most t queries to f, the relative lossiness of C f is at most L/m ≤ ℓ/n + O(log t)/n. In particular, no black-box method making a polynomial t = poly(n) number of queries can amplify relative lossiness by more than an O(logn)/n additive term. We show that this is tight by giving a simple construction (cascading with some randomization) that achieves such amplification.}, author = {Pietrzak, Krzysztof Z and Rosen, Alon and Segev, Gil}, location = {Taormina, Sicily, Italy}, pages = {458 -- 475}, publisher = {Springer}, title = {{Lossy functions do not amplify well}}, doi = {10.1007/978-3-642-28914-9_26}, volume = {7194}, year = {2012}, } @inproceedings{3284, abstract = {We study the complexity of valued constraint satisfaction problems (VCSP). A problem from VCSP is characterised by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimise the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well-understood, see Raghavendra [FOCS’08]. However, there is no characterisation of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimisation perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e. relations), such languages have been called conservative and studied by Bulatov [LICS’03] and recently by Barto [LICS’11]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [AIJ’06] for languages over Boolean domains, by Deineko et al. [JACM’08] for {0,1}-valued languages (a.k.a Max-CSP), and by Takhanov [STACS’10] for {0,∞}-valued languages containing all finite- valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimorphisms), then any instance can be solved in polynomial time (via a new algorithm developed in this paper), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains is significantly harder than the Boolean case. The polynomial-time algorithm we present for the tractable cases is a generalisation of the submodular minimisation problem and a result of Cohen et al. [TCS’08]. Our results generalise previous results by Takhanov [STACS’10] and (a subset of results) by Cohen et al. [AIJ’06] and Deineko et al. [JACM’08]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [JACM’08], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.}, author = {Vladimir Kolmogorov and Živný, Stanislav}, pages = {750 -- 759}, publisher = {SIAM}, title = {{The complexity of conservative valued CSPs}}, year = {2012}, } @article{330, abstract = {A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. }, author = {Shavel, Alexey and Cadavid, Doris and Ibáñez, Maria and Carrete, Alex and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {3}, pages = {1438 -- 1441}, publisher = {ACS}, title = {{Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor}}, doi = {10.1021/ja209688a}, volume = {134}, year = {2012}, } @article{3317, abstract = {The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission.}, author = {Eggermann, Emmanuel and Bucurenciu, Iancu and Goswami, Sarit and Jonas, Peter M}, journal = {Nature Reviews Neuroscience}, number = {1}, pages = {7 -- 21}, publisher = {Nature Publishing Group}, title = {{Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses}}, doi = {10.1038/nrn3125}, volume = {13}, year = {2012}, } @article{3314, abstract = {We introduce two-level discounted and mean-payoff games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted or mean-payoff game and the lower level game is a (undiscounted) reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. For both discounted and mean-payoff two-level games, we show the existence of pure memoryless optimal strategies for both players and an ordered field property. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP. We also give an alternate strategy improvement algorithm to compute the value. © 2012 World Scientific Publishing Company.}, author = {Chatterjee, Krishnendu and Majumdar, Ritankar}, journal = {International Journal of Foundations of Computer Science}, number = {3}, pages = {609 -- 625}, publisher = {World Scientific Publishing}, title = {{Discounting and averaging in games across time scales}}, doi = {10.1142/S0129054112400308}, volume = {23}, year = {2012}, } @article{3115, abstract = {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.