TY - JOUR
AB - We propose a new memetic strategy that can solve the multi-physics, complex inverse problems, formulated as the multi-objective optimization ones, in which objectives are misfits between the measured and simulated states of various governing processes. The multi-deme structure of the strategy allows for both, intensive, relatively cheap exploration with a moderate accuracy and more accurate search many regions of Pareto set in parallel. The special type of selection operator prefers the coherent alternative solutions, eliminating artifacts appearing in the particular processes. The additional accuracy increment is obtained by the parallel convex searches applied to the local scalarizations of the misfit vector. The strategy is dedicated for solving ill-conditioned problems, for which inverting the single physical process can lead to the ambiguous results. The skill of the selection in artifact elimination is shown on the benchmark problem, while the whole strategy was applied for identification of oil deposits, where the misfits are related to various frequencies of the magnetic and electric waves of the magnetotelluric measurements. 2016 Elsevier B.V.
AU - Gajda-Zagorska, Ewa P
AU - Schaefer, Robert
AU - Smołka, Maciej
AU - Pardo, David
AU - Alvarez Aramberri, Julen
ID - 1152
JF - Journal of Computational Science
SN - 18777503
TI - A multi objective memetic inverse solver reinforced by local optimization methods
VL - 18
ER -
TY - THES
AB - This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results.
AU - Daca, Przemyslaw
ID - 1155
TI - Statistical and logical methods for property checking
ER -
TY - JOUR
AB - Auxin steers numerous physiological processes in plants, making the tight control of its endogenous levels and spatiotemporal distribution a necessity. This regulation is achieved by different mechanisms, including auxin biosynthesis, metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic acid (c-CA) as a novel and unique addition to a small group of endogenous molecules affecting in planta auxin concentrations. c-CA is the photo-isomerization product of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes characteristic for high auxin levels, including inhibition of primary root growth, induction of root hairs, and promotion of adventitious and lateral rooting. By molecular docking and receptor binding assays, we showed that c-CA itself is neither an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux. Auxin signaling reporters detected changes in spatiotemporal distribution of the auxin response along the root of c-CA-treated plants, and long-distance auxin transport assays showed no inhibition of rootward auxin transport. Overall, these results suggest that the phenotypes of c-CA-treated plants are the consequence of a local change in auxin accumulation, induced by the inhibition of auxin efflux. This work reveals a novel mechanism how plants may regulate auxin levels and adds a novel, naturally occurring molecule to the chemical toolbox for the studies of auxin homeostasis.
AU - Steenackers, Ward
AU - Klíma, Petr
AU - Quareshy, Mussa
AU - Cesarino, Igor
AU - Kumpf, Robert
AU - Corneillie, Sander
AU - Araújo, Pedro
AU - Viaene, Tom
AU - Goeminne, Geert
AU - Nowack, Moritz
AU - Ljung, Karin
AU - Friml, Jirí
AU - Blakeslee, Joshua
AU - Novák, Ondřej
AU - Zažímalová, Eva
AU - Napier, Richard
AU - Boerjan, Wout
AU - Vanholme, Bartel
ID - 1159
IS - 1
JF - Plant Physiology
SN - 00320889
TI - Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation
VL - 173
ER -
TY - JOUR
AB - We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined be-tween two concentric independently rotating cylinders - consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying out systematic bifurcation analysis. Without magnetic field, we find steady flow patterns, previously observed with a simple fluid, such as those containing normal one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states. However, when a symmetry-breaking transverse magnetic field is present, all flow states exhibit stimulated, finite two-fold mode. Various bifurcations between steady and unsteady states can occur, corresponding to the transitions between the two-cell and one-cell states. While unsteady, axially oscillating flow states can arise, we also detect the emergence of new unsteady flow states. In particular, we uncover two new states: one contains only the azimuthally oscillating solution in the configuration of the twin-cell flow state, and an-other a rotating flow state. Topologically, these flow states are a limit cycle and a quasiperiodic solution on a two-torus, respectively. Emergence of new flow states in addition to observed ones with classical fluid, indicates that richer but potentially more controllable dynamics in ferrofluidic flows, as such flow states depend on the external magnetic field.
