@article{1373, author = {Martin, Olivier and Zagórski, Marcin P}, journal = {Physics of Life Reviews}, pages = {168 -- 171}, publisher = {Elsevier}, title = {{Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"}}, doi = {10.1016/j.plrev.2016.06.006}, volume = {17}, year = {2016}, } @article{1377, abstract = {We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.}, author = {Kolmogorov, Vladimir and Pock, Thomas and Rolinek, Michal}, journal = {SIAM Journal on Imaging Sciences}, number = {2}, pages = {605 -- 636}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Total variation on a tree}}, doi = {10.1137/15M1010257}, volume = {9}, year = {2016}, } @inproceedings{1378, abstract = {We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M.}, author = {Dotterrer, Dominic and Kaufman, Tali and Wagner, Uli}, location = {Medford, MA, USA}, pages = {35.1 -- 35.10}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{On expansion and topological overlap}}, doi = {10.4230/LIPIcs.SoCG.2016.35}, volume = {51}, year = {2016}, } @inproceedings{1379, abstract = {We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.}, author = {Burton, Benjamin and De Mesmay, Arnaud N and Wagner, Uli}, location = {Medford, MA, USA}, pages = {24.1 -- 24.15}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Finding non-orientable surfaces in 3-manifolds}}, doi = {10.4230/LIPIcs.SoCG.2016.24}, volume = {51}, year = {2016}, } @article{1380, abstract = {We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP.}, author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James}, journal = {Journal of the ACM}, number = {3}, publisher = {ACM}, title = {{On the complexity of the orbit problem}}, doi = {10.1145/2857050}, volume = {63}, year = {2016}, } @inproceedings{1381, abstract = {Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.}, author = {Mabillard, Isaac and Wagner, Uli}, location = {Medford, MA, USA}, pages = {51.1 -- 51.12}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range}}, doi = {10.4230/LIPIcs.SoCG.2016.51}, volume = {51}, year = {2016}, } @article{1382, abstract = {Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.}, author = {Ellis, Thomas and Field, David}, journal = {Annals of Botany}, number = {7}, pages = {1133 -- 1140}, publisher = {Oxford University Press}, title = {{Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae}}, doi = {10.1093/aob/mcw043}, volume = {117}, year = {2016}, } @inproceedings{1389, abstract = {The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be described in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can equivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear differential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision.}, author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James}, booktitle = {LICS '16}, location = {New York, NY, USA}, pages = {515 -- 524}, publisher = {IEEE}, title = {{On recurrent reachability for continuous linear dynamical systems}}, doi = {10.1145/2933575.2934548}, year = {2016}, } @inproceedings{1390, abstract = {The goal of automatic program repair is to identify a set of syntactic changes that can turn a program that is incorrect with respect to a given specification into a correct one. Existing program repair techniques typically aim to find any program that meets the given specification. Such “best-effort” strategies can end up generating a program that is quite different from the original one. Novel techniques have been proposed to compute syntactically minimal program fixes, but the smallest syntactic fix to a program can still significantly alter the original program’s behaviour. We propose a new approach to program repair based on program distances, which can quantify changes not only to the program syntax but also to the program semantics. We call this the quantitative program repair problem where the “optimal” repair is derived using multiple distances. We implement a solution to the quantitative repair problem in a prototype tool called Qlose (Quantitatively close), using the program synthesizer Sketch. We evaluate the effectiveness of different distances in obtaining desirable repairs by evaluating Qlose on programs taken from educational tools such as CodeHunt and edX.}, author = {D'Antoni, Loris and Samanta, Roopsha and Singh, Rishabh}, location = {Toronto, Canada}, pages = {383 -- 401}, publisher = {Springer}, title = {{QLOSE: Program repair with quantitative objectives}}, doi = {10.1007/978-3-319-41540-6_21}, volume = {9780}, year = {2016}, } @article{1394, abstract = {The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show that empirical growth rate distributions recently obtained in experiments at single-cell resolution can be explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the higher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of a large bacterial population that captures this trade-off. The scaling relationships observed in experiments encode, in such frameworks, for the same distance from the maximum achievable growth rate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being grounded on genome-scale metabolic network reconstructions, these results allow for multiple implications and extensions in spite of the underlying conceptual simplicity.}, author = {De Martino, Daniele and Capuani, Fabrizio and De Martino, Andrea}, journal = {Physical Biology}, number = {3}, publisher = {IOP Publishing}, title = {{Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli}}, doi = {10.1088/1478-3975/13/3/036005}, volume = {13}, year = {2016}, } @article{1408, abstract = {The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status.