@inproceedings{11832, abstract = {In this paper, we study the problem of opening centers to cluster a set of clients in a metric space so as to minimize the sum of the costs of the centers and of the cluster radii, in a dynamic environment where clients arrive and depart, and the solution must be updated efficiently while remaining competitive with respect to the current optimal solution. We call this dynamic sum-of-radii clustering problem. We present a data structure that maintains a solution whose cost is within a constant factor of the cost of an optimal solution in metric spaces with bounded doubling dimension and whose worst-case update time is logarithmic in the parameters of the problem.}, author = {Henzinger, Monika H and Leniowski, Dariusz and Mathieu, Claire}, booktitle = {25th Annual European Symposium on Algorithms}, isbn = {978-3-95977-049-1}, issn = {1868-8969}, location = {Vienna, Austria}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Dynamic clustering to minimize the sum of radii}}, doi = {10.4230/LIPICS.ESA.2017.48}, volume = {87}, year = {2017}, } @inproceedings{11874, abstract = {We consider the problem of maintaining an approximately maximum (fractional) matching and an approximately minimum vertex cover in a dynamic graph. Starting with the seminal paper by Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. There remains, however, a polynomial gap between the best known worst case update time and the best known amortised update time for this problem, even after allowing for randomisation. Specifically, Bernstein and Stein [ICALP 2015, SODA 2016] have the best known worst case update time. They present a deterministic data structure with approximation ratio (3/2 + ∊) and worst case update time O(m1/4/ ∊2), where m is the number of edges in the graph. In recent past, Gupta and Peng [FOCS 2013] gave a deterministic data structure with approximation ratio (1+ ∊) and worst case update time No known randomised data structure beats the worst case update times of these two results. In contrast, the paper by Onak and Rubinfeld [STOC 2010] gave a randomised data structure with approximation ratio O(1) and amortised update time O(log2 n), where n is the number of nodes in the graph. This was later improved by Baswana, Gupta and Sen [FOCS 2011] and Solomon [FOCS 2016], leading to a randomised date structure with approximation ratio 2 and amortised update time O(1). We bridge the polynomial gap between the worst case and amortised update times for this problem, without using any randomisation. We present a deterministic data structure with approximation ratio (2 + ∊) and worst case update time O(log3 n), for all sufficiently small constants ∊.}, author = {Bhattacharya, Sayan and Henzinger, Monika H and Nanongkai, Danupon}, booktitle = {28th Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {Barcelona, Spain}, pages = {470 -- 489}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time}}, doi = {10.1137/1.9781611974782.30}, year = {2017}, } @inproceedings{11873, abstract = {We study the problem of computing a minimum cut in a simple, undirected graph and give a deterministic O(m log2 n log log2 n) time algorithm. This improves both on the best previously known deterministic running time of O(m log12 n) (Kawarabayashi and Thorup [12]) and the best previously known randomized running time of O(mlog3n) (Karger [11]) for this problem, though Karger's algorithm can be further applied to weighted graphs. Our approach is using the Kawarabayashi and Tho- rup graph compression technique, which repeatedly finds low-conductance cuts. To find these cuts they use a diffusion-based local algorithm. We use instead a flow- based local algorithm and suitably adjust their framework to work with our flow-based subroutine. Both flow and diffusion based methods have a long history of being applied to finding low conductance cuts. Diffusion algorithms have several variants that are naturally local while it is more complicated to make flow methods local. Some prior work has proven nice properties for local flow based algorithms with respect to improving or cleaning up low conductance cuts. Our flow subroutine, however, is the first that is both local and produces low conductance cuts. Thus, it may be of independent interest.}, author = {Henzinger, Monika H and Rao, Satish and Wang, Di}, booktitle = {28th Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {Barcelona, Spain}, pages = {1919--1938}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Local flow partitioning for faster edge connectivity}}, doi = {10.1137/1.9781611974782.125}, year = {2017}, } @inproceedings{11831, abstract = {Graph Sparsification aims at compressing large graphs into smaller ones while (approximately) preserving important characteristics of the input graph. In this work we study Vertex Sparsifiers, i.e., sparsifiers whose goal is to reduce the number of vertices. Given a weighted graph G=(V,E), and a terminal set K with |K|=k, a quality-q vertex cut sparsifier of G is a graph H with K contained in V_H that preserves the value of minimum cuts separating any bipartition of K, up to a factor of q. We show that planar graphs with all the k terminals lying on the same face admit quality-1 vertex cut sparsifier of size O(k^2) that are also planar. Our result extends to vertex flow and distance sparsifiers. It improves the previous best known bound of O(k^2 2^(2k)) for cut and flow sparsifiers by an exponential factor, and matches an Omega(k^2) lower-bound for this class of graphs. We also study vertex reachability sparsifiers for directed graphs. Given a digraph G=(V,E) and a terminal set K, a vertex reachability sparsifier of G is a digraph H=(V_H,E_H), K contained in V_H that preserves all reachability information among terminal pairs. We introduce the notion of reachability-preserving minors, i.e., we require H to be a minor of G. Among others, for general planar digraphs, we construct reachability-preserving minors of size O(k^2 log^2 k). We complement our upper-bound by showing that there exists an infinite family of acyclic planar digraphs such that any reachability-preserving minor must have Omega(k^2) vertices.}, author = {Goranci, Gramoz and Henzinger, Monika H and Peng, Pan}, booktitle = {25th Annual European Symposium on Algorithms}, isbn = {978-3-95977-049-1}, issn = {1868-8969}, location = {Vienna, Austria}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Improved guarantees for vertex sparsification in planar graphs}}, doi = {10.4230/LIPICS.ESA.2017.44}, volume = {87}, year = {2017}, } @article{11903, abstract = {Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1−1/e). (2) On the positive side we present (i) an 𝑂(𝑛√)-approximation algorithm for general concave externality functions, (ii) an O(log m)-approximation algorithm for linear externality functions, and (iii) a 518(1−1/𝑒)-approximation algorithm for 2-hop step function externalities. We also improve the result from [7] for 1-hop step function externalities by giving a 12(1−1/𝑒)-approximation algorithm.}, author = {Bhattacharya, Sayan and Dvořák, Wolfgang and Henzinger, Monika H and Starnberger, Martin}, issn = {1433-0490}, journal = {Theory of Computing Systems}, number = {4}, pages = {948--986}, publisher = {Springer Nature}, title = {{Welfare maximization with friends-of-friends network externalities}}, doi = {10.1007/s00224-017-9759-8}, volume = {61}, year = {2017}, } @article{1191, abstract = {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.}, author = {Kollár, Richard and Novak, Sebastian}, journal = {Bulletin of Mathematical Biology}, number = {3}, pages = {525--559}, publisher = {Springer}, title = {{Existence of traveling waves for the generalized F–KPP equation}}, doi = {10.1007/s11538-016-0244-3}, volume = {79}, year = {2017}, } @article{11976, abstract = {The way organic multistep synthesis is performed is changing due to the adoption of flow chemical techniques, which has enabled the development of improved methods to make complex molecules. The modular nature of the technique provides not only access to target molecules via linear flow approaches but also for the targeting of structural cores with single systems. This perspective article summarizes the state of the art of continuous multistep synthesis and discusses the main challenges and opportunities in this area.