AU - Altmeyer, Sebastian
AU - Do, Younghae
AU - Lai, Ying
ID - 1160
JF - Scientific Reports
SN - 20452322
TI - Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio
VL - 7
ER -
TY - JOUR
AB - Selected universal experimental properties of high-temperature superconducting (HTS) cuprates have been singled out in the last decade. One of the pivotal challenges in this field is the designation of a consistent interpretation framework within which we can describe quantitatively the universal features of those systems. Here we analyze in a detailed manner the principal experimental data and compare them quantitatively with the approach based on a single-band model of strongly correlated electrons supplemented with strong antiferromagnetic (super)exchange interaction (the so-called t−J−U model). The model rationale is provided by estimating its microscopic parameters on the basis of the three-band approach for the Cu-O plane. We use our original full Gutzwiller wave-function solution by going beyond the renormalized mean-field theory (RMFT) in a systematic manner. Our approach reproduces very well the observed hole doping (δ) dependence of the kinetic-energy gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer features of the cuprates. The calculated Fermi velocity in the nodal direction is practically δ-independent and its universal value agrees very well with that determined experimentally. Also, a weak doping dependence of the Fermi wave vector leads to an almost constant value of the effective mass in a pure superconducting phase which is both observed in experiment and reproduced within our approach. An assessment of the currently used models (t−J, Hubbard) is carried out and the results of the canonical RMFT as a zeroth-order solution are provided for comparison to illustrate the necessity of the introduced higher-order contributions.
AU - Spałek, Jozef
AU - Zegrodnik, Michał
AU - Kaczmarczyk, Jan
ID - 1162
IS - 2
JF - Physical Review B - Condensed Matter and Materials Physics
SN - 24699950
TI - Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment
VL - 95
ER -
TY - JOUR
AB - Optimum experimental design theory has recently been extended for parameter estimation in copula models. The use of these models allows one to gain in flexibility by considering the model parameter set split into marginal and dependence parameters. However, this separation also leads to the natural issue of estimating only a subset of all model parameters. In this work, we treat this problem with the application of the (Formula presented.)-optimality to copula models. First, we provide an extension of the corresponding equivalence theory. Then, we analyze a wide range of flexible copula models to highlight the usefulness of (Formula presented.)-optimality in many possible scenarios. Finally, we discuss how the usage of the introduced design criterion also relates to the more general issue of copula selection and optimal design for model discrimination.
AU - Perrone, Elisa
AU - Rappold, Andreas
AU - Müller, Werner
ID - 1168
IS - 3
JF - Statistical Methods and Applications
TI - D inf s optimality in copula models
VL - 26
ER -
TY - JOUR
AB - Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies.
AU - Novak, Sebastian
AU - Kollár, Richard
ID - 1169
IS - 1
JF - Genetics
SN - 00166731
TI - Spatial gene frequency waves under genotype dependent dispersal
VL - 205
ER -
TY - JOUR
AB - We introduce the Voronoi functional of a triangulation of a finite set of points in the Euclidean plane and prove that among all geometric triangulations of the point set, the Delaunay triangulation maximizes the functional. This result neither extends to topological triangulations in the plane nor to geometric triangulations in three and higher dimensions.