}, author = {Berberich, Eric and Halperin, Dan and Kerber, Michael and Pogalnikova, Roza}, journal = {Discrete & Computational Geometry}, number = {4}, pages = {964 -- 989}, publisher = {Springer}, title = {{Deconstructing approximate offsets}}, doi = {10.1007/s00454-012-9441-5}, volume = {48}, year = {2012}, } @article{3331, abstract = {Computing the topology of an algebraic plane curve C means computing a combinatorial graph that is isotopic to C and thus represents its topology in R2. We prove that, for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology of the induced curve can be computed with bit operations ( indicates that we omit logarithmic factors). Our analysis improves the previous best known complexity bounds by a factor of n2. The improvement is based on new techniques to compute and refine isolating intervals for the real roots of polynomials, and on the consequent amortized analysis of the critical fibers of the algebraic curve.}, author = {Kerber, Michael and Sagraloff, Michael}, journal = { Journal of Symbolic Computation}, number = {3}, pages = {239 -- 258}, publisher = {Elsevier}, title = {{A worst case bound for topology computation of algebraic curves}}, doi = {10.1016/j.jsc.2011.11.001}, volume = {47}, year = {2012}, } @article{346, abstract = {Arrays of vertically aligned ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires (NWs) were prepared by means of the combination of two solution-growth processes. First, single-crystal ZnO NWs with controlled n-type doping were grown on conducting substrates by a low-cost, high-yield and seed-free electrochemical route. These NWs were covered by a titanium oxide shell of tunable thickness mediating successive adsorption-hydrolysis-condensation steps. Using this atomic-layer growth procedure, titania shells with controlled thickness and the anatase TiO2 phase were obtained after sintering at 450 °C. Higher sintering temperatures resulted in the formation of ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs by the interdiffusion of Zn and Ti ions at the ZnO–TiO2 interface. The performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs towards photoelectrochemical (PEC) water splitting was investigated as a function of the titania shell thickness. Furthermore, the performance of such core–shell NWs as photoelectrodes in dye-sensitized solar cells was also characterized. The TiO2 presence at the ZnO : Cl surface promoted a two-fold increase on the produced photocurrent densities, probing their potential for PEC and optoelectronic applications. Electrochemical impedance spectroscopy was used to corroborate the lower resistance for charge transfer between the NWs and the electrolyte in the presence of the TiO2 shell.}, author = {Fan, Jiandong and Zamani, Reza and Fábrega, Cristina and Shavel, Alexey and Flox, Cristina and Ibáñez, Maria and Andreu, Teresa and López, Amtonio and Arbiol, Jordi and Morante, Joan and Cabot, Andreu}, journal = {Journal of Physics D: Applied Physics}, number = {41}, publisher = {IOP Publishing Ltd.}, title = {{Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness}}, doi = {10.1088/0022-3727/45/41/415301}, volume = {45}, year = {2012}, } @article{3168, abstract = {The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk.}, author = {Feret, Jérôme and Henzinger, Thomas A and Koeppl, Heinz and Petrov, Tatjana}, journal = {Theoretical Computer Science}, pages = {137 -- 164}, publisher = {Elsevier}, title = {{Lumpability abstractions of rule based systems}}, doi = {10.1016/j.tcs.2011.12.059}, volume = {431}, year = {2012}, } @article{377, abstract = {The potential to control the composition and crystal phase at the nanometer scale enable the production of nanocrystalline materials with enhanced functionalities and new applications. In the present work, we detail a novel colloidal synthesis route to prepare nanoparticles of the ternary semiconductor Cu2GeSe3 (CGSe) with nanometer-scale control over their crystal phases. We also demonstrate the structural effect on the thermoelectric properties of bottom-up-prepared CGSe nanomaterials. By careful adjustment of the nucleation and growth temperatures, pure orthorhombic CGSe nanoparticles with cationic order or polytypic CGSe nanoparticles with disordered cation positions can be produced. In this second type of nanoparticle, a high density of twins can be created to periodically change the atomic plane stacking, forming a hexagonal wurtzite CGSe phase. The high yield of the synthetic routes reported here allows the production of single-phase and multiphase CGSe nanoparticles in the gram scale, which permits characterization of the thermoelectric properties of these materials. Reduced thermal conductivities and a related 2.5-fold increase of the thermoelectric figure of merit for multiphase nanomaterials compared to pure-phase CGSe are systematically obtained. These results are discussed in terms of the density and efficiency of phonon scattering centers in both types of materials.