@article{6649,
abstract = {While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.
},
author = {Benedikter, Niels P and Nam, Phan Thành and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
publisher = {Springer},
title = {{Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime}},
doi = {10.1007/s00220-019-03505-5},
year = {2019},
}
@article{6795,
abstract = {The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations.},
author = {Trubenova, Barbora and Hager, Reinmar},
issn = {20457758},
journal = {Ecology and Evolution},
publisher = {Wiley},
title = {{Green beards in the light of indirect genetic effects}},
doi = {10.1002/ece3.5484},
year = {2019},
}
@inproceedings{6884,
abstract = {In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the "bank" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. },
author = {Avni, Guy and Henzinger, Thomas A and Zikelic, Dorde},
location = {Aachen, Germany},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Bidding mechanisms in graph games}},
doi = {10.4230/LIPICS.MFCS.2019.11},
volume = {138},
year = {2019},
}
@inproceedings{6889,
abstract = {We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. },
author = {Chatterjee, Krishnendu and Piterman, Nir},
location = {Amsterdam, Netherlands},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Combinations of Qualitative Winning for Stochastic Parity Games}},
doi = {10.4230/LIPICS.CONCUR.2019.6},
volume = {140},
year = {2019},
}
@inproceedings{6822,
abstract = {In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher
bidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called
randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one.},
author = {Avni, Guy and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Novotny, Petr},
booktitle = { Proceedings of the 13th International Conference of Reachability Problems},
isbn = {978-303030805-6},
issn = {0302-9743},
location = {Brussels, Belgium},
pages = {1--12},
publisher = {Springer},
title = {{Bidding games on Markov decision processes}},
doi = {10.1007/978-3-030-30806-3_1},
volume = {11674},
year = {2019},
}
@inproceedings{6935,
abstract = {This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does
preprocessing help in the CONGEST model.},
author = {Foerster, Klaus-Tycho and Korhonen, Janne and Rybicki, Joel and Schmid, Stefan},
booktitle = {Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing},
isbn = {9781450362177},
location = {Toronto, ON, Canada},
pages = {259--261},
publisher = {ACM},
title = {{Does preprocessing help under congestion?}},
doi = {10.1145/3293611.3331581},
year = {2019},
}
@inproceedings{6942,
abstract = {Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of 𝜔 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees.},
author = {Ashok, Pranav and Brázdil, Tomáš and Chatterjee, Krishnendu and Křetínský, Jan and Lampert, Christoph and Toman, Viktor},
booktitle = {16th International Conference on Quantitative Evaluation of Systems},
isbn = {9783030302801},
issn = {0302-9743},
location = {Glasgow, United Kingdom},
pages = {109--128},
publisher = {Springer Nature},
title = {{Strategy representation by decision trees with linear classifiers}},
doi = {10.1007/978-3-030-30281-8_7},
volume = {11785},
year = {2019},
}
@article{6978,
abstract = {In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.},
author = {Budanur, Nazmi B and Dogra, Akshunna and Hof, Björn},
journal = {Physical Review Fluids},
number = {10},
pages = {102401},
publisher = {American Physical Society},
title = {{Geometry of transient chaos in streamwise-localized pipe flow turbulence}},
doi = {10.1103/PhysRevFluids.4.102401},
volume = {4},
year = {2019},
}
@article{6980,
abstract = {Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development.},
author = {Petridou, Nicoletta and Heisenberg, Carl-Philipp J},
issn = {0261-4189},
journal = {The EMBO Journal},
number = {20},
publisher = {EMBO},
title = {{Tissue rheology in embryonic organization}},
doi = {10.15252/embj.2019102497},
volume = {38},
year = {2019},
}
@article{7015,
abstract = {We modify the "floating crystal" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential.},
author = {Lewin, Mathieu and Lieb, Elliott H. and Seiringer, Robert},
issn = {2469-9950},
journal = {Physical Review B},
number = {3},
publisher = {APS},
title = {{Floating Wigner crystal with no boundary charge fluctuations}},
doi = {10.1103/physrevb.100.035127},
volume = {100},
year = {2019},
}
@inproceedings{6985,
abstract = {In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets.},