AU - Edelsbrunner, Herbert
AU - Glazyrin, Alexey
AU - Musin, Oleg
AU - Nikitenko, Anton
ID - 1173
IS - 5
JF - Combinatorica
SN - 02099683
TI - The Voronoi functional is maximized by the Delaunay triangulation in the plane
VL - 37
ER -
TY - CONF
AB - Security of cryptographic applications is typically defined by security games. The adversary, within certain resources, cannot win with probability much better than 0 (for unpredictability applications, like one-way functions) or much better than 1/2 (indistinguishability applications for instance encryption schemes). In so called squared-friendly applications the winning probability of the adversary, for different values of the application secret randomness, is not only close to 0 or 1/2 on average, but also concentrated in the sense that its second central moment is small. The class of squared-friendly applications, which contains all unpredictability applications and many indistinguishability applications, is particularly important for key derivation. Barak et al. observed that for square-friendly applications one can beat the "RT-bound", extracting secure keys with significantly smaller entropy loss. In turn Dodis and Yu showed that in squared-friendly applications one can directly use a "weak" key, which has only high entropy, as a secure key. In this paper we give sharp lower bounds on square security assuming security for "weak" keys. We show that any application which is either (a) secure with weak keys or (b) allows for entropy savings for keys derived by universal hashing, must be square-friendly. Quantitatively, our lower bounds match the positive results of Dodis and Yu and Barak et al. (TCC\'13, CRYPTO\'11) Hence, they can be understood as a general characterization of squared-friendly applications. While the positive results on squared-friendly applications where derived by one clever application of the Cauchy-Schwarz Inequality, for tight lower bounds we need more machinery. In our approach we use convex optimization techniques and some theory of circular matrices.
AU - Skórski, Maciej
ID - 1174
SN - 18688969
TI - Lower bounds on key derivation for square-friendly applications
VL - 66
ER -
TY - CONF
AB - We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure.
AU - Alwen, Joel F
AU - De Rezende, Susanna
AU - Nordstrom, Jakob
AU - Vinyals, Marc
ED - Papadimitriou, Christos
ID - 1175
SN - 18688969
TI - Cumulative space in black-white pebbling and resolution
VL - 67
ER -
TY - CONF
AB - The algorithm Argon2i-B of Biryukov, Dinu and Khovratovich is currently being considered by the IRTF (Internet Research Task Force) as a new de-facto standard for password hashing. An older version (Argon2i-A) of the same algorithm was chosen as the winner of the recent Password Hashing Competition. An important competitor to Argon2i-B is the recently introduced Balloon Hashing (BH) algorithm of Corrigan-Gibs, Boneh and Schechter. A key security desiderata for any such algorithm is that evaluating it (even using a custom device) requires a large amount of memory amortized across multiple instances. Alwen and Blocki (CRYPTO 2016) introduced a class of theoretical attacks against Argon2i-A and BH. While these attacks yield large asymptotic reductions in the amount of memory, it was not, a priori, clear if (1) they can be extended to the newer Argon2i-B, (2) the attacks are effective on any algorithm for practical parameter ranges (e.g., 1GB of memory) and (3) if they can be effectively instantiated against any algorithm under realistic hardware constrains. In this work we answer all three of these questions in the affirmative for all three algorithms. This is also the first work to analyze the security of Argon2i-B. In more detail, we extend the theoretical attacks of Alwen and Blocki (CRYPTO 2016) to the recent Argon2i-B proposal demonstrating severe asymptotic deficiencies in its security. Next we introduce several novel heuristics for improving the attack's concrete memory efficiency even when on-chip memory bandwidth is bounded. We then simulate our attacks on randomly sampled Argon2i-A, Argon2i-B and BH instances and measure the resulting memory consumption for various practical parameter ranges and for a variety of upperbounds on the amount of parallelism available to the attacker. Finally we describe, implement, and test a new heuristic for applying the Alwen-Blocki attack to functions employing a technique developed by Corrigan-Gibs et al. for improving concrete security of memory-hard functions. We analyze the collected data and show the effects various parameters have on the memory consumption of the attack. In particular, we can draw several interesting conclusions about the level of security provided by these functions. · For the Alwen-Blocki attack to fail against practical memory parameters, Argon2i-B must be instantiated with more than 10 passes on memory - beyond the "paranoid" parameter setting in the current IRTF proposal. · The technique of Corrigan-Gibs for improving security can also be overcome by the Alwen-Blocki attack under realistic hardware constraints. · On a positive note, both the asymptotic and concrete security of Argon2i-B seem to improve on that of Argon2i-A.