}, author = {Ibáñez, Maria and Zamani, Reza and Li, Wenhua and Cadavid, Doris and Gorse, Stéphane and Katchoi, Nebll and Shavel, Alexey and López, Antonioo and Morante, Joan and Arbiol, Jordi and Cabot, Andreu}, journal = {Chemistry of Materials}, number = {23}, pages = {4615 -- 4622}, publisher = {American Chemical Society}, title = {{Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials}}, doi = {10.1021/cm303252q}, volume = {24}, year = {2012}, } @article{3846, abstract = {We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A}, journal = {Journal of Computer and System Sciences}, number = {2}, pages = {394 -- 413}, publisher = {Elsevier}, title = {{A survey of stochastic ω regular games}}, doi = {10.1016/j.jcss.2011.05.002}, volume = {78}, year = {2012}, } @article{387, abstract = {In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society.}, author = {Alpichshev, Zhanybek and Biswas, Rudro and Balatsky, Alexander and Analytis, James and Chu, Jiunhaw and Fisher, Ian and Kapitulnik, Aharon}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{STM imaging of impurity resonances on Bi 2Se 3}}, doi = {10.1103/PhysRevLett.108.206402}, volume = {108}, year = {2012}, } @article{3110, abstract = {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. }, author = {Dai, Mingqiu and Zhang, Chen and Urszula Kania and Chen, Fang and Xue, Qin and McCray, Tyra and Li, Gang and Qin, Genji and Wakeley, Michelle and Terzaghi, William and Wan, Jianmin and Zhao, Yunde and Xu, Jian and Jirí Friml and Deng, Xing W and Wang, Haiyang}, journal = {Plant Cell}, number = {6}, pages = {2497 -- 2514}, publisher = {American Society of Plant Biologists}, title = {{A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis}}, doi = {10.1105/tpc.112.098905}, volume = {24}, year = {2012}, } @article{3113, abstract = {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.}, author = {Martinière, Alexandre and Lavagi, Irene and Nageswaran, Gayathri and Rolfe, Daniel J and Maneta-Peyret, Lilly and Luu, Doan-Trung and Botchway, Stanley W and Webb, Stephen E and Mongrand, Sebastien and Maurel, Christophe and Martin-Fernandez, Marisa L and Kleine-Vehn, Jürgen and Jirí Friml and Moreau, Patrick and Runions, John}, journal = {PNAS}, number = {31}, pages = {12805 -- 12810}, publisher = {National Academy of Sciences}, title = {{Cell wall constrains lateral diffusion of plant plasma membrane proteins}}, doi = {10.1073/pnas.1202040109}, volume = {109}, year = {2012}, } @article{3114, abstract = {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.}, author = {Ding, Zhaojun and Wang, Bangjun and Moreno, Ignacio and Dupláková, Nikoleta and Sibu Simon and Carraro, Nicola and Reemmer, Jesica and Pěnčík, Aleš and Xu Chen and Tejos, Ricardo I and Skůpa, Petr and Pollmann, Stephan and Mravec, Jozef and Petrášek, Jan and Zažímalová, Eva and Honys, David and Rolčík, Jakub and Murphy, Angus S and Orellana, Ariel and Geisler, Markus and Jirí Friml}, journal = {Nature Communications}, number = {AN 941}, publisher = {Nature Publishing Group}, title = {{ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis}}, doi = {10.1038/ncomms1941}, volume = {3}, year = {2012}, } @article{3111, abstract = {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.}, author = {Lin, Deshu and Nagawa, Shingo and Chen, Jisheng and Cao, Lingyan and Xu Chen and Xu, Tongda and Hongjiang Li and Dhonukshe, Pankaj and Yamamuro, Chizuko and Jirí Friml and Scheres, Ben and Fu, Ying and Yang, Zhenbiao}, journal = {Current Biology}, number = {14}, pages = {1319 -- 1325}, publisher = {Cell Press}, title = {{A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots}}, doi = {10.1016/j.cub.2012.05.019}, volume = {22}, year = {2012}, } @article{3112, abstract = {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 = {Xu Chen and Naramoto, Satoshi and Robert, Stéphanie and Tejos, Ricardo and Löfke, Christian and Lin, Deshu and Yang, Zhenbiao and Jirí Friml}, journal = {Current Biology}, number = {14}, pages = {1326 -- 1332}, publisher = {Cell Press}, title = {{ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots}}, doi = {10.1016/j.cub.2012.05.020}, volume = {22}, year = {2012}, } @article{3128, abstract = {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). }, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, journal = {Formal Methods in System Design}, number = {2}, pages = {268 -- 284}, publisher = {Springer}, title = {{A survey of partial-observation stochastic parity games}}, doi = {10.1007/s10703-012-0164-2}, volume = {43}, year = {2012}, } @inproceedings{3125, abstract = {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.