author = {Hasani, Ramin and Amini, Alexander and Lechner, Mathias and Naser, Felix and Grosu, Radu and Rus, Daniela},
booktitle = {Proceedings of the International Joint Conference on Neural Networks},
isbn = {9781728119854},
location = {Budapest, Hungary},
publisher = {IEEE},
title = {{Response characterization for auditing cell dynamics in long short-term memory networks}},
doi = {10.1109/ijcnn.2019.8851954},
year = {2019},
}
@article{6997,
author = {Zhang, Yuzhou and Friml, Jiří},
issn = {0028-646x},
journal = {New Phytologist},
publisher = {Wiley},
title = {{Auxin guides roots to avoid obstacles during gravitropic growth}},
doi = {10.1111/nph.16203},
year = {2019},
}
@article{7034,
abstract = {We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus.},
author = {Fulek, Radoslav and Kynčl, Jan},
issn = {1439-6912},
journal = {Combinatorica},
publisher = {Springer Nature},
title = {{Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4}},
doi = {10.1007/s00493-019-3905-7},
year = {2019},
}
@unpublished{7084,
abstract = {URu2Si2 exhibits a clear phase transition at THO=17.5 K to a low-temperature phase known as "hidden order" (HO). Even the most basic information needed to construct a theory of this state---such as the number of components in the order parameter---has been lacking. Here we use resonant ultrasound spectroscopy (RUS) and machine learning to determine that the order parameter of HO is one-dimensional (singlet), ruling out a large class of theories based on two-dimensional (doublet) order parameters. This strict constraint is independent of any microscopic mechanism, and independent of other symmetries that HO may break. Our technique is general for second-order phase transitions, and can discriminate between nematic (singlet) versus loop current (doublet) order in the high-\Tc cuprates, and conventional (singlet) versus the proposed px+ipy (doublet) superconductivity in Sr2RuO4. The machine learning framework we develop should be readily adaptable to other spectroscopic techniques where missing resonances confound traditional analysis, such as NMR. },
author = {Ghosh, Sayak and Matty, Michael and Baumbach, Ryan and Bauer, Eric D. and Modic, Kimberly A and Shekhter, Arkady and Mydosh, J. A. and Kim, Eun-Ah and Ramshaw, B. J.},
booktitle = {arXiv:1903.00552},
title = {{Single-component order parameter in URu2Si2 uncovered by resonant ultrasound spectroscopy and machine learning}},
year = {2019},
}
@article{6788,
abstract = {We consider the Nelson model with ultraviolet cutoff, which describes the interaction between non-relativistic particles and a positive or zero mass quantized scalar field. We take the non-relativistic particles to obey Fermi statistics and discuss the time evolution in a mean-field limit of many fermions. In this case, the limit is known to be also a semiclassical limit. We prove convergence in terms of reduced density matrices of the many-body state to a tensor product of a Slater determinant with semiclassical structure and a coherent state, which evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations.},
author = {Leopold, Nikolai K and Petrat, Sören P},
issn = {1424-0661},
journal = {Annales Henri Poincare},
publisher = {Springer Nature},
title = {{Mean-field dynamics for the Nelson model with fermions}},
doi = {10.1007/s00023-019-00828-w},
year = {2019},
}
@misc{7154,
author = {Guseinov, Ruslan},
publisher = {IST Austria},
title = {{Supplementary data for "Programming temporal morphing of self-actuated shells"}},
doi = {10.15479/AT:ISTA:7154},
year = {2019},
}
@article{5907,
abstract = {Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.},
author = {Mócsai, Réka and Figl, Rudolf and Troschl, Clemens and Strasser, Richard and Svehla, Elisabeth and Windwarder, Markus and Thader, Andreas and Altmann, Friedrich},
journal = {Scientific Reports},
number = {1},
publisher = {Nature Publishing Group},
title = {{N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated}},
doi = {10.1038/s41598-018-36884-1},
volume = {9},
year = {2019},
}
@article{6102,
abstract = {Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior.},
author = {Le Feber, B. and Sipe, J. E. and Wulf, Matthias and Kuipers, L. and Rotenberg, N.},
issn = {20477538},
journal = {Light: Science and Applications},
number = {1},
publisher = {Springer Nature},
title = {{A full vectorial mapping of nanophotonic light fields}},
doi = {10.1038/s41377-019-0124-3},
volume = {8},
year = {2019},
}
@article{6025,