AU - Alwen, Joel F
AU - Blocki, Jeremiah
ID - 1176
SN - 978-150905761-0
TI - Towards practical attacks on Argon2i and balloon hashing
ER -
TY - CONF
AB - For any pair (X, Z) of correlated random variables we can think of Z as a randomized function of X. If the domain of Z is small, one can make this function computationally efficient by allowing it to be only approximately correct. In folklore this problem is known as simulating auxiliary inputs. This idea of simulating auxiliary information turns out to be a very usefull tool, finding applications in complexity theory, cryptography, pseudorandomness and zero-knowledge. In this paper we revisit this problem, achieving the following results: (a) We present a novel boosting algorithm for constructing the simulator. This boosting proof is of independent interest, as it shows how to handle “negative mass” issues when constructing probability measures by shifting distinguishers in descent algorithms. Our technique essentially fixes the flaw in the TCC’14 paper “How to Fake Auxiliary Inputs”. (b) The complexity of our simulator is better than in previous works, including results derived from the uniform min-max theorem due to Vadhan and Zheng. To achieve (s,ϵ) -indistinguishability we need the complexity O(s⋅25ℓϵ−2) in time/circuit size, which improve previous bounds by a factor of ϵ−2. In particular, with we get meaningful provable security for the EUROCRYPT’09 leakage-resilient stream cipher instantiated with a standard 256-bit block cipher, like
AU - Skórski, Maciej
ID - 1178
TI - Simulating auxiliary inputs, revisited
VL - 9985
ER -
TY - JOUR
AB - In this article we define an algebraic vertex of a generalized polyhedron and show that the set of algebraic vertices is the smallest set of points needed to define the polyhedron. We prove that the indicator function of a generalized polytope P is a linear combination of indicator functions of simplices whose vertices are algebraic vertices of P. We also show that the indicator function of any generalized polyhedron is a linear combination, with integer coefficients, of indicator functions of cones with apices at algebraic vertices and line-cones. The concept of an algebraic vertex is closely related to the Fourier–Laplace transform. We show that a point v is an algebraic vertex of a generalized polyhedron P if and only if the tangent cone of P, at v, has non-zero Fourier–Laplace transform.
AU - Akopyan, Arseniy
AU - Bárány, Imre
AU - Robins, Sinai
ID - 1180
JF - Advances in Mathematics
SN - 00018708
TI - Algebraic vertices of non-convex polyhedra
VL - 308
ER -
TY - JOUR
AB - We construct efficient authentication protocols and message authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work—starting with the (Formula presented.) protocol of Hopper and Blum in 2001—until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle attacks. A MAC implies such a (two-round) protocol.
AU - Kiltz, Eike
AU - Pietrzak, Krzysztof Z
AU - Venturi, Daniele
AU - Cash, David
AU - Jain, Abhishek
ID - 1187
IS - 4
JF - Journal of Cryptology
TI - Efficient authentication from hard learning problems
VL - 30
ER -
TY - JOUR
AB - Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed.
AU - Kollár, Richard
AU - Novak, Sebastian
ID - 1191
IS - 3
JF - Bulletin of Mathematical Biology
TI - Existence of traveling waves for the generalized F–KPP equation
VL - 79
ER -
TY - CONF
AB - The main result of this paper is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even Δ-matroid constraints allows us to extend the tractability result to a larger class of Δ-matroids that includes many classes that were known to be tractable before, namely co-independent, compact, local and binary.
AU - Kazda, Alexandr
AU - Kolmogorov, Vladimir
AU - Rolinek, Michal
ID - 1192
SN - 978-161197478-2
TI - Even delta-matroids and the complexity of planar Boolean CSPs
ER -
TY - CONF
AB - Termination is one of the basic liveness properties, and we study the termination problem for probabilistic programs with real-valued variables. Previous works focused on the qualitative problem that asks whether an input program terminates with probability~1 (almost-sure termination). A powerful approach for this qualitative problem is the notion of ranking supermartingales with respect to a given set of invariants. The quantitative problem (probabilistic termination) asks for bounds on the termination probability. A fundamental and conceptual drawback of the existing approaches to address probabilistic termination is that even though the supermartingales consider the probabilistic behavior of the programs, the invariants are obtained completely ignoring the probabilistic aspect. In this work we address the probabilistic termination problem for linear-arithmetic probabilistic programs with nondeterminism. We define the notion of {\em stochastic invariants}, which are constraints along with a probability bound that the constraints hold. We introduce a concept of {\em repulsing supermartingales}. First, we show that repulsing supermartingales can be used to obtain bounds on the probability of the stochastic invariants. Second, we show the effectiveness of repulsing supermartingales in the following three ways: (1)~With a combination of ranking and repulsing supermartingales we can compute lower bounds on the probability of termination; (2)~repulsing supermartingales provide witnesses for refutation of almost-sure termination; and (3)~with a combination of ranking and repulsing supermartingales we can establish persistence properties of probabilistic programs. We also present results on related computational problems and an experimental evaluation of our approach on academic examples.