}, author = {Pieber, Bartholomäus and Gilmore, Kerry and Seeberger, Peter H.}, issn = {2063-0212}, journal = {Journal of Flow Chemistry}, number = {3-4}, pages = {129--136}, publisher = {AKJournals}, title = {{Integrated flow processing - challenges in continuous multistep synthesis}}, doi = {10.1556/1846.2017.00016}, volume = {7}, year = {2017}, } @article{1211, abstract = {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.}, author = {Budanur, Nazmi B and Cvitanović, Predrag}, journal = {Journal of Statistical Physics}, number = {3-4}, pages = {636--655}, publisher = {Springer}, title = {{Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system}}, doi = {10.1007/s10955-016-1672-z}, volume = {167}, year = {2017}, } @article{123, abstract = {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.}, author = {Waitukaitis, Scott R and Zuiderwijk, Antal and Souslov, Anton and Coulais, Corentin and Van Hecke, Martin}, journal = {Nature Physics}, number = {11}, pages = {1095 -- 1099}, publisher = {Nature Publishing Group}, title = {{Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing}}, doi = {10.1038/nphys4194}, volume = {13}, year = {2017}, } @inproceedings{12571, abstract = {We consider the problems of maintaining approximate maximum matching and minimum vertex cover in a dynamic graph. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized 2-approximation dynamic algorithm for this problem that has amortized update time of O(1) with high probability. We consider the natural open question of derandomizing this result. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya, Henzinger and Italiano [SODA 2015]; it had an approximation ratio of (2+ϵ) and an amortized update time of O(logn/ϵ2). Our result can be generalized to give a fully dynamic O(f3)-approximation algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional matching problems, where every hyperedge has at most f vertices.}, author = {Bhattacharya, Sayan and Chakrabarty, Deeparnab and Henzinger, Monika H}, booktitle = {19th International Conference on Integer Programming and Combinatorial Optimization}, isbn = {9783319592497}, issn = {0302-9743}, location = {Waterloo, ON, Canada}, pages = {86--98}, publisher = {Springer Nature}, title = {{Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time}}, doi = {10.1007/978-3-319-59250-3_8}, volume = {10328}, year = {2017}, } @article{1113, abstract = {A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth.}, author = {Fulek, Radoslav and Pelsmajer, Michael and Schaefer, Marcus}, journal = {Journal of Graph Algorithms and Applications}, number = {1}, pages = {135 -- 154}, publisher = {Brown University}, title = {{Hanani-Tutte for radial planarity}}, doi = {10.7155/jgaa.00408}, volume = {21}, year = {2017}, } @article{169, abstract = {We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3.}, author = {Browning, Timothy D and Kumaraswamy, Vinay and Steiner, Rapael}, journal = {International Mathematics Research Notices}, publisher = {Oxford University Press}, title = {{Twisted Linnik implies optimal covering exponent for S3}}, doi = {10.1093/imrn/rnx116}, year = {2017}, } @article{172, abstract = {We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg.}, author = {Browning, Timothy D and Schindler, Damaris}, journal = {International Mathematics Research Notices}, publisher = {Oxford University Press}, title = {{Strong approximation and a conjecture of Harpaz and Wittenberg}}, doi = {10.1093/imrn/rnx252}, year = {2017}, } @article{393, abstract = {We use a three-pulse ultrafast optical spectroscopy to study the relaxation processes in a frustrated Mott insulator Na2IrO3. By being able to independently produce the out-of-equilibrium bound states (excitons) of doublons and holons with the first pulse and suppress the underlying antiferromagnetic order with the second one, we were able to elucidate the relaxation mechanism of quasiparticles in this system. By observing the difference in the exciton dynamics in the magnetically ordered and disordered phases we found that the mass of this quasiparticle is mostly determined by its interaction with the surrounding spins. }, author = {Alpichshev, Zhanybek and Sie, Edbert and Mahmood, Fahad and Cao, Gang and Gedik, Nuh}, journal = {Physical Review B}, number = {23}, publisher = {American Physical Society}, title = {{Origin of the exciton mass in the frustrated Mott insulator Na2IrO3}}, doi = {10.1103/PhysRevB.96.235141}, volume = {96}, year = {2017}, } @article{392, abstract = {We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static.}, author = {Vishik, Inna and Mahmood, Fahad and Alpichshev, Zhanybek and Gedik, Nuh and Higgins, Joshu and Greene, Richard}, journal = {Physical Review B}, number = {11}, publisher = {American Physical Society}, title = {{Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ}}, doi = {10.1103/PhysRevB.95.115125}, volume = {95}, year = {2017}, } @article{443, abstract = {Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited.}, author = {Hardie, Rae and Van Dam, Ellen and Cowley, Mark and Han, Ting and Balaban, Seher and Pajic, Marina and Pinese, Mark and Iconomou, Mary and Shearer, Robert and Mckenna, Jessie and Miller, David and Waddell, Nicola and Pearson, John and Grimmond, Sean and Sazanov, Leonid A and Biankin, Andrew and Villas Boas, Silas and Hoy, Andrew and Turner, Nigel and Saunders, Darren}, journal = {Cancer & Metabolism}, number = {2}, publisher = {BioMed Central}, title = {{Mitochondrial mutations and metabolic adaptation in pancreatic cancer}}, doi = {10.1186/s40170-017-0164-1}, volume = {5}, year = {2017}, } @article{445, abstract = {The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase.}, author = {Maksym Serbyn and Abanin, Dimitry A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {1}, publisher = {American Physical Society}, title = {{Loschmidt echo in many body localized phases}}, doi = {10.1103/PhysRevB.96.014202}, volume = {96}, year = {2017}, } @article{453, abstract = {Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.}, author = {Fallesen, Todd and Roostalu, Johanna and Düllberg, Christian F and Pruessner, Gunnar and Surrey, Thomas}, journal = {Biophysical Journal}, number = {9}, pages = {2055 -- 2067}, publisher = {Biophysical Society}, title = {{Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement}}, doi = {10.1016/j.bpj.2017.09.006}, volume = {113}, year = {2017}, } @article{464, abstract = {The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years.}, author = {Chatterjee, Krishnendu and Henzinger, Monika H and Loitzenbauer, Veronika}, issn = {1860-5974}, journal = {Logical Methods in Computer Science}, number = {3}, publisher = {International Federation of Computational Logic}, title = {{Improved algorithms for parity and Streett objectives}}, doi = {10.23638/LMCS-13(3:26)2017}, volume = {13}, year = {2017}, } @article{470, abstract = {This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios.}, author = {Jeschke, Stefan and Wojtan, Christopher J}, issn = {07300301}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Water wave packets}}, doi = {10.1145/3072959.3073678}, volume = {36}, year = {2017}, } @article{471, abstract = {We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. }, author = {Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Petrov, Tatjana}, issn = {15293785}, journal = {ACM Transactions on Computational Logic (TOCL)}, number = {2}, publisher = {ACM}, title = {{Faster statistical model checking for unbounded temporal properties}}, doi = {10.1145/3060139}, volume = {18}, year = {2017}, } @article{481, abstract = {We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.}, author = {Biedl, Therese and Huber, Stefan and Palfrader, Peter}, journal = {International Journal of Computational Geometry and Applications}, number = {3-4}, pages = {211 -- 229}, publisher = {World Scientific Publishing}, title = {{Planar matchings for weighted straight skeletons}}, doi = {10.1142/S0218195916600050}, volume = {26}, year = {2017}, } @article{484, abstract = {We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory.}, author = {Nam, Phan and Napiórkowski, Marcin M}, issn = {10950761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {3}, pages = {683 -- 738}, publisher = {International Press}, title = {{Bogoliubov correction to the mean-field dynamics of interacting bosons}}, doi = {10.4310/ATMP.2017.v21.n3.a4}, volume = {21}, year = {2017}, } @article{483, abstract = {We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices.}, author = {Bourgade, Paul and Erdös, László and Yau, Horng and Yin, Jun}, issn = {10950761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {3}, pages = {739 -- 800}, publisher = {International Press}, title = {{Universality for a class of random band matrices}}, doi = {10.4310/ATMP.2017.v21.n3.a5}, volume = {21}, year = {2017}, } @article{514, abstract = {Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.}, author = {Simonnet, Jean and Nassar, Mérie and Stella, Federico and Cohen, Ivan and Mathon, Bertrand and Boccara, Charlotte and Miles, Richard and Fricker, Desdemona}, issn = {20411723}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum}}, doi = {10.1038/ncomms16032}, volume = {8}, year = {2017}, } @article{515, abstract = {The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.}, author = {Letts, James A and Sazanov, Leonid A}, issn = {15459993}, journal = {Nature Structural and Molecular Biology}, number = {10}, pages = {800 -- 808}, publisher = {Nature Publishing Group}, title = {{Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain}}, doi = {10.1038/nsmb.3460}, volume = {24}, year = {2017}, } @article{513, abstract = {We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction.}, author = {Klotz, Lukasz and Lemoult, Grégoire M and Frontczak, Idalia and Tuckerman, Laurette and Wesfreid, José}, journal = {Physical Review Fluids}, number = {4}, publisher = {American Physical Society}, title = {{Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence}}, doi = {10.1103/PhysRevFluids.2.043904}, volume = {2}, year = {2017}, } @article{521, abstract = {Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension.}, author = {Austin, Kyle and Virk, Ziga}, issn = {01668641}, journal = {Topology and its Applications}, pages = {45 -- 57}, publisher = {Elsevier}, title = {{Higson compactification and dimension raising}}, doi = {10.1016/j.topol.2016.10.005}, volume = {215}, year = {2017}, } @article{525, abstract = {The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity. }, author = {Daniel von Wangenheim and Goh, Tatsuaki and Dietrich, Daniela and Bennett, Malcolm J}, journal = {Current Biology}, number = {5}, pages = {R172 -- R174}, publisher = {Cell Press}, title = {{Plant biology: Building barriers… in roots}}, doi = {10.1016/j.cub.2017.01.060}, volume = {27}, year = {2017}, } @article{534, 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}, issn = {01795376}, journal = {Discrete & Computational Geometry}, number = {4}, pages = {871 -- 888}, publisher = {Springer}, title = {{Finding non-orientable surfaces in 3-Manifolds}}, doi = {10.1007/s00454-017-9900-0}, volume = {58}, year = {2017}, } @article{538, abstract = {Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. }, author = {Kainrath, Stephanie and Stadler, Manuela and Gschaider-Reichhart, Eva and Distel, Martin and Janovjak, Harald L}, journal = {Angewandte Chemie}, number = {16}, pages = {4679 -- 4682}, publisher = {Wiley}, title = {{Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen}}, doi = {10.1002/ange.201611998}, volume = {129}, year = {2017}, } @article{540, abstract = {RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host.}, author = {Khamina, Kseniya and Lercher, Alexander and Caldera, Michael and Schliehe, Christopher and Vilagos, Bojan and Sahin, Mehmet and Kosack, Lindsay and Bhattacharya, Anannya and Májek, Peter and Stukalov, Alexey and Sacco, Roberto and James, Leo and Pinschewer, Daniel and Bennett, Keiryn and Menche, Jörg and Bergthaler, Andreas}, issn = {15537366}, journal = {PLoS Pathogens}, number = {12}, publisher = {Public Library of Science}, title = {{Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein}}, doi = {10.1371/journal.ppat.1006758}, volume = {13}, year = {2017}, } @article{466, abstract = {We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. }, author = {Chatterjee, Krishnendu and Křetínská, Zuzana and Kretinsky, Jan}, issn = {18605974}, journal = {Logical Methods in Computer Science}, number = {2}, publisher = {International Federation of Computational Logic}, title = {{Unifying two views on multiple mean-payoff objectives in Markov decision processes}}, doi = {10.23638/LMCS-13(2:15)2017}, volume = {13}, year = {2017}, } @article{467, abstract = {Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, issn = {15293785}, journal = {ACM Transactions on Computational Logic (TOCL)}, number = {4}, publisher = {ACM}, title = {{Nested weighted automata}}, doi = {10.1145/3152769}, volume = {18}, year = {2017}, } @article{465, abstract = {The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. }, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Otop, Jan}, issn = {18605974}, journal = {Logical Methods in Computer Science}, number = {3}, publisher = {International Federation of Computational Logic}, title = {{Edit distance for pushdown automata}}, doi = {10.23638/LMCS-13(3:23)2017}, volume = {13}, year = {2017}, } @article{512, abstract = {The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. }, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin}, issn = {20452322}, journal = {Scientific Reports}, number = {1}, publisher = {Nature Publishing Group}, title = {{Amplification on undirected population structures: Comets beat stars}}, doi = {10.1038/s41598-017-00107-w}, volume = {7}, year = {2017}, } @article{10416, abstract = {A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.}, author = {Chatterjee, Krishnendu and Choudhary, Bhavya and Pavlogiannis, Andreas}, issn = {2475-1421}, journal = {Proceedings of the ACM on Programming Languages}, location = {Los Angeles, CA, United States}, number = {POPL}, publisher = {Association for Computing Machinery}, title = {{Optimal Dyck reachability for data-dependence and Alias analysis}}, doi = {10.1145/3158118}, volume = {2}, year = {2017}, } @misc{5455, abstract = {A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks.}, author = {Chatterjee, Krishnendu and Choudhary, Bhavya and Pavlogiannis, Andreas}, issn = {2664-1690}, pages = {37}, publisher = {IST Austria}, title = {{Optimal Dyck reachability for data-dependence and alias analysis}}, doi = {10.15479/AT:IST-2017-870-v1-1}, year = {2017}, } @techreport{5450, abstract = {In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.}, author = {Barbara Petritsch}, publisher = {IST Austria}, title = {{Implementing the institutional data repository IST DataRep}}, year = {2017}, } @article{10417, abstract = {We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class. We introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.}, author = {Chalupa, Marek and Chatterjee, Krishnendu and Pavlogiannis, Andreas and Sinha, Nishant and Vaidya, Kapil}, issn = {2475-1421}, journal = {Proceedings of the ACM on Programming Languages}, location = {Los Angeles, CA, United States}, number = {POPL}, publisher = {Association for Computing Machinery}, title = {{Data-centric dynamic partial order reduction}}, doi = {10.1145/3158119}, volume = {2}, year = {2017}, } @misc{5456, abstract = {We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class. We introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence. 1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence. 2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. Finally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.}, author = {Chalupa, Marek and Chatterjee, Krishnendu and Pavlogiannis, Andreas and Sinha, Nishant and Vaidya, Kapil}, issn = {2664-1690}, pages = {36}, publisher = {IST Austria}, title = {{Data-centric dynamic partial order reduction}}, doi = {10.15479/AT:IST-2017-872-v1-1}, year = {2017}, } @inproceedings{551, abstract = {Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. }, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Nowak, Martin}, booktitle = {Leibniz International Proceedings in Informatics}, isbn = {978-395977046-0}, location = {Aalborg, Denmark}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs}}, doi = {10.4230/LIPIcs.MFCS.2017.61}, volume = {83}, year = {2017}, } @inproceedings{552, abstract = {Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).