abstract = {Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation.},
author = {Capek, Daniel and Smutny, Michael and Tichy, Alexandra Madelaine and Morri, Maurizio and Janovjak, Harald L and Heisenberg, Carl-Philipp J},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration}},
doi = {10.7554/eLife.42093},
volume = {8},
year = {2019},
}
@article{6032,
abstract = {The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids.},
author = {Kazda, Alexandr and Kolmogorov, Vladimir and Rolinek, Michal},
journal = {ACM Transactions on Algorithms},
number = {2},
publisher = {ACM},
title = {{Even delta-matroids and the complexity of planar boolean CSPs}},
doi = {10.1145/3230649},
volume = {15},
year = {2019},
}
@inproceedings{6056,
abstract = {In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs.},
author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Pourdamghani, Arash},
booktitle = {IEEE International Conference on Blockchain and Cryptocurrency},
location = {Seoul, Korea},
publisher = {IEEE},
title = {{Probabilistic smart contracts: Secure randomness on the blockchain}},
doi = {10.1109/BLOC.2019.8751326},
year = {2019},
}
@article{6260,
abstract = {Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.},
author = {Oochi, A and Hajny, Jakub and Fukui, K and Nakao, Y and Gallei, Michelle C and Quareshy, M and Takahashi, K and Kinoshita, T and Harborough, SR and Kepinski, S and Kasahara, H and Napier, RM and Friml, Jiří and Hayashi, KI},
issn = {0032-0889},
journal = {Plant Physiology},
number = {2},
pages = {1152--1165},
publisher = {ASPB},
title = {{Pinstatic acid promotes auxin transport by inhibiting PIN internalization}},
doi = {10.1104/pp.19.00201},
volume = {180},
year = {2019},
}
@inproceedings{6556,
abstract = {Motivated by fixed-parameter tractable (FPT) problems in computational topology, we consider the treewidth tw(M) of a compact, connected 3-manifold M, defined to be the minimum treewidth of the face pairing graph of any triangulation T of M. In this setting the relationship between the topology of a 3-manifold and its treewidth is of particular interest. First, as a corollary of work of Jaco and Rubinstein, we prove that for any closed, orientable 3-manifold M the treewidth tw(M) is at most 4g(M)-2, where g(M) denotes Heegaard genus of M. In combination with our earlier work with Wagner, this yields that for non-Haken manifolds the Heegaard genus and the treewidth are within a constant factor. Second, we characterize all 3-manifolds of treewidth one: These are precisely the lens spaces and a single other Seifert fibered space. Furthermore, we show that all remaining orientable Seifert fibered spaces over the 2-sphere or a non-orientable surface have treewidth two. In particular, for every spherical 3-manifold we exhibit a triangulation of treewidth at most two. Our results further validate the parameter of treewidth (and other related parameters such as cutwidth or congestion) to be useful for topological computing, and also shed more light on the scope of existing FPT-algorithms in the field.},
author = {Huszár, Kristóf and Spreer, Jonathan},
booktitle = {35th International Symposium on Computational Geometry (SoCG 2019)},
isbn = {978-3-95977-104-7},
issn = {1868-8969},
keyword = {computational 3-manifold topology, fixed-parameter tractability, layered triangulations, structural graph theory, treewidth, cutwidth, Heegaard genus},
location = {Portland, Oregon, United States},
pages = {44:1--44:20},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik},
title = {{3-manifold triangulations with small treewidth}},
doi = {10.4230/LIPIcs.SoCG.2019.44},
volume = {129},
year = {2019},
}
@article{6563,
abstract = {This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋.},
author = {Filakovský, Marek and Vokřínek, Lukas},
issn = {16153383},
journal = {Foundations of Computational Mathematics},
publisher = {Springer Nature},
title = {{Are two given maps homotopic? An algorithmic viewpoint}},
doi = {10.1007/s10208-019-09419-x},
year = {2019},
}
@article{6575,
abstract = {Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit.},
author = {Choi, Soonwon and Turner, Christopher J. and Pichler, Hannes and Ho, Wen Wei and Michailidis, Alexios and Papić, Zlatko and Serbyn, Maksym and Lukin, Mikhail D. and Abanin, Dmitry A.},
issn = {10797114},
journal = {Physical Review Letters},
number = {22},
publisher = {APS Physics},
title = {{Emergent SU(2) dynamics and perfect quantum many-body scars}},
doi = {10.1103/PhysRevLett.122.220603},