AU - Chatterjee, Krishnendu
AU - Novotny, Petr
AU - Zikelic, Djordje
ID - 1194
IS - 1
SN - 07308566
TI - Stochastic invariants for probabilistic termination
VL - 52
ER -
TY - JOUR
AB - We consider a model of fermions interacting via point interactions, defined via a certain weighted Dirichlet form. While for two particles the interaction corresponds to infinite scattering length, the presence of further particles effectively decreases the interaction strength. We show that the model becomes trivial in the thermodynamic limit, in the sense that the free energy density at any given particle density and temperature agrees with the corresponding expression for non-interacting particles.
AU - Moser, Thomas
AU - Seiringer, Robert
ID - 1198
IS - 3
JF - Letters in Mathematical Physics
SN - 03779017
TI - Triviality of a model of particles with point interactions in the thermodynamic limit
VL - 107
ER -
TY - JOUR
AB - Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.
AU - Barton, Nicholas H
ID - 1199
JF - Heredity
TI - How does epistasis influence the response to selection?
VL - 118
ER -
TY - JOUR
AB - The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix.
AU - Bao, Zhigang
AU - Erdös, László
AU - Schnelli, Kevin
ID - 1207
IS - 3
JF - Communications in Mathematical Physics
SN - 00103616
TI - Local law of addition of random matrices on optimal scale
VL - 349
ER -
TY - JOUR
AB - We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd.
AU - Zwiernik, Piotr
AU - Uhler, Caroline
AU - Richards, Donald
ID - 1208
IS - 4
JF - Journal of the Royal Statistical Society. Series B: Statistical Methodology
SN - 13697412
TI - Maximum likelihood estimation for linear Gaussian covariance models
VL - 79
ER -
TY - JOUR
AB - Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.
AU - Budanur, Nazmi B
AU - Cvitanović, Predrag
ID - 1211
IS - 3-4
JF - Journal of Statistical Physics
TI - Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system
VL - 167
ER -
TY - JOUR
AB - Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.
AU - Sauerzopf, Ulrich
AU - Sacco, Roberto
AU - Novarino, Gaia
AU - Niello, Marco
AU - Weidenauer, Ana
AU - Praschak Rieder, Nicole
AU - Sitte, Harald
AU - Willeit, Matthaeus
ID - 1228
IS - 1
JF - European Journal of Neuroscience
TI - Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence
VL - 45
ER -
TY - JOUR
AB - The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics.
AU - Waitukaitis, Scott R
AU - Zuiderwijk, Antal
AU - Souslov, Anton
AU - Coulais, Corentin
AU - Van Hecke, Martin
ID - 123
IS - 11
JF - Nature Physics
TI - Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing
VL - 13
ER -
TY - JOUR
AB - We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor ½ cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.
AU - Akopyan, Arseniy
AU - Vysotsky, Vladislav
ID - 909
IS - 7
JF - The American Mathematical Monthly
SN - 00029890
TI - On the lengths of curves passing through boundary points of a planar convex shape
VL - 124
ER -
TY - JOUR
AB - Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.
AU - Novak, Sebastian
AU - Barton, Nicholas H
ID - 910
IS - 2
JF - Genetics
TI - When does frequency-independent selection maintain genetic variation?
VL - 207
ER -
TY - CONF
AB - We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset.