}, author = {Chatterjee, Krishnendu and Henzinger, Monika H and Svozil, Alexander}, booktitle = {Leibniz International Proceedings in Informatics}, isbn = {978-395977046-0}, location = {Aalborg, Denmark}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Faster algorithms for mean-payoff parity games}}, doi = {10.4230/LIPIcs.MFCS.2017.39}, volume = {83}, year = {2017}, } @inproceedings{553, abstract = {We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. }, author = {Chatterjee, Krishnendu and Hansen, Kristofer and Ibsen-Jensen, Rasmus}, booktitle = {Leibniz International Proceedings in Informatics}, isbn = {978-395977046-0}, location = {Aalborg, Denmark}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Strategy complexity of concurrent safety games}}, doi = {10.4230/LIPIcs.MFCS.2017.55}, volume = {83}, year = {2017}, } @article{560, abstract = {In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.}, author = {Gerencser, Mate and Jentzen, Arnulf and Salimova, Diyora}, issn = {13645021}, journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences}, number = {2207}, publisher = {Royal Society of London}, title = {{On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions}}, doi = {10.1098/rspa.2017.0104}, volume = {473}, year = {2017}, } @article{568, abstract = {We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).}, author = {Franek, Peter and Krcál, Marek}, issn = {15320073}, journal = {Homology, Homotopy and Applications}, number = {2}, pages = {313 -- 342}, publisher = {International Press}, title = {{Persistence of zero sets}}, doi = {10.4310/HHA.2017.v19.n2.a16}, volume = {19}, year = {2017}, } @article{570, abstract = {Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. }, author = {Lagator, Mato and Sarikas, Srdjan and Acar, Hande and Bollback, Jonathan P and Guet, Calin C}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Regulatory network structure determines patterns of intermolecular epistasis}}, doi = {10.7554/eLife.28921}, volume = {6}, year = {2017}, } @article{569, abstract = {The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.}, author = {Spira, Felix and Cuylen Haering, Sara and Mehta, Shalin and Samwer, Matthias and Reversat, Anne and Verma, Amitabh and Oldenbourg, Rudolf and Sixt, Michael K and Gerlich, Daniel}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments}}, doi = {10.7554/eLife.30867}, volume = {6}, year = {2017}, } @article{572, abstract = {In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.}, author = {Olatunji, Damilola and Geelen, Danny and Verstraeten, Inge}, journal = {International Journal of Molecular Sciences}, number = {12}, publisher = {MDPI}, title = {{Control of endogenous auxin levels in plant root development}}, doi = {10.3390/ijms18122587}, volume = {18}, year = {2017}, } @inproceedings{313, abstract = {Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.}, author = {Camus, Nicolas and Yakaboylu, Enderalp and Fechner, Lutz and Klaiber, Michael and Laux, Martin and Mi, Yonghao and Hatsagortsyan, Karen and Pfeifer, Thomas and Keitel, Cristoph and Moshammer, Robert}, issn = {17426588}, location = {Kazan, Russian Federation}, number = {1}, publisher = {American Physical Society}, title = {{Experimental evidence for Wigner's tunneling time}}, doi = {10.1088/1742-6596/999/1/012004}, volume = {999}, year = {2017}, } @article{601, abstract = {The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. }, author = {Xu, Youwei and Bernecky, Carrie A and Lee, Chung and Maier, Kerstin and Schwalb, Björn and Tegunov, Dimitri and Plitzko, Jürgen and Urlaub, Henning and Cramer, Patrick}, issn = {20411723}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex}}, doi = {10.1038/ncomms15741}, volume = {8}, year = {2017}, } @article{6013, abstract = {The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”}, author = {Camus, Nicolas and Yakaboylu, Enderalp and Fechner, Lutz and Klaiber, Michael and Laux, Martin and Mi, Yonghao and Hatsagortsyan, Karen Z. and Pfeifer, Thomas and Keitel, Christoph H. and Moshammer, Robert}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {2}, publisher = {American Physical Society}, title = {{Experimental evidence for quantum tunneling time}}, doi = {10.1103/PhysRevLett.119.023201}, volume = {119}, year = {2017}, } @inproceedings{605, abstract = {Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.}, author = {Brody, Joshua and Dziembowski, Stefan and Faust, Sebastian and Pietrzak, Krzysztof Z}, editor = {Kalai, Yael and Reyzin, Leonid}, isbn = {978-331970499-9}, location = {Baltimore, MD, United States}, pages = {56 -- 81}, publisher = {Springer}, title = {{Position based cryptography and multiparty communication complexity}}, doi = {10.1007/978-3-319-70500-2_3}, volume = {10677}, year = {2017}, } @inbook{604, abstract = {In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.}, author = {Lemeshko, Mikhail and Schmidt, Richard}, booktitle = {Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero }, editor = {Dulieu, Oliver and Osterwalder, Andreas}, issn = {20413181}, pages = {444 -- 495}, publisher = {The Royal Society of Chemistry}, title = {{Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets}}, doi = {10.1039/9781782626800-00444}, volume = {11}, year = {2017}, } @inproceedings{609, abstract = {Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover.}, author = {Alwen, Joel F and Tackmann, Björn}, editor = {Kalai, Yael and Reyzin, Leonid}, isbn = {978-331970499-9}, location = {Baltimore, MD, United States}, pages = {493 -- 526}, publisher = {Springer}, title = {{Moderately hard functions: Definition, instantiations, and applications}}, doi = {10.1007/978-3-319-70500-2_17}, volume = {10677}, year = {2017}, } @article{610, abstract = {The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.}, author = {Goaoc, Xavier and Mabillard, Isaac and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, journal = {Israel Journal of Mathematics}, number = {2}, pages = {841 -- 866}, publisher = {Springer}, title = {{On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result}}, doi = {10.1007/s11856-017-1607-7}, volume = {222}, year = {2017}, } @article{6115, abstract = {Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.}, author = {Fenk, Lorenz A. and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {16}, pages = {4195--4200}, publisher = {National Academy of Sciences}, title = {{Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans}}, doi = {10.1073/pnas.1618934114}, volume = {114}, year = {2017}, } @article{6117, abstract = {Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates responses to pathogens or tissue damage, and drives autoimmune diseases. Little is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter their response properties and contribution to behaviour. Using unbiased genetic screens, we delineate an IL-17 signalling pathway and show that it acts in the RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to input from oxygen sensors, and renders sustained escape from 21% oxygen transient and contingent on additional stimuli. Over-activating IL-17 receptors abnormally heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in adults can rescue mutant defects within 6 h. These findings reveal a non-immunological role of IL-17 modulating circuit function and behaviour.}, author = {Chen, Changchun and Itakura, Eisuke and Nelson, Geoffrey M. and Sheng, Ming and Laurent, Patrick and Fenk, Lorenz A. and Butcher, Rebecca A. and Hegde, Ramanujan S. and de Bono, Mario}, issn = {0028-0836}, journal = {Nature}, number = {7639}, pages = {43--48}, publisher = {Springer Nature}, title = {{IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses}}, doi = {10.1038/nature20818}, volume = {542}, year = {2017}, } @article{6113, author = {Oda, Shigekazu and Toyoshima, Yu and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {23}, pages = {E4658--E4665}, publisher = {National Academy of Sciences}, title = {{Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans}}, doi = {10.1073/pnas.1614596114}, volume = {114}, year = {2017}, } @article{613, abstract = {Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.