volume = {122},
year = {2019},
}
@article{6607,
abstract = {Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically.},
author = {Nguyen, Chi Huu and Glüxam, Tobias and Schlerka, Angela and Bauer, Katharina and Grandits, Alexander M. and Hackl, Hubert and Dovey, Oliver and Zöchbauer-Müller, Sabine and Cooper, Jonathan L. and Vassiliou, George S. and Stoiber, Dagmar and Wieser, Rotraud and Heller, Gerwin},
journal = {Scientific Reports},
number = {1},
publisher = {Nature Publishing Group},
title = {{SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness}},
doi = {10.1038/s41598-019-45579-0},
volume = {9},
year = {2019},
}
@article{6412,
abstract = {Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.},
author = {Moussa, Hagar F. and Bsteh, Daniel and Yelagandula, Ramesh and Pribitzer, Carina and Stecher, Karin and Bartalska, Katarina and Michetti, Luca and Wang, Jingkui and Zepeda-Martinez, Jorge A. and Elling, Ulrich and Stuckey, Jacob I. and James, Lindsey I. and Frye, Stephen V. and Bell, Oliver},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing}},
doi = {10.1038/s41467-019-09628-6},
volume = {10},
year = {2019},
}
@inproceedings{6493,
abstract = {We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements.},
author = {Garcia Soto, Miriam and Henzinger, Thomas A and Schilling, Christian and Zeleznik, Luka},
booktitle = {31st International Conference on Computer-Aided Verification},
isbn = {9783030255398},
issn = {0302-9743},
keyword = {Synthesis, Linear hybrid automaton, Membership},
location = {New York City, NY, USA},
pages = {297--314},
publisher = {Springer},
title = {{Membership-based synthesis of linear hybrid automata}},
doi = {10.1007/978-3-030-25540-4_16},
volume = {11561},
year = {2019},
}
@article{6506,
abstract = {How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.},
author = {Noda-García, Lianet and Davidi, Dan and Korenblum, Elisa and Elazar, Assaf and Putintseva, Ekaterina and Aharoni, Asaph and Tawfik, Dan S.},
issn = {2058-5276},
journal = {Nature Microbiology},
publisher = {Springer Nature},
title = {{Chance and pleiotropy dominate genetic diversity in complex bacterial environments}},
doi = {10.1038/s41564-019-0412-y},
year = {2019},
}
@inproceedings{6462,
abstract = {A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles.},
author = {Avni, Guy and Bloem, Roderick and Chatterjee, Krishnendu and Henzinger, Thomas A and Konighofer, Bettina and Pranger, Stefan},
booktitle = {31st International Conference on Computer-Aided Verification},
isbn = {9783030255398},
issn = {0302-9743},
location = {New York, NY, United States},
pages = {630--649},
publisher = {Springer},
title = {{Run-time optimization for learned controllers through quantitative games}},
doi = {10.1007/978-3-030-25540-4_36},
volume = {11561},
year = {2019},
}
@inproceedings{6378,
abstract = {In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin.},
author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Pourdamghani, Arash},
booktitle = {Proceedings of the 34th ACM Symposium on Applied Computing},
isbn = {9781450359337},
location = {Limassol, Cyprus},
pages = {374--381},
publisher = {ACM},
title = {{Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving}},
doi = {10.1145/3297280.3297319},
volume = {Part F147772},
year = {2019},
}
@article{6380,
abstract = {There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. },
author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Okati, Nastaran and Pavlogiannis, Andreas},
issn = {2475-1421},
journal = {Proceedings of the ACM on Programming Languages},
number = {POPL},
publisher = {ACM},
title = {{Efficient parameterized algorithms for data packing}},
doi = {10.1145/3290366},
volume = {3},
year = {2019},
}
@article{6486,
abstract = {Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.},
author = {Kühnen, Jakob and Scarselli, Davide and Hof, Björn},
issn = {1528901X},
journal = {Journal of Fluids Engineering},
number = {11},
publisher = {ASME},
title = {{Relaminarization of pipe flow by means of 3D-printed shaped honeycombs}},
doi = {10.1115/1.4043494},
volume = {141},
year = {2019},
}
@article{6366,
abstract = {Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl.},
author = {Bellstaedt, Julia and Trenner, Jana and Lippmann, Rebecca and Poeschl, Yvonne and Zhang, Xixi and Friml, Jiří and Quint, Marcel and Delker, Carolin},
issn = {0032-0889},
journal = {Plant Physiology},
number = {2},
pages = {757--766},
publisher = {ASPB},
title = {{A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls}},