}, author = {Franek, Peter and Krcál, Marek}, journal = {Discrete & Computational Geometry}, number = {1}, pages = {126 -- 164}, publisher = {Springer}, title = {{On computability and triviality of well groups}}, doi = {10.1007/s00454-016-9794-2}, volume = {56}, year = {2016}, } @article{1409, author = {Abbott, Richard and Barton, Nicholas H and Good, Jeffrey}, journal = {Molecular Ecology}, number = {11}, pages = {2325 -- 2332}, publisher = {Wiley-Blackwell}, title = {{Genomics of hybridization and its evolutionary consequences}}, doi = {10.1111/mec.13685}, volume = {25}, year = {2016}, } @article{1410, abstract = {The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.}, author = {Ugalde, José and Rodríguez Furlán, Cecilia and De Rycke, Riet and Norambuena, Lorena and Friml, Jirí and León, Gabriel and Tejos, Ricardo}, journal = {Plant Science}, pages = {10 -- 19}, publisher = {Elsevier}, title = {{Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development}}, doi = {10.1016/j.plantsci.2016.05.014}, volume = {250}, year = {2016}, } @article{1411, abstract = {We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn on a compact two-dimensional surface M with boundary. Each αi and each βj is either an arc meeting the boundary of M at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise such that the total number of crossings of the ai with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. The proofs rely, among other things, on a result concerning simultaneous planar drawings of graphs by Erten and Kobourov.}, author = {Matoušek, Jiří and Sedgwick, Eric and Tancer, Martin and Wagner, Uli}, journal = {Israel Journal of Mathematics}, number = {1}, pages = {37 -- 79}, publisher = {Springer}, title = {{Untangling two systems of noncrossing curves}}, doi = {10.1007/s11856-016-1294-9}, volume = {212}, year = {2016}, } @article{1412, abstract = {Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods.}, author = {Goldade, Ryan and Batty, Christopher and Wojtan, Christopher J}, journal = {Computer Graphics Forum}, number = {2}, pages = {233 -- 242}, publisher = {Wiley-Blackwell}, title = {{A practical method for high-resolution embedded liquid surfaces}}, doi = {10.1111/cgf.12826}, volume = {35}, year = {2016}, } @article{1413, abstract = {This paper generalizes the well-known Diffusion Curves Images (DCI), which are composed of a set of Bezier curves with colors specified on either side. These colors are diffused as Laplace functions over the image domain, which results in smooth color gradients interrupted by the Bezier curves. Our new formulation allows for more color control away from the boundary, providing a similar expressive power as recent Bilaplace image models without introducing associated issues and computational costs. The new model is based on a special Laplace function blending and a new edge blur formulation. We demonstrate that given some user-defined boundary curves over an input raster image, fitting colors and edge blur from the image to the new model and subsequent editing and animation is equally convenient as with DCIs. Numerous examples and comparisons to DCIs are presented.}, author = {Jeschke, Stefan}, journal = {Computer Graphics Forum}, number = {2}, pages = {71 -- 79}, publisher = {Wiley-Blackwell}, title = {{Generalized diffusion curves: An improved vector representation for smooth-shaded images}}, doi = {10.1111/cgf.12812}, volume = {35}, year = {2016}, } @article{1414, abstract = {In this paper, we present a method to model hyperelasticity that is well suited for representing the nonlinearity of real-world objects, as well as for estimating it from deformation examples. Previous approaches suffer several limitations, such as lack of integrability of elastic forces, failure to enforce energy convexity, lack of robustness of parameter estimation, or difficulty to model cross-modal effects. Our method avoids these problems by relying on a general energy-based definition of elastic properties. The accuracy of the resulting elastic model is maximized by defining an additive model of separable energy terms, which allow progressive parameter estimation. In addition, our method supports efficient modeling of extreme nonlinearities thanks to energy-limiting constraints. We combine our energy-based model with an optimization method to estimate model parameters from force-deformation examples, and we show successful modeling of diverse deformable objects, including cloth, human finger skin, and internal human anatomy in a medical imaging application.}, author = {Miguel Villalba, Eder and Miraut, David and Otaduy, Miguel}, journal = {Computer Graphics Forum}, number = {2}, pages = {385 -- 396}, publisher = {Wiley-Blackwell}, title = {{Modeling and estimation of energy-based hyperelastic objects}}, doi = {10.1111/cgf.12840}, volume = {35}, year = {2016}, } @article{1415, abstract = {The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation.}, author = {Ferstl, Florian and Ando, Ryoichi and Wojtan, Christopher J and Westermann, Rüdiger and Thuerey, Nils}, journal = {Computer Graphics Forum}, number = {2}, pages = {225 -- 232}, publisher = {Wiley-Blackwell}, title = {{Narrow band FLIP for liquid simulations}}, doi = {10.1111/cgf.12825}, volume = {35}, year = {2016}, } @article{1416, abstract = {Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven.}, author = {Van Loon, Erik and Katsnelson, Mikhail and Chomaz, Lauriane and Lemeshko, Mikhail}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {19}, publisher = {American Physical Society}, title = {{Interaction-driven Lifshitz transition with dipolar fermions in optical lattices}}, doi = {10.1103/PhysRevB.93.195145}, volume = {93}, year = {2016}, } @article{1417, abstract = {Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.}, author = {Simon, Sibu and Skůpa, Petr and Viaene, Tom and Zwiewka, Marta and Tejos, Ricardo and Klíma, Petr and Čarná, Mária and Rolčík, Jakub and De Rycke, Riet and Moreno, Ignacio and Dobrev, Petre and Orellana, Ariel and Zažímalová, Eva and Friml, Jirí}, journal = {New Phytologist}, number = {1}, pages = {65 -- 74}, publisher = {Wiley-Blackwell}, title = {{PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis}}, doi = {10.1111/nph.14019}, volume = {211}, year = {2016}, }