}, author = {Chait, Remy P and Ruess, Jakob and Bergmiller, Tobias and Tkacik, Gasper and Guet, Calin C}, issn = {20411723}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{Shaping bacterial population behavior through computer interfaced control of individual cells}}, doi = {10.1038/s41467-017-01683-1}, volume = {8}, year = {2017}, } @article{615, abstract = {We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law.}, author = {Erdös, László and Schnelli, Kevin}, issn = {02460203}, journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics}, number = {4}, pages = {1606 -- 1656}, publisher = {Institute of Mathematical Statistics}, title = {{Universality for random matrix flows with time dependent density}}, doi = {10.1214/16-AIHP765}, volume = {53}, year = {2017}, } @article{618, abstract = {Background: Increasing temperatures are predicted to strongly impact host-parasite interactions, but empirical tests are rare. Host species that are naturally exposed to a broad temperature spectrum offer the possibility to investigate the effects of elevated temperatures on hosts and parasites. Using three-spined sticklebacks, Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776), originating from a cold and a warm water site of a volcanic lake, we subjected sympatric and allopatric host-parasite combinations to cold and warm conditions in a fully crossed design. We predicted that warm temperatures would promote the development of the parasites, while the hosts might benefit from cooler temperatures. We further expected adaptations to the local temperature and mutual adaptations of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster at warm temperatures and stickleback hosts at cold temperatures. On a finer scale, we observed that parasites were able to exploit their hosts more efficiently at the parasite’s temperature of origin. In contrast, host tolerance towards parasite infection was higher when sticklebacks were infected with parasites at the parasite’s ‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite infection induced a stronger immune response. Conclusions: Our results suggest that increasing environmental temperatures promote the parasite rather than the host and that host tolerance is dependent on the interaction between parasite infection and temperature. Sticklebacks might use tolerance mechanisms towards parasite infection in combination with their high plasticity towards temperature changes to cope with increasing parasite infection pressures and rising temperatures.}, author = {Franke, Frederik and Armitage, Sophie and Kutzer, Megan and Kurtz, Joachim and Scharsack, Jörn}, issn = {17563305}, journal = {Parasites & Vectors}, number = {252}, publisher = {BioMed Central}, title = {{Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association }}, doi = {10.1186/s13071-017-2192-7}, volume = {10}, year = {2017}, } @article{626, abstract = {Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.}, author = {Barton, Nicholas H and Etheridge, Alison and Véber, Amandine}, issn = {00405809}, journal = {Theoretical Population Biology}, pages = {50 -- 73}, publisher = {Academic Press}, title = {{The infinitesimal model: Definition derivation and implications}}, doi = {10.1016/j.tpb.2017.06.001}, volume = {118}, year = {2017}, } @inbook{625, abstract = {In the analysis of reactive systems a quantitative objective assigns a real value to every trace of the system. The value decision problem for a quantitative objective requires a trace whose value is at least a given threshold, and the exact value decision problem requires a trace whose value is exactly the threshold. We compare the computational complexity of the value and exact value decision problems for classical quantitative objectives, such as sum, discounted sum, energy, and mean-payoff for two standard models of reactive systems, namely, graphs and graph games.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, booktitle = {Models, Algorithms, Logics and Tools}, editor = {Aceto, Luca and Bacci, Giorgio and Ingólfsdóttir, Anna and Legay, Axel and Mardare, Radu}, isbn = {978-3-319-63120-2}, issn = {0302-9743}, pages = {367 -- 381}, publisher = {Springer}, title = {{The cost of exactness in quantitative reachability}}, doi = {10.1007/978-3-319-63121-9_18}, volume = {10460}, year = {2017}, } @article{624, abstract = {Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.}, author = {Nikolic, Nela and Didara, Zrinka and Moll, Isabella}, issn = {21678359}, journal = {PeerJ}, number = {9}, publisher = {PeerJ}, title = {{MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations}}, doi = {10.7717/peerj.3830}, volume = {2017}, year = {2017}, } @inproceedings{628, abstract = {We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. The motivation is that several classical textbook algorithms have quite efficient expected-runtime complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since the main focus of expected-runtime analysis is to obtain efficient bounds, we consider bounds that are either logarithmic, linear or almost-linear (O(log n), O(n), O(n · log n), respectively, where n represents the input size). Our main contribution is an efficient (simple linear-time algorithm) sound approach for deriving such expected-runtime bounds for the analysis of recurrence relations induced by randomized algorithms. The experimental results show that our approach can efficiently derive asymptotically optimal expected-runtime bounds for recurrences of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select, Coupon-Collector, where the worst-case bounds are either inefficient (such as linear as compared to logarithmic expected-runtime complexity, or quadratic as compared to linear or almost-linear expected-runtime complexity), or ineffective.}, author = {Chatterjee, Krishnendu and Fu, Hongfei and Murhekar, Aniket}, editor = {Majumdar, Rupak and Kunčak, Viktor}, isbn = {978-331963386-2}, location = {Heidelberg, Germany}, pages = {118 -- 139}, publisher = {Springer}, title = {{Automated recurrence analysis for almost linear expected runtime bounds}}, doi = {10.1007/978-3-319-63387-9_6}, volume = {10426}, year = {2017}, } @inproceedings{630, abstract = {Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.}, author = {Sauermann, Stefan and David, Veronika and Schlögl, Alois and Egelkraut, Reinhard and Frohner, Matthias and Pohn, Birgit and Urbauer, Philipp and Mense, Alexander}, isbn = {978-161499758-0}, location = {Vienna, Austria}, pages = {356 -- 362}, publisher = {IOS Press}, title = {{Biosignals standards and FHIR: The way to go}}, doi = {10.3233/978-1-61499-759-7-356}, volume = {236}, year = {2017}, } @article{632, abstract = {We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. }, author = {Lewin, Mathieu and Nam, Phan and Rougerie, Nicolas}, journal = {Proceedings of the American Mathematical Society}, number = {6}, pages = {2441 -- 2454}, publisher = {American Mathematical Society}, title = {{A note on 2D focusing many boson systems}}, doi = {10.1090/proc/13468}, volume = {145}, year = {2017}, } @inproceedings{635, abstract = {Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is dominated by memory cost. As memory, unlike computation, costs about the same across different platforms, MHFs cannot be evaluated at significantly lower cost on dedicated hardware like ASICs. MHFs have found widespread applications including password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt, a simple candidate MHF designed by Percival, and described in RFC 7914. It has been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and has been an inspiration for Argon2d, one of the winners of the recent password-hashing competition. Despite its popularity, no rigorous lower bounds on its memory complexity are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w and n are the output length and number of invocations of the underlying hash function, respectively. High cmc is a strong security target for MHFs introduced by Alwen and Serbinenko (STOC’15) which implies high memory cost even for adversaries who can amortize the cost over many evaluations and evaluate the underlying hash functions many times in parallel. Our proof is the first showing optimal memory-hardness for any MHF. Our result improves both quantitatively and qualitatively upon the recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of Ω(n2w/ log2 n) for a restricted class of adversaries.