AU - Royer, Amélie
AU - Kolesnikov, Alexander
AU - Lampert, Christoph
ID - 911
TI - Probabilistic image colorization
ER -
TY - JOUR
AB - We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.
AU - Deuchert, Andreas
ID - 912
IS - 8
JF - Journal of Mathematical Physics
SN - 00222488
TI - A lower bound for the BCS functional with boundary conditions at infinity
VL - 58
ER -
TY - JOUR
AB - Pools of air cooled by partial rain evaporation span up to several hundreds of kilometers in nature and typically last less than 1 day, ultimately losing their identity to the large-scale flow. These fundamentally differ in character from the radiatively-driven dry pools defining convective aggregation. Advancement in remote sensing and in computer capabilities has promoted exploration of how precipitation-induced cold pool processes modify the convective spectrum and life cycle. This contribution surveys current understanding of such cold pools over the tropical and subtropical oceans. In shallow convection with low rain rates, the cold pools moisten, preserving the near-surface equivalent potential temperature or increasing it if the surface moisture fluxes cannot ventilate beyond the new surface layer; both conditions indicate downdraft origin air from within the boundary layer. When rain rates exceed ∼ 2 mm h−1, convective-scale downdrafts can bring down drier air of lower equivalent potential temperature from above the boundary layer. The resulting density currents facilitate the lifting of locally thermodynamically favorable air and can impose an arc-shaped mesoscale cloud organization. This organization allows clouds capable of reaching 4–5 km within otherwise dry environments. These are more commonly observed in the northern hemisphere trade wind regime, where the flow to the intertropical convergence zone is unimpeded by the equator. Their near-surface air properties share much with those shown from cold pools sampled in the equatorial Indian Ocean. Cold pools are most effective at influencing the mesoscale organization when the atmosphere is moist in the lower free troposphere and dry above, suggesting an optimal range of water vapor paths. Outstanding questions on the relationship between cold pools, their accompanying moisture distribution and cloud cover are detailed further. Near-surface water vapor rings are documented in one model inside but near the cold pool edge; these are not consistent with observations, but do improve with smaller horizontal grid spacings.
AU - Zuidema, Paquita
AU - Torri, Giuseppe
AU - MULLER, Caroline J
AU - Chandra, Arunchandra
ID - 9137
IS - 6
JF - Surveys in Geophysics
KW - Geochemistry and Petrology
KW - Geophysics
SN - 0169-3298
TI - A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment
VL - 38
ER -
TY - JOUR
AB - Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.
AU - Holloway, Christopher E.
AU - Wing, Allison A.
AU - Bony, Sandrine
AU - MULLER, Caroline J
AU - Masunaga, Hirohiko
AU - L’Ecuyer, Tristan S.
AU - Turner, David D.
AU - Zuidema, Paquita
ID - 9138
IS - 6
JF - Surveys in Geophysics
KW - Geochemistry and Petrology
KW - Geophysics
SN - 0169-3298
TI - Observing convective aggregation
VL - 38
ER -
TY - JOUR
AB - Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.
AU - Giehr, Julia
AU - Grasse, Anna V
AU - Cremer, Sylvia
AU - Heinze, Jürgen
AU - Schrempf, Alexandra
ID - 914
IS - 7
JF - Royal Society Open Science
SN - 20545703
TI - Ant queens increase their reproductive efforts after pathogen infection
VL - 4
ER -
TY - CONF
AB - We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.