}, author = {Sharmanska, Viktoriia and Quadrianto, Novi and Lampert, Christoph}, location = {Florence, Italy}, number = {PART 5}, pages = {242 -- 255}, publisher = {Springer}, title = {{Augmented attribute representations}}, doi = {10.1007/978-3-642-33715-4_18}, volume = {7576}, year = {2012}, } @inproceedings{3129, abstract = {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. Using 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. }, author = {Busaryev, Oleksiy and Cabello, Sergio and Chen, Chao and Dey, Tamal and Wang, Yusu}, location = {Helsinki, Finland}, pages = {189 -- 200}, publisher = {Springer}, title = {{Annotating simplices with a homology basis and its applications}}, doi = {10.1007/978-3-642-31155-0_17}, volume = {7357}, year = {2012}, } @inproceedings{3126, abstract = {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. }, author = {Müller, Andreas and Nowozin, Sebastian and Lampert, Christoph}, location = {Graz, Austria}, pages = {205 -- 215}, publisher = {Springer}, title = {{Information theoretic clustering using minimal spanning trees}}, doi = {10.1007/978-3-642-32717-9_21}, volume = {7476}, year = {2012}, } @inproceedings{3155, abstract = {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.}, author = {Delahaye, Benoît and Fahrenberg, Uli and Henzinger, Thomas A and Legay, Axel and Nickovic, Dejan}, location = {Stockholm, Sweden}, pages = {203 -- 218}, publisher = {Springer}, title = {{Synchronous interface theories and time triggered scheduling}}, doi = {10.1007/978-3-642-30793-5_13}, volume = {7273}, year = {2012}, } @article{3159, abstract = {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.}, author = {Mileyko, Yuriy and Edelsbrunner, Herbert and Price, Charles and Weitz, Joshua}, journal = {PLoS One}, number = {6}, publisher = {Public Library of Science}, title = {{Hierarchical ordering of reticular networks}}, doi = {10.1371/journal.pone.0036715}, volume = {7}, year = {2012}, } @article{3156, abstract = {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.}, author = {Ugelvig, Line V and Andersen, Anne and Boomsma, Jacobus and Nash, David}, journal = {Molecular Ecology}, number = {13}, pages = {3224 -- 3236}, publisher = {Wiley-Blackwell}, title = {{Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion}}, doi = {10.1111/j.1365-294X.2012.05592.x}, volume = {21}, year = {2012}, } @article{3158, abstract = {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.}, author = {Schachtner, Hannah and Li, Ang and Stevenson, David and Calaminus, Simon and Thomas, Steven and Watson, Steve and Sixt, Michael K and Wedlich Söldner, Roland and Strathdee, Douglas and Machesky, Laura}, journal = {European Journal of Cell Biology}, number = {11-12}, pages = {923 -- 929}, publisher = {Elsevier}, title = {{Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo}}, doi = {10.1016/j.ejcb.2012.04.002}, volume = {91}, year = {2012}, } @article{3248, abstract = {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.}, author = {Lampert, Christoph and Peters, Jan}, issn = {1861-8219}, journal = {Journal of Real-Time Image Processing}, number = {1}, pages = {31 -- 41}, publisher = {Springer}, title = {{Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components}}, doi = {10.1007/s11554-010-0168-3}, volume = {7}, year = {2012}, } @article{3247, abstract = {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.}, author = {Vilaça, Sibelle and Fernandes Redondo, Rodrigo A and Lins, Lívia and Santos, Fabrício}, journal = {Conservation Genetics}, number = {1}, pages = {293 -- 298}, publisher = {Springer}, title = {{Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)}}, doi = {10.1007/s10592-011-0262-5}, volume = {13}, year = {2012}, } @article{3245, abstract = {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.}, author = {Behrndt, Martin and Heisenberg, Carl-Philipp J}, journal = {Developmental Cell}, number = {1}, pages = {3 -- 4}, publisher = {Cell Press}, title = {{Spurred by resistance mechanosensation in collective migration}}, doi = {10.1016/j.devcel.2011.12.018}, volume = {22}, year = {2012}, } @article{3262, abstract = {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.