doi = {10.1104/pp.18.01377},
volume = {180},
year = {2019},
}
@article{6671,
abstract = {In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.},
author = {Boissonnat, Jean-Daniel and Lieutier, André and Wintraecken, Mathijs},
issn = {2367-1734},
journal = {Journal of Applied and Computational Topology},
publisher = {Springer Nature},
title = {{The reach, metric distortion, geodesic convexity and the variation of tangent spaces}},
doi = {10.1007/s41468-019-00029-8},
year = {2019},
}
@article{6638,
abstract = {The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one.},
author = {Silva, André and Arroyo Guevara, Alan M and Richter, Bruce and Lee, Orlando},
journal = {Discrete Mathematics},
publisher = {Elsevier},
title = {{Graphs with at most one crossing}},
doi = {10.1016/j.disc.2019.06.031},
year = {2019},
}
@article{6657,
abstract = {In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as "gold" and "green" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.},
author = {Danowski, Patrick},
journal = {VOEB-Mitteilungen},
number = {1},
pages = {59--65},
publisher = {Mitteilungen der VOEB},
title = {{An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors}},
doi = {10.31263/voebm.v72i1.2276},
volume = {72},
year = {2019},
}
@inproceedings{6676,
abstract = {It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.
Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.},
author = {Alistarh, Dan-Adrian and Aspnes, James and Ellen, Faith and Gelashvili, Rati and Zhu, Leqi},
booktitle = {Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019},
isbn = {9781450367059},
location = {Phoenix, AZ, United States},
pages = {986--996},
publisher = {ACM Press},
title = {{Why extension-based proofs fail}},
doi = {10.1145/3313276.3316407},
year = {2019},
}
@article{6784,
abstract = {Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems.},
author = {Ruess, Jakob and Pleska, Maros and Guet, Calin C and Tkačik, Gašper},
issn = {1553-7358},
journal = {PLoS Computational Biology},
number = {7},
publisher = {Public Library of Science},
title = {{Molecular noise of innate immunity shapes bacteria-phage ecologies}},
doi = {10.1371/journal.pcbi.1007168},
volume = {15},
year = {2019},
}
@article{6796,
abstract = {Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.},
author = {Stella, Federico and Urdapilleta, Eugenio and Luo, Yifan and Treves, Alessandro},
issn = {10981063},
journal = {Hippocampus},
publisher = {Wiley},
title = {{Partial coherence and frustration in self-organizing spherical grids}},
doi = {10.1002/hipo.23144},
year = {2019},
}
@article{6835,
abstract = {We derive the Hasse principle and weak approximation for fibrations of certain varieties in the spirit of work by Colliot-Thélène–Sansuc and Harpaz–Skorobogatov–Wittenberg. Our varieties are defined through polynomials in many variables and part of our work is devoted to establishing Schinzel's hypothesis for polynomials of this kind. This last part is achieved by using arguments behind Birch's well-known result regarding the Hasse principle for complete intersections with the notable difference that we prove our result in 50% fewer variables than in the classical Birch setting. We also study the problem of square-free values of an integer polynomial with 66.6% fewer variables than in the Birch setting.},
author = {Destagnol, Kevin N and Sofos, Efthymios},
issn = {0007-4497},
journal = {Bulletin des Sciences Mathematiques},
publisher = {Elsevier},
title = {{Rational points and prime values of polynomials in moderately many variables}},
doi = {10.1016/j.bulsci.2019.102794},
volume = {156},
year = {2019},
}
@inproceedings{6885,
abstract = {A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. },
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
location = {Amsterdam, Netherlands},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Long-run average behavior of vector addition systems with states}},
doi = {10.4230/LIPICS.CONCUR.2019.27},
volume = {140},
year = {2019},
}
@article{6828,
abstract = {In this paper we construct a family of exact functors from the category of Whittaker modules of the simple complex Lie algebra of type to the category of finite-dimensional modules of the graded affine Hecke algebra of type . Using results of Backelin [2] and of Arakawa-Suzuki [1], we prove that these functors map standard modules to standard modules (or zero) and simple modules to simple modules (or zero). Moreover, we show that each simple module of the graded affine Hecke algebra appears as the image of a simple Whittaker module. Since the Whittaker category contains the BGG category as a full subcategory, our results generalize results of Arakawa-Suzuki [1], which in turn generalize Schur-Weyl duality between finite-dimensional representations of and representations of the symmetric group .},