}, author = {Alwen, Joel F and Chen, Binchi and Pietrzak, Krzysztof Z and Reyzin, Leonid and Tessaro, Stefano}, editor = {Coron, Jean-Sébastien and Buus Nielsen, Jesper}, isbn = {978-331956616-0}, location = {Paris, France}, pages = {33 -- 62}, publisher = {Springer}, title = {{Scrypt is maximally memory hard}}, doi = {10.1007/978-3-319-56617-7_2}, volume = {10212}, year = {2017}, } @inproceedings{636, abstract = {Signal regular expressions can specify sequential properties of real-valued signals based on threshold conditions, regular operations, and duration constraints. In this paper we endow them with a quantitative semantics which indicates how robustly a signal matches or does not match a given expression. First, we show that this semantics is a safe approximation of a distance between the signal and the language defined by the expression. Then, we consider the robust matching problem, that is, computing the quantitative semantics of every segment of a given signal relative to an expression. We present an algorithm that solves this problem for piecewise-constant and piecewise-linear signals and show that for such signals the robustness map is a piecewise-linear function. The availability of an indicator describing how robustly a signal segment matches some regular pattern provides a general framework for quantitative monitoring of cyber-physical systems.}, author = {Bakhirkin, Alexey and Ferrere, Thomas and Maler, Oded and Ulus, Dogan}, editor = {Abate, Alessandro and Geeraerts, Gilles}, isbn = {978-331965764-6}, location = {Berlin, Germany}, pages = {189 -- 206}, publisher = {Springer}, title = {{On the quantitative semantics of regular expressions over real-valued signals}}, doi = {10.1007/978-3-319-65765-3_11}, volume = {10419}, year = {2017}, } @inproceedings{640, abstract = {Data-independent Memory Hard Functions (iMHFS) are finding a growing number of applications in security; especially in the domain of password hashing. An important property of a concrete iMHF is specified by fixing a directed acyclic graph (DAG) Gn on n nodes. The quality of that iMHF is then captured by the following two pebbling complexities of Gn: – The parallel cumulative pebbling complexity Π∥cc(Gn) must be as high as possible (to ensure that the amortized cost of computing the function on dedicated hardware is dominated by the cost of memory). – The sequential space-time pebbling complexity Πst(Gn) should be as close as possible to Π∥cc(Gn) (to ensure that using many cores in parallel and amortizing over many instances does not give much of an advantage). In this paper we construct a family of DAGs with best possible parameters in an asymptotic sense, i.e., where Π∥cc(Gn) = Ω(n2/ log(n)) (which matches a known upper bound) and Πst(Gn) is within a constant factor of Π∥cc(Gn). Our analysis relies on a new connection between the pebbling complexity of a DAG and its depth-robustness (DR) – a well studied combinatorial property. We show that high DR is sufficient for high Π∥cc. Alwen and Blocki (CRYPTO’16) showed that high DR is necessary and so, together, these results fully characterize DAGs with high Π∥cc in terms of DR. Complementing these results, we provide new upper and lower bounds on the Π∥cc of several important candidate iMHFs from the literature. We give the first lower bounds on the memory hardness of the Catena and Balloon Hashing functions in a parallel model of computation and we give the first lower bounds of any kind for (a version) of Argon2i. Finally we describe a new class of pebbling attacks improving on those of Alwen and Blocki (CRYPTO’16). By instantiating these attacks we upperbound the Π∥cc of the Password Hashing Competition winner Argon2i and one of the Balloon Hashing functions by O (n1.71). We also show an upper bound of O(n1.625) for the Catena functions and the two remaining Balloon Hashing functions.}, author = {Alwen, Joel F and Blocki, Jeremiah and Pietrzak, Krzysztof Z}, editor = {Coron, Jean-Sébastien and Buus Nielsen, Jesper}, isbn = {978-331956616-0}, location = {Paris, France}, pages = {3 -- 32}, publisher = {Springer}, title = {{Depth-robust graphs and their cumulative memory complexity}}, doi = {10.1007/978-3-319-56617-7_1}, volume = {10212}, year = {2017}, } @misc{6426, abstract = {Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent asynchronous computation threads. We show that specifications and correctness proofs for asynchronous programs can be structured by introducing the fiction, for proof purposes, that intermediate, non-quiescent states of asynchronous operations can be ignored. Then, the task of specification becomes relatively simple and the task of verification can be naturally decomposed into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure of an asynchronous program, the atomic effect of non-atomic operations and the synchronous effect of asynchronous operations. This structuring of specifications and proofs corresponds to the introduction of multiple layers of stepwise refinement for asynchronous programs. We present the first proof rule, called synchronization, to reduce asynchronous invocations on a lower layer to synchronous invocations on a higher layer. We implemented our proof method in CIVL and evaluated it on a collection of benchmark programs.}, author = {Henzinger, Thomas A and Kragl, Bernhard and Qadeer, Shaz}, issn = {2664-1690}, pages = {28}, publisher = {IST Austria}, title = {{Synchronizing the asynchronous}}, doi = {10.15479/AT:IST-2018-853-v2-2}, year = {2017}, } @article{642, abstract = {Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable.}, author = {Gerencser, Mate and Gyöngy, István}, issn = {00255718}, journal = {Mathematics of Computation}, number = {307}, pages = {2373 -- 2397}, publisher = {American Mathematical Society}, title = {{Localization errors in solving stochastic partial differential equations in the whole space}}, doi = {10.1090/mcom/3201}, volume = {86}, year = {2017}, } @inproceedings{645, abstract = {Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks.}, author = {Ashok, Pranav and Chatterjee, Krishnendu and Daca, Przemyslaw and Kretinsky, Jan and Meggendorfer, Tobias}, editor = {Majumdar, Rupak and Kunčak, Viktor}, isbn = {978-331963386-2}, location = {Heidelberg, Germany}, pages = {201 -- 221}, publisher = {Springer}, title = {{Value iteration for long run average reward in markov decision processes}}, doi = {10.1007/978-3-319-63387-9_10}, volume = {10426}, year = {2017}, } @article{644, abstract = {An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.}, author = {Kolmogorov, Vladimir and Krokhin, Andrei and Rolinek, Michal}, journal = {SIAM Journal on Computing}, number = {3}, pages = {1087 -- 1110}, publisher = {SIAM}, title = {{The complexity of general-valued CSPs}}, doi = {10.1137/16M1091836}, volume = {46}, year = {2017}, } @inproceedings{646, abstract = {We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations.}, author = {Kuske, Jan and Swoboda, Paul and Petra, Stefanie}, editor = {Lauze, François and Dong, Yiqiu and Bjorholm Dahl, Anders}, isbn = {978-331958770-7}, location = {Kolding, Denmark}, pages = {235 -- 246}, publisher = {Springer}, title = {{A novel convex relaxation for non binary discrete tomography}}, doi = {10.1007/978-3-319-58771-4_19}, volume = {10302}, year = {2017}, } @inproceedings{648, abstract = {Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method.}, author = {Skórski, Maciej}, editor = {Jäger, Gerhard and Steila, Silvia}, isbn = {978-331955910-0}, location = {Bern, Switzerland}, pages = {600 -- 613}, publisher = {Springer}, title = {{On the complexity of breaking pseudoentropy}}, doi = {10.1007/978-3-319-55911-7_43}, volume = {10185}, year = {2017}, } @inproceedings{650, abstract = {In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy.}, author = {Skórski, Maciej}, editor = {Jäger, Gerhard and Steila, Silvia}, issn = {03029743}, location = {Bern, Switzerland}, pages = {586 -- 599}, publisher = {Springer}, title = {{A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds}}, doi = {10.1007/978-3-319-55911-7_42}, volume = {10185}, year = {2017}, } @inproceedings{6519, abstract = {Graph games with omega-regular winning conditions provide a mathematical framework to analyze a wide range of problems in the analysis of reactive systems and programs (such as the synthesis of reactive systems, program repair, and the verification of branching time properties). Parity conditions are canonical forms to specify omega-regular winning conditions. Graph games with parity conditions are equivalent to mu-calculus model checking, and thus a very important algorithmic problem. Symbolic algorithms are of great significance because they provide scalable algorithms for the analysis of large finite-state systems, as well as algorithms for the analysis of infinite-state systems with finite quotient. A set-based symbolic algorithm uses the basic set operations and the one-step predecessor operators. We consider graph games with n vertices and parity conditions with c priorities (equivalently, a mu-calculus formula with c alternations of least and greatest fixed points). While many explicit algorithms exist for graph games with parity conditions, for set-based symbolic algorithms there are only two algorithms (notice that we use space to refer to the number of sets stored by a symbolic algorithm): (a) the basic algorithm that requires O(n^c) symbolic operations and linear space; and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two set-based symbolic algorithms for parity games: (a) our first algorithm requires O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic operations and only linear space. We also present the first linear space set-based symbolic algorithm for parity games that requires at most a sub-exponential number of symbolic operations. }, author = {Chatterjee, Krishnendu and Dvorák, Wolfgang and Henzinger, Monika H and Loitzenbauer, Veronika}, location = {Stockholm, Sweden}, publisher = {Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik}, title = {{Improved set-based symbolic algorithms for parity games}}, doi = {10.4230/LIPICS.CSL.2017.18}, volume = {82}, year = {2017}, } @inproceedings{6517, abstract = {A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle.}, author = {Fulek, Radoslav}, location = {Phuket, Thailand}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Embedding graphs into embedded graphs}}, doi = {10.4230/LIPICS.ISAAC.2017.34}, volume = {92}, year = {2017}, } @article{653, abstract = {The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease.}, author = {Makohon Moore, Alvin and Zhang, Ming and Reiter, Johannes and Božić, Ivana and Allen, Benjamin and Kundu, Deepanjan and Chatterjee, Krishnendu and Wong, Fay and Jiao, Yuchen and Kohutek, Zachary and Hong, Jungeui and Attiyeh, Marc and Javier, Breanna and Wood, Laura and Hruban, Ralph and Nowak, Martin and Papadopoulos, Nickolas and Kinzler, Kenneth and Vogelstein, Bert and Iacobuzio Donahue, Christine}, issn = {10614036}, journal = {Nature Genetics}, number = {3}, pages = {358 -- 366}, publisher = {Nature Publishing Group}, title = {{Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer}}, doi = {10.1038/ng.3764}, volume = {49}, year = {2017}, } @inproceedings{6527, abstract = {A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs. Essentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called "depth-robustness") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice. In this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we: *Prove that their depth-robustness is asymptotically maximal. *Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF. *Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. We find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice. Along the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT). }, author = {Alwen, Joel F and Blocki, Jeremiah and Harsha, Ben}, booktitle = {Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security}, isbn = {9781450349468}, location = {Dallas, TX, USA}, pages = {1001--1017}, publisher = {ACM Press}, title = {{Practical graphs for optimal side-channel resistant memory-hard functions}}, doi = {10.1145/3133956.3134031}, year = {2017}, } @article{654, abstract = {In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.}, author = {Kicheva, Anna and Rivron, Nicolas}, issn = {09501991}, journal = {Development}, number = {5}, pages = {733 -- 736}, publisher = {Company of Biologists}, title = {{Creating to understand – developmental biology meets engineering in Paris}}, doi = {10.1242/dev.144915}, volume = {144}, year = {2017}, } @inproceedings{6526, abstract = {This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity.}, author = {Skórski, Maciej}, booktitle = {2017 IEEE International Symposium on Information Theory (ISIT)}, isbn = {9781509040964}, location = {Aachen, Germany}, publisher = {IEEE}, title = {{On the complexity of estimating Rènyi divergences}}, doi = {10.1109/isit.2017.8006529}, year = {2017}, } @article{655, abstract = {The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell.}, author = {Renault, Thibaud and Abraham, Anthony and Bergmiller, Tobias and Paradis, Guillaume and Rainville, Simon and Charpentier, Emmanuelle and Guet, Calin C and Tu, Yuhai and Namba, Keiichi and Keener, James and Minamino, Tohru and Erhardt, Marc}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Bacterial flagella grow through an injection diffusion mechanism}}, doi = {10.7554/eLife.23136}, volume = {6}, year = {2017}, } @article{657, abstract = {Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.}, author = {Möller, Barbara and Ten Hove, Colette and Xiang, Daoquan and Williams, Nerys and López, Lorena and Yoshida, Saiko and Smit, Margot and Datla, Raju and Weijers, Dolf}, issn = {00278424}, journal = {PNAS}, number = {12}, pages = {E2533 -- E2539}, publisher = {National Academy of Sciences}, title = {{Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo}}, doi = {10.1073/pnas.1616493114}, volume = {114}, year = {2017}, } @article{658, abstract = {With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.}, author = {Der, Ralf and Martius, Georg S}, issn = {16625218}, journal = {Frontiers in Neurorobotics}, number = {MAR}, publisher = {Frontiers Research Foundation}, title = {{Self organized behavior generation for musculoskeletal robots}}, doi = {10.3389/fnbot.2017.00008}, volume = {11}, year = {2017}, } @article{659, abstract = {Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching.}, author = {Kage, Frieda and Winterhoff, Moritz and Dimchev, Vanessa and Müller, Jan and Thalheim, Tobias and Freise, Anika and Brühmann, Stefan and Kollasser, Jana and Block, Jennifer and Dimchev, Georgi A and Geyer, Matthias and Schnittler, Hams and Brakebusch, Cord and Stradal, Theresia and Carlier, Marie and Sixt, Michael K and Käs, Josef and Faix, Jan and Rottner, Klemens}, issn = {20411723}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{FMNL formins boost lamellipodial force generation}}, doi = {10.1038/ncomms14832}, volume = {8}, year = {2017}, } @article{660, abstract = {Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth.}, author = {Rickman, Jamie and Düllberg, Christian F and Cade, Nicholas and Griffin, Lewis and Surrey, Thomas}, issn = {00278424}, journal = {PNAS}, number = {13}, pages = {3427 -- 3432}, publisher = {National Academy of Sciences}, title = {{Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation}}, doi = {10.1073/pnas.1620274114}, volume = {114}, year = {2017}, } @article{662, abstract = {We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.}, author = {Shi, Liang and Hof, Björn and Rampp, Markus and Avila, Marc}, issn = {10706631}, journal = {Physics of Fluids}, number = {4}, publisher = {American Institute of Physics}, title = {{Hydrodynamic turbulence in quasi Keplerian rotating flows}}, doi = {10.1063/1.4981525}, volume = {29}, year = {2017}, } @inproceedings{663, abstract = {In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. }, author = {Kong, Hui and Bogomolov, Sergiy and Schilling, Christian and Jiang, Yu and Henzinger, Thomas A}, booktitle = {Proceedings of the 20th International Conference on Hybrid Systems}, isbn = {978-145034590-3}, location = {Pittsburgh, PA, United States}, pages = {163 -- 172}, publisher = {ACM}, title = {{Safety verification of nonlinear hybrid systems based on invariant clusters}}, doi = {10.1145/3049797.3049814}, year = {2017}, } @article{668, abstract = {Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading.}, author = {Horsthemke, Markus and Bachg, Anne and Groll, Katharina and Moyzio, Sven and Müther, Barbara and Hemkemeyer, Sandra and Wedlich Söldner, Roland and Sixt, Michael K and Tacke, Sebastian and Bähler, Martin and Hanley, Peter}, issn = {00219258}, journal = {Journal of Biological Chemistry}, number = {17}, pages = {7258 -- 7273}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion}}, doi = {10.1074/jbc.M116.766923}, volume = {292}, year = {2017}, } @article{669, abstract = {The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. }, author = {Synek, Lukáš and Vukašinović, Nemanja and Kulich, Ivan and Hála, Michal and Aldorfová, Klára and Fendrych, Matyas and Žárský, Viktor}, issn = {00320889}, journal = {Plant Physiology}, number = {1}, pages = {223 -- 240}, publisher = {American Society of Plant Biologists}, title = {{EXO70C2 is a key regulatory factor for optimal tip growth of pollen}}, doi = {10.1104/pp.16.01282}, volume = {174}, year = {2017}, } @inproceedings{6679, abstract = {Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption [1]. In this paper, we examine the paradigm of PSCL decoding from both theoretical and practical standpoints: (i) by changing the construction of the code, we are able to improve the performance at no additional computational, latency or memory cost, (ii) we present an optimal scheme to allocate cyclic redundancy checks (CRCs), and (iii) we provide an upper bound on the list size that allows MAP performance.}, author = {Hashemi, Seyyed Ali and Mondelli, Marco and Hassani, Hamed and Urbanke, Ruediger and Gross, Warren}, booktitle = {2017 IEEE Global Communications Conference}, location = {Singapore, Singapore}, pages = {1--7}, publisher = {IEEE}, title = {{Partitioned list decoding of polar codes: Analysis and improvement of finite length performance}}, doi = {10.1109/glocom.2017.8254940}, year = {2017}, } @article{671, abstract = {Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation.}, author = {Hilbe, Christian and Martinez, Vaquero and Chatterjee, Krishnendu and Nowak, Martin}, issn = {00278424}, journal = {PNAS}, number = {18}, pages = {4715 -- 4720}, publisher = {National Academy of Sciences}, title = {{Memory-n strategies of direct reciprocity}}, doi = {10.1073/pnas.1621239114}, volume = {114}, year = {2017}, } @article{670, abstract = {We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears.}, author = {Schreck, Camille and Rohmer, Damien and Hahmann, Stefanie}, issn = {01677055}, journal = {Computer Graphics Forum}, number = {2}, pages = {95 -- 106}, publisher = {Wiley}, title = {{Interactive paper tearing}}, doi = {10.1111/cgf.13110}, volume = {36}, year = {2017}, } @article{672, abstract = {Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration.}, author = {Vaahtomeri, Kari and Brown, Markus and Hauschild, Robert and De Vries, Ingrid and Leithner, Alexander F and Mehling, Matthias and Kaufmann, Walter and Sixt, Michael K}, issn = {22111247}, journal = {Cell Reports}, number = {5}, pages = {902 -- 909}, publisher = {Cell Press}, title = {{Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia}}, doi = {10.1016/j.celrep.2017.04.027}, volume = {19}, year = {2017}, } @inproceedings{6729, abstract = {Consider the problem of constructing a polar code of block length N for the transmission over a given channel W. Typically this requires to compute the reliability of all the N synthetic channels and then to include those that are sufficiently reliable. However, we know from [1], [2] that there is a partial order among the synthetic channels. Hence, it is natural to ask whether we can exploit it to reduce the computational burden of the construction problem. We show that, if we take advantage of the partial order [1], [2], we can construct a polar code by computing the reliability of roughly N/ log 3/2 N synthetic channels. Such a set of synthetic channels is universal, in the sense that it allows one to construct polar codes for any W, and it can be identified by solving a maximum matching problem on a bipartite graph. Our proof technique consists in reducing the construction problem to the problem of computing the maximum cardinality of an antichain for a suitable partially ordered set. As such, this method is general and it can be used to further improve the complexity of the construction problem in case a new partial order on the synthetic channels of polar codes is discovered.}, author = {Mondelli, Marco and Hassani, S. Hamed and Urbanke, Rudiger}, booktitle = {2017 IEEE International Symposium on Information Theory }, isbn = {9781509040964}, issn = {2157-8117}, location = {Aachen, Germany}, pages = {1853--1857}, publisher = {IEEE}, title = {{Construction of polar codes with sublinear complexity}}, doi = {10.1109/isit.2017.8006850}, year = {2017}, } @article{6730, abstract = {We introduce a new approach to proving that a sequence of deterministic linear codes achieves capacity on an erasure channel under maximum a posteriori decoding. Rather than relying on the precise structure of the codes, our method exploits code symmetry. In particular, the technique applies to any sequence of linear codes where the blocklengths are strictly increasing, the code rates converge, and the permutation group of each code is doubly transitive. In other words, we show that symmetry alone implies near-optimal performance. An important consequence of this result is that a sequence of Reed-Muller codes with increasing block length and converging rate achieves capacity. This possibility has been suggested previously in the literature but it has only been proven for cases where the limiting code rate is 0 or 1. Moreover, these results extend naturally to all affine-invariant codes and, thus, to extended primitive narrow-sense BCH codes. This also resolves, in the affirmative, the existence question for capacity-achieving sequences of binary cyclic codes. The primary tools used in the proof are the sharp threshold property for symmetric monotone Boolean functions and the area theorem for extrinsic information transfer functions.}, author = {Kudekar, Shrinivas and Kumar, Santhosh and Mondelli, Marco and Pfister, Henry D. and Sasoglu, Eren and Urbanke, Ridiger L.}, issn = {1557-9654}, journal = {IEEE Transactions on Information Theory}, number = {7}, pages = {4298--4316}, publisher = {IEEE}, title = {{Reed–Muller codes achieve capacity on erasure channels}}, doi = {10.1109/tit.2017.2673829}, volume = {63}, year = {2017}, } @inproceedings{6731, abstract = {We present a rate-compatible polar coding scheme that achieves the capacity of any family of channels. Our solution generalizes the previous results [1], [2] that provide capacity-achieving rate-compatible polar codes for a degraded family of channels. The motivation for our extension comes from the fact that in many practical scenarios, e.g., MIMO systems and non-Gaussian interference, the channels cannot be ordered by degradation. The main technical contribution of this paper consists in removing the degradation condition. To do so, we exploit the ideas coming from the construction of universal polar codes. Our scheme possesses the usual attractive features of polar codes: low complexity code construction, encoding, and decoding; super-polynomial scaling of the error probability with the block length; and absence of error floors. On the negative side, the scaling of the gap to capacity with the block length is slower than in standard polar codes, and we prove an upper bound on the scaling exponent.}, author = {Mondelli, Marco and Hassani, Hamed and Maric, Ivana and Hui, Dennis and Hong, Song-Nam}, booktitle = {2017 IEEE Wireless Communications and Networking Conference Workshops }, isbn = {9781509059089}, location = {San Francisco, CA, USA}, publisher = {IEEE}, title = {{Capacity-achieving rate-compatible polar codes for general channels}}, doi = {10.1109/wcncw.2017.7919107}, year = {2017}, }