}, author = {Tkacik, Gasper and Walczak, Aleksandra and Bialek, William}, journal = { Physical Review E statistical nonlinear and soft matter physics }, number = {4}, publisher = {American Institute of Physics}, title = {{Optimizing information flow in small genetic networks. III. A self-interacting gene}}, doi = {10.1103/PhysRevE.85.041903}, volume = {85}, year = {2012}, } @article{3257, abstract = {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.}, author = {Kolmogorov, Vladimir}, journal = {Discrete Applied Mathematics}, number = {4-5}, pages = {416 -- 426}, publisher = {Elsevier}, title = {{Generalized roof duality and bisubmodular functions}}, doi = {10.1016/j.dam.2011.10.026}, volume = {160}, year = {2012}, } @inbook{3277, abstract = {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.}, author = {de Vladar, Harold and Chela Flores, Julian}, booktitle = {Life on Earth and other planetary bodies}, pages = {387 -- 405}, publisher = {Springer}, title = {{Can the evolution of multicellularity be anticipated in the exploration of the solar system?}}, doi = {10.1007/978-94-007-4966-5_22}, volume = {24}, year = {2012}, } @inproceedings{3279, abstract = {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. }, author = {Jain, Abhishek and Pietrzak, Krzysztof Z and Tentes, Aris}, location = {Taormina, Sicily, Italy}, pages = {369 -- 382}, publisher = {Springer}, title = {{Hardness preserving constructions of pseudorandom functions}}, doi = {10.1007/978-3-642-28914-9_21}, volume = {7194}, year = {2012}, } @article{3274, abstract = {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.}, author = {Rieckh, Georg and Kreuzer, Wolfgang and Waubke, Holger and Balazs, Peter}, journal = { Engineering Analysis with Boundary Elements}, number = {6}, pages = {960 -- 967}, publisher = {Elsevier}, title = {{A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil}}, doi = {10.1016/j.enganabound.2011.12.014}, volume = {36}, year = {2012}, } @article{3289, abstract = {Viral manipulation of transduction pathways associated with key cellular functions such as survival, response to microbial infection, and cytoskeleton reorganization can provide the supportive milieu for a productive infection. Here, we demonstrate that vaccinia virus (VACV) infection leads to activation of the stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK) 4/7 (MKK4/7)-c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the stimulation of this pathway requires postpenetration, prereplicative events in the viral replication cycle. Although the formation of intracellular mature virus (IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an accentuated deregulation of microtubule and actin network organization in infected JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery and enhanced enveloped particle release. Furthermore, VACV infection induced alterations in the cell contractility and morphology, and cell migration was reduced in the JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell contractility and cell migration, such as microtubule-associated protein 1B and paxillin, respectively, was not detected in the VACV-infected KO cells. In sum, our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in cytoskeleton reorganization during VACV infection. }, author = {Pereira, Anna and Leite, Flávia and Brasil, Bruno and Soares Martins, Jamaria and Torres, Alice and Pimenta, Paulo and Souto Padrón, Thais and Tranktman, Paula and Ferreira, Paulo and Kroon, Erna and Bonjardim, Cláudio}, journal = {Journal of Virology}, number = {1}, pages = {172 -- 184}, publisher = {ASM}, title = {{A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization}}, doi = {10.1128/JVI.05638-11}, volume = {86}, year = {2012}, } @article{3310, abstract = {The theory of persistent homology opens up the possibility to reason about topological features of a space or a function quantitatively and in combinatorial terms. We refer to this new angle at a classical subject within algebraic topology as a point calculus, which we present for the family of interlevel sets of a real-valued function. Our account of the subject is expository, devoid of proofs, and written for non-experts in algebraic topology.}, author = {Bendich, Paul and Cabello, Sergio and Edelsbrunner, Herbert}, journal = {Pattern Recognition Letters}, number = {11}, pages = {1436 -- 1444}, publisher = {Elsevier}, title = {{A point calculus for interlevel set homology}}, doi = {10.1016/j.patrec.2011.10.007}, volume = {33}, year = {2012}, } @article{338, abstract = {The ample chemical and structural freedom of quaternary compounds permits engineering materials that fulfill the requirements of a wide variety of applications. In this work, the mechanisms to achieve unprecedented size, shape, and composition control in quaternary nanocrystals are detailed. The described procedure allows obtaining tetrahedral and penta-tetrahedral quaternary nanocrystals with tuned size distributions and controlled compositions from a plethora of I 2-II-IV-VI 4 semiconductors.