AU - Swoboda, Paul
AU - Andres, Bjoern
ID - 915
SN - 978-153860457-1
TI - A message passing algorithm for the minimum cost multicut problem
VL - 2017
ER -
TY - JOUR
AB - Previous numerical studies of the dissipation of internal tides in idealized settings suggest the existence of a critical latitude (~29°) where dissipation is enhanced. But observations only indicate a modest enhancement at this latitude. To resolve this difference between observational and numerical results, the authors study the latitudinal dependence of internal tides’ dissipation in more realistic conditions. In particular, the ocean is not a quiescent medium; the presence of large-scale currents or mesoscale eddies can impact the propagation and dissipation of internal tides. This paper investigates the impact of a weak background mean current in numerical simulations. The authors focus on the local dissipation of high spatial mode internal waves near their generation site. The vertical profile of dissipation and its variation with latitude without the mean current are consistent with earlier studies. But adding a weak mean current has a major impact on the latitudinal distribution of dissipation. The peak at the critical latitude disappears, and the dissipation is closer to a constant, albeit with two weak peaks at ~25° and ~35° latitude. This disappearance results from the Doppler shift of the internal tides’ frequency, which hinders the nonlinear transfer of energy to small-scale secondary waves via the parametric subharmonic instability (PSI). The new two weak peaks correspond to the Doppler-shifted critical latitudes of the left- and right-propagating waves. The results are confirmed in simulations with simple sinusoidal topography. Thus, although nonlinear transfers via PSI are efficient at dissipating internal tides, the exact location of the dissipation is sensitive to large-scale oceanic conditions.
AU - Richet, O.
AU - MULLER, Caroline J
AU - Chomaz, J.-M.
ID - 9152
IS - 6
JF - Journal of Physical Oceanography
KW - Oceanography
SN - 0022-3670
TI - Impact of a mean current on the internal tide energy dissipation at the critical latitude
VL - 47
ER -
TY - CONF
AB - We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each.
AU - Swoboda, Paul
AU - Rother, Carsten
AU - Abu Alhaija, Carsten
AU - Kainmueller, Dagmar
AU - Savchynskyy, Bogdan
ID - 916
SN - 978-153860457-1
TI - A study of lagrangean decompositions and dual ascent solvers for graph matching
VL - 2017
ER -
TY - CONF
AB - We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers.
AU - Swoboda, Paul
AU - Kuske, Jan
AU - Savchynskyy, Bogdan
ID - 917
SN - 978-153860457-1
TI - A dual ascent framework for Lagrangean decomposition of combinatorial problems
VL - 2017
ER -
TY - JOUR
AB - An electro-optomechanical device capable of microwave-to-optics conversion has recently been demonstrated, with the vision of enabling optical networks of superconducting qubits. Here we present an improved converter design that uses a three-dimensional microwave cavity for coupling between the microwave transmission line and an integrated LC resonator on the converter chip. The new design simplifies the optical assembly and decouples it from the microwave part of the setup. Experimental demonstrations show that the modular device assembly allows us to flexibly tune the microwave coupling to the converter chip while maintaining small loss. We also find that electromechanical experiments are not impacted by the additional microwave cavity. Our design is compatible with a high-finesse optical cavity and will improve optical performance.
AU - Menke, Tim
AU - Burns, Peter
AU - Higginbotham, Andrew P
AU - Kampel, N S
AU - Peterson, Robert
AU - Cicak, Katarina
AU - Simmonds, Raymond
AU - Regal, Cindy
AU - Lehnert, Konrad
ID - 93
IS - 9
JF - Review of Scientific Instruments
TI - Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device
VL - 88
ER -
TY - THES
AB - The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.
AU - Adamowski, Maciek
ID - 938
TI - Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana
ER -
TY - JOUR
AB - We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding.
AU - Midya, Bikashkali
AU - Konotop, Vladimir
ID - 939
IS - 3
JF - Physical Review Letters
SN - 00319007
TI - Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons
VL - 119
ER -
TY - JOUR
AB - We introduce a method for breaking Lorentz reciprocity based upon the noncommutation of frequency conversion and delay. The method requires no magnetic materials or resonant physics, allowing for the design of scalable and broadband nonreciprocal circuits. With this approach, two types of gyrators - universal building blocks for linear, nonreciprocal circuits - are constructed. Using one of these gyrators, we create a circulator with >15 dB of isolation across the 5-9 GHz band. Our designs may be readily extended to any platform with suitable frequency conversion elements, including semiconducting devices for telecommunication or an on-chip superconducting implementation for quantum information processing.