author = {Brown, Adam},
issn = {0021-8693},
journal = {Journal of Algebra},
pages = {261--289},
publisher = {Elsevier},
title = {{Arakawa-Suzuki functors for Whittaker modules}},
doi = {10.1016/j.jalgebra.2019.07.027},
volume = {538},
year = {2019},
}
@article{6900,
abstract = {Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks.},
author = {Cepeda Humerez, Sarah A and Ruess, Jakob and Tkačik, Gašper},
issn = {15537358},
journal = {PLoS computational biology},
number = {9},
pages = {e1007290},
publisher = {Public Library of Science},
title = {{Estimating information in time-varying signals}},
doi = {10.1371/journal.pcbi.1007290},
volume = {15},
year = {2019},
}
@inproceedings{6931,
abstract = {Consider a distributed system with n processors out of which f can be Byzantine faulty. In the
approximate agreement task, each processor i receives an input value xi and has to decide on an
output value yi such that
1. the output values are in the convex hull of the non-faulty processors’ input values,
2. the output values are within distance d of each other.
Classically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.
In this work, we study the task in a discrete setting, where input values with some structure
expressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to
output vertices that are within distance d of each other in G, but still remain in the graph-induced
convex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with
a deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,
we show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,
where ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a
variant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact
variants of these and related tasks over a large class of combinatorial structures.},
author = {Nowak, Thomas and Rybicki, Joel},
booktitle = {33rd International Symposium on Distributed Computing},
keyword = {consensus, approximate agreement, Byzantine faults, chordal graphs, lattice agreement},
location = {Budapest, Hungary},
pages = {29:1----29:17},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik},
title = {{Byzantine approximate agreement on graphs}},
doi = {10.4230/LIPICS.DISC.2019.29},
volume = {146},
year = {2019},
}
@article{6936,
abstract = {A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.
},
author = {Ovaskainen, Otso and Rybicki, Joel and Abrego, Nerea},
issn = {1600-0587},
journal = {Ecography},
number = {11},
pages = {1877--1886},
publisher = {Wiley},
title = {{What can observational data reveal about metacommunity processes?}},
doi = {10.1111/ecog.04444},
volume = {42},
year = {2019},
}
@article{6986,
abstract = {Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. },
author = {Li, Penghui},
issn = {0002-9939},
journal = {Proceedings of the American Mathematical Society},
number = {11},
pages = {4597--4604},
publisher = {AMS},
title = {{A colimit of traces of reflection groups}},
doi = {10.1090/proc/14586},
volume = {147},
year = {2019},
}
@article{7004,
abstract = {We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds.},
author = {Rapcak, Miroslav and Soibelman, Yan and Yang, Yaping and Zhao, Gufang},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
publisher = {Springer Nature},
title = {{Cohomological Hall algebras, vertex algebras and instantons}},
doi = {10.1007/s00220-019-03575-5},
year = {2019},
}
@article{6955,
abstract = {We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential.},
author = {Schmickler, C.H. and Hammer, H.-W. and Volosniev, Artem},
issn = {0370-2693},
journal = {Physics Letters B},
publisher = {Elsevier},
title = {{Universal physics of bound states of a few charged particles}},
doi = {10.1016/j.physletb.2019.135016},
volume = {798},
year = {2019},
}
@article{6943,
abstract = {Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration.},
author = {Hörmayer, Lukas and Friml, Jiří},
issn = {1369-5266},
journal = {Current Opinion in Plant Biology},
number = {12},
pages = {124--130},
publisher = {Elsevier},
title = {{Targeted cell ablation-based insights into wound healing and restorative patterning}},
doi = {10.1016/j.pbi.2019.08.006},
volume = {52},
year = {2019},
}