}, author = {Ibáñez, Maria and Zamani, Reza and Li, Wenhua and Shavel, Alexey and Arbiol, Jordi and Morante, Joan and Cabot, Andreu}, journal = {Crystal Growth and Design }, number = {3}, pages = {1085 -- 1090}, publisher = {American Chemical Society (ACS)}, title = {{Extending the nanocrystal synthesis control to quaternary compositions}}, doi = {10.1021/cg201709c}, volume = {12}, year = {2012}, } @article{339, abstract = {A high-yield and upscalable colloidal synthesis route for the production of quaternary I 2-II-IV-VI 4 nanocrystals, particularly stannite Cu 2+xCd 1-xSnSe 4, with narrow size distribution and precisely controlled composition is presented. It is also shown here how the diversity of valences in the constituent elements allows an effective control of their electrical conductivity through the adjustment of the cation ratios. At the same time, while the crystallographic complexity of quaternary chalcogenides is associated with intrinsically low thermal conductivities, the reduction of the lattice dimensions to the nanoscale further reduces the materials thermal conductivity. In the specific case of the stannite crystal structure, a convenient slab distribution of the valence band maximum states permits a partial decoupling of the p-type electrical conductivity from both the Seebeck coefficient and the thermal conductivity. Combining these features, we demonstrate how an initial optimization of the nanocrystals Cd/Cu ratio allowed us to obtain low-temperature solution-processed materials with ZT values up to 0.71 at 685 K.}, author = {Ibáñez, Maria and Cadavid, Doris and Zamani, Reza and García Castelló, Nuria and Izquierdo Roca, Victora and Li, Wenhua and Fairbrother, Andrew and Prades, Joan and Shavel, Alexey and Arbiol, Jordi and Pérez Rodríguez, Alejandro and Morante, Joan and Cabot, Andreu}, journal = {Chemistry of Materials}, number = {3}, pages = {562 -- 570}, publisher = {American Chemical Society}, title = {{Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4}}, doi = {10.1021/cm2031812}, volume = {24}, year = {2012}, } @article{340, abstract = {A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. }, author = {Shavel, Alexey and Cadavid, Doris and Ibáñez, Maria and Carrete, Alex and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {3}, pages = {1438 -- 1441}, publisher = {ACS}, title = {{Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor}}, doi = {10.1021/ja209688a}, volume = {134}, year = {2012}, } @article{345, abstract = {Nanocomposites are highly promising materials to enhance the efficiency of current thermoelectric devices. A straightforward and at the same time highly versatile and controllable approach to produce nanocomposites is the assembly of solution-processed nanocrystal building blocks. The convenience of this bottom-up approach to produce nanocomposites with homogeneous phase distributions and adjustable composition is demonstrated here by blending Ag2Te and PbTe colloidal nanocrystals to form Ag2Te–PbTe bulk nanocomposites. The thermoelectric properties of these nanocomposites are analyzed in the temperature range from 300 to 700 K. The evolution of their electrical conductivity and Seebeck coefficient is discussed in terms of the blend composition and the characteristics of the constituent materials. }, author = {Cadavid, Doris and Ibáñez, Maria and Gorsse, Stéphane and López, Antonio and Cirera, Albert and Morante, Joan and Cabot, Andreu}, journal = {Journal of Nanoparticle Research}, number = {12}, publisher = {Kluwer}, title = {{Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe}}, doi = {10.1007/s11051-012-1328-0}, volume = {14}, year = {2012}, } @article{347, abstract = {A synthetic route for producing Cu 2ZnGeSe 4 nanocrystals with narrow size distributions and controlled composition is presented. These nanocrystals were used to produce densely packed nanomaterials by hot-pressing. From the characterization of the thermoelectric properties of these nanomaterials, Cu 2ZnGeSe 4 is demonstrated to show excellent thermoelectric properties. A very preliminary adjustment of the nanocrystal composition