AU - Rosenthal, Eric
AU - Chapman, Benjamin
AU - Higginbotham, Andrew P
AU - Kerckhoff, Joseph
AU - Lehnert, Konrad
ID - 94
IS - 14
JF - APS Physics, Physical Review Letters
TI - Breaking Lorentz reciprocity with frequency conversion and delay
VL - 119
ER -
TY - JOUR
AB - Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation.
AU - Zagórski, Marcin P
AU - Tabata, Yoji
AU - Brandenberg, Nathalie
AU - Lutolf, Matthias
AU - Tkacik, Gasper
AU - Bollenbach, Tobias
AU - Briscoe, James
AU - Kicheva, Anna
ID - 943
IS - 6345
JF - Science
SN - 00368075
TI - Decoding of position in the developing neural tube from antiparallel morphogen gradients
VL - 356
ER -
TY - JOUR
AB - While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.
AU - Huylmans, Ann K
AU - Macon, Ariana
AU - Vicoso, Beatriz
ID - 945
IS - 10
JF - Molecular Biology and Evolution
SN - 07374038
TI - Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome
VL - 34
ER -
TY - JOUR
AB - Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.
AU - Von Wangenheim, Daniel
AU - Hauschild, Robert
AU - Fendrych, Matyas
AU - Barone, Vanessa
AU - Benková, Eva
AU - Friml, Jirí
ID - 946
JF - eLife
TI - Live tracking of moving samples in confocal microscopy for vertically grown roots
VL - 6
ER -
TY - JOUR
AB - Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.
AU - De Martino, Daniele
AU - Capuani, Fabrizio
AU - De Martino, Andrea
ID - 947
IS - 1
JF - Physical Review E Statistical Nonlinear and Soft Matter Physics
SN - 24700045
TI - Quantifying the entropic cost of cellular growth control
VL - 96
ER -
TY - CONF
AB - Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\in [0,1] such that if\PO's budget exceeds $t$, he can win the game, and if\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games.
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Chonev, Ventsislav K
ID - 950
SN - 1868-8969
TI - Infinite-duration bidding games
VL - 85
ER -
TY - JOUR
AB - Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo
AU - Schmidt, Tom
AU - Barton, Nicholas H
AU - Rasic, Gordana
AU - Turley, Andrew
AU - Montgomery, Brian
AU - Iturbe Ormaetxe, Inaki
AU - Cook, Peter
AU - Ryan, Peter
AU - Ritchie, Scott
AU - Hoffmann, Ary
AU - O’Neill, Scott
AU - Turelli, Michael
ID - 951
IS - 5
JF - PLoS Biology
SN - 15449173
TI - Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti
VL - 15
ER -
TY - JOUR
AB - A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area.
AU - Turelli, Michael
AU - Barton, Nicholas H
ID - 952
JF - Theoretical Population Biology
SN - 00405809
TI - Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti
VL - 115
ER -
TY - JOUR
AB - The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.
AU - Charlesworth, Deborah
AU - Barton, Nicholas H
AU - Charlesworth, Brian
ID - 953
IS - 1855
JF - Proceedings of the Royal Society of London Series B Biological Sciences
TI - The sources of adaptive evolution
VL - 284
ER -
TY - JOUR
AB - Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.
AU - Lagator, Mato
AU - Paixao, Tiago
AU - Barton, Nicholas H
AU - Bollback, Jonathan P
AU - Guet, Calin C
ID - 954
JF - eLife
SN - 2050084X
TI - On the mechanistic nature of epistasis in a canonical cis-regulatory element
VL - 6
ER -
TY - JOUR
AB - Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.
AU - Friedlander, Tamar
AU - Prizak, Roshan
AU - Barton, Nicholas H
AU - Tkacik, Gasper
ID - 955
IS - 1
JF - Nature Communications
SN - 20411723
TI - Evolution of new regulatory functions on biophysically realistic fitness landscapes
VL - 8
ER -
TY - JOUR
AB - We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance.
AU - Carlen, Eric
AU - Maas, Jan
ID - 956
IS - 5
JF - Journal of Functional Analysis
SN - 00221236
TI - Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance
VL - 273
ER -