has already resulted in a figure of merit of up to 0.55 at 450°C. }, author = {Ibáñez, Maria and Zamani, Reza and Lalonde, Aaron and Cadavid, Doris and Li, Wenhua and Shavel, Alexey and Arbiol, Jordi and Morante, Joan and Gorsse, Stéphane and Snyder, G Jeffrey and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {9}, pages = {4060 -- 4063}, publisher = {ACS}, title = {{Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties}}, doi = {10.1021/ja211952z}, volume = {134}, year = {2012}, } @article{3836, abstract = {Hierarchical Timing Language (HTL) is a coordination language for distributed, hard real-time applications. HTL is a hierarchical extension of Giotto and, like its predecessor, based on the logical execution time (LET) paradigm of real-time programming. Giotto is compiled into code for a virtual machine, called the EmbeddedMachine (or E machine). If HTL is targeted to the E machine, then the hierarchicalprogram structure needs to be flattened; the flattening makes separatecompilation difficult, and may result in E machinecode of exponential size. In this paper, we propose a generalization of the E machine, which supports a hierarchicalprogram structure at runtime through real-time trigger mechanisms that are arranged in a tree. We present the generalized E machine, and a modular compiler for HTL that generates code of linear size. The compiler may generate code for any part of a given HTL program separately in any order.}, author = {Ghosal, Arkadeb and Iercan, Daniel and Kirsch, Christoph and Henzinger, Thomas A and Sangiovanni Vincentelli, Alberto}, journal = {Science of Computer Programming}, number = {2}, pages = {96 -- 112}, publisher = {Elsevier}, title = {{Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code}}, doi = {10.1016/j.scico.2010.06.004}, volume = {77}, year = {2012}, } @article{2972, abstract = {Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objectives. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is logspace-equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games.}, author = {Chatterjee, Krishnendu and Doyen, Laurent}, journal = {Theoretical Computer Science}, pages = {49 -- 60}, publisher = {Elsevier}, title = {{Energy parity games}}, doi = {10.1016/j.tcs.2012.07.038}, volume = {458}, year = {2012}, } @article{2967, abstract = {For programs whose data variables range over Boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this article, we consider algorithmic verification of programs that use Boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over an unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) PSPACE-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly nested loops. The second result establishes connections to automata and logics defining languages over data words.}, author = {Alur, Rajeev and Cerny, Pavol and Weinstein, Scott}, journal = {ACM Transactions on Computational Logic (TOCL)}, number = {3}, publisher = {ACM}, title = {{Algorithmic analysis of array-accessing programs}}, doi = {10.1145/2287718.2287727}, volume = {13}, year = {2012}, } @article{492, abstract = {Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.}, author = {Galkovskyi, Taras and Mileyko, Yuriy and Bucksch, Alexander and Moore, Brad and Symonova, Olga and Price, Charles and Topp, Chrostopher and Iyer Pascuzzi, Anjali and Zurek, Paul and Fang, Suqin and Harer, John and Benfey, Philip and Weitz, Joshua}, journal = {BMC Plant Biology}, publisher = {BioMed Central}, title = {{GiA Roots: Software for the high throughput analysis of plant root system architecture}}, doi = {10.1186/1471-2229-12-116}, volume = {12}, year = {2012}, } @article{493, abstract = {The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.}, author = {Tangermann, Michael and Müller, Klaus and Aertsen, Ad and Birbaumer, Niels and Braun, Christoph and Brunner, Clemens and Leeb, Robert and Mehring, Carsten and Miller, Kai and Müller Putz, Gernot and Nolte, Guido and Pfurtscheller, Gert and Preissl, Hubert and Schalk, Gerwin and Schlögl, Alois and Vidaurre, Carmen and Waldert, Stephan and Blankertz, Benjamin}, journal = {Frontiers in Neuroscience}, publisher = {Frontiers Research Foundation}, title = {{Review of the BCI competition IV}}, doi = {10.3389/fnins.2012.00055}, volume = {6}, year = {2012}, } @inproceedings{495, abstract = {An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice.}, author = {Kruckman, Alex and Rubin, Sasha and Sheridan, John and Zax, Ben}, booktitle = {Proceedings GandALF 2012}, location = {Napoli, Italy}, pages = {238 -- 246}, publisher = {Open Publishing Association}, title = {{A Myhill Nerode theorem for automata with advice}}, doi = {10.4204/EPTCS.96.18}, volume = {96}, year = {2012}, } @article{498, abstract = {Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.}, author = {Pickup, Melinda and Field, David and Rowell, David and Young, Andrew}, journal = {Evolutionary Applications}, number = {8}, pages = {913 -- 924}, publisher = {Wiley-Blackwell}, title = {{Predicting local adaptation in fragmented plant populations: Implications for restoration genetics}}, doi = {10.1111/j.1752-4571.2012.00284.x}, volume = {5}, year = {2012}, } @inproceedings{496, abstract = {We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations.}, author = {Rabinovich, Alexander and Rubin, Sasha}, location = {Dubrovnik, Croatia}, publisher = {IEEE}, title = {{Interpretations in trees with countably many branches}}, doi = {10.1109/LICS.2012.65}, year = {2012}, } @article{494, abstract = {We solve the longstanding open problems of the blow-up involved in the translations, when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW). For the NBW to NCW translation, the currently known upper bound is 2o(nlog n) and the lower bound is 1.5n. We improve the upper bound to n2n and describe a matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight. Both of our upper-bound constructions are based on a simple subset construction, do not involve intermediate automata with richer acceptance conditions, and can be implemented symbolically. We continue and solve the open problems of translating nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to DCW. Going via an intermediate NBW is not optimal and we describe direct, simple, and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions are variants of the subset construction, providing a unified approach for translating all common classes of automata to NCW and DCW. Beyond the theoretical importance of the results, we point to numerous applications of the new constructions. In particular, they imply a simple subset-construction based translation, when possible, of LTL to deterministic Büchi word automata.}, author = {Boker, Udi and Kupferman, Orna}, journal = {ACM Transactions on Computational Logic (TOCL)}, number = {4}, publisher = {ACM}, title = {{Translating to Co-Büchi made tight, unified, and useful}}, doi = {10.1145/2362355.2362357}, volume = {13}, year = {2012}, } @article{506, author = {Sixt, Michael K}, journal = {Journal of Cell Biology}, number = {3}, pages = {347 -- 349}, publisher = {Rockefeller University Press}, title = {{Cell migration: Fibroblasts find a new way to get ahead}}, doi = {10.1083/jcb.201204039}, volume = {197}, year = {2012}, } @inproceedings{497, abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.}, author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish}, location = {Fontainebleau, France}, pages = {167 -- 182}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Faster algorithms for alternating refinement relations}}, doi = {10.4230/LIPIcs.CSL.2012.167}, volume = {16}, year = {2012}, } @inproceedings{3165, abstract = {Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is Õ(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n·m) boundary by presenting a new technique that reduces the running time to O(n 2). This bound also leads to O(n 2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n 3)), and (3) in Markov decision processes (improving for m > n 4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n 2), which is an improvement over earlier bounds for m > n 4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.}, author = {Chatterjee, Krishnendu and Henzinger, Monika H}, booktitle = {Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {Kyoto, Japan}, pages = {1386 -- 1399}, publisher = {SIAM}, title = {{An O(n2) time algorithm for alternating Büchi games}}, doi = {10.1137/1.9781611973099.109}, year = {2012}, } @inproceedings{2956, abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and parity objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two-player pushdown games. Finally we also show that all the problems have the same computational complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.}, author = {Chatterjee, Krishnendu and Velner, Yaron}, booktitle = {Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science}, location = {Dubrovnik, Croatia }, publisher = {IEEE}, title = {{Mean payoff pushdown games}}, doi = {10.1109/LICS.2012.30}, year = {2012}, }