@article{1663,
abstract = {CREB-binding protein (CBP) and p300 are transcriptional coactivators involved in numerous biological processes that affect cell growth, transformation, differentiation, and development. In this study, we provide evidence of the involvement of homeodomain-interacting protein kinase 2 (HIPK2) in the regulation of CBP activity. We show that HIPK2 interacts with and phosphorylates several regions of CBP. We demonstrate that serines 2361, 2363, 2371, 2376, and 2381 are responsible for the HIPK2-induced mobility shift of CBP C-terminal activation domain. Moreover, we show that HIPK2 strongly potentiates the transcriptional activity of CBP. However, our data suggest that HIPK2 activates CBP mainly by counteracting the repressive action of cell cycle regulatory domain 1 (CRD1), located between amino acids 977 and 1076, independently of CBP phosphorylation. Our findings thus highlight a complex regulation of CBP activity by HIPK2, which might be relevant for the control of specific sets of target genes involved in cellular proliferation, differentiation and apoptosis.},
author = {Kovács, Krisztián and Steinmann, Myriam and Halfon, Olivier and Magistretti, Pierre and Cardinaux, Jean},
journal = {Cellular Signalling},
number = {11},
pages = {2252 -- 2260},
publisher = {Elsevier},
title = {{Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2}},
doi = {10.1016/j.cellsig.2015.08.001},
volume = {27},
year = {2015},
}
@article{1664,
abstract = {Over a century of research into the origin of turbulence in wall-bounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At moderate flow speeds, turbulence is confined to localized patches; it is only at higher speeds that the entire flow becomes turbulent. The origin of the different states encountered during this transition, the front dynamics of the turbulent regions and the transformation to full turbulence have yet to be explained. By combining experiments, theory and computer simulations, here we uncover a bifurcation scenario that explains the transformation to fully turbulent pipe flow and describe the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows.},
author = {Barkley, Dwight and Song, Baofang and Vasudevan, Mukund and Lemoult, Grégoire M and Avila, Marc and Hof, Björn},
journal = {Nature},
number = {7574},
pages = {550 -- 553},
publisher = {Nature Publishing Group},
title = {{The rise of fully turbulent flow}},
doi = {10.1038/nature15701},
volume = {526},
year = {2015},
}
@article{1665,
abstract = {Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome.},
author = {Landau, Dan and Tausch, Eugen and Taylor Weiner, Amaro and Stewart, Chip and Reiter, Johannes and Bahlo, Jasmin and Kluth, Sandra and Božić, Ivana and Lawrence, Michael and Böttcher, Sebastian and Carter, Scott and Cibulskis, Kristian and Mertens, Daniel and Sougnez, Carrie and Rosenberg, Mara and Hess, Julian and Edelmann, Jennifer and Kless, Sabrina and Kneba, Michael and Ritgen, Matthias and Fink, Anna and Fischer, Kirsten and Gabriel, Stacey and Lander, Eric and Nowak, Martin and Döhner, Hartmut and Hallek, Michael and Neuberg, Donna and Getz, Gad and Stilgenbauer, Stephan and Wu, Catherine},
journal = {Nature},
number = {7574},
pages = {525 -- 530},
publisher = {Nature Publishing Group},
title = {{Mutations driving CLL and their evolution in progression and relapse}},
doi = {10.1038/nature15395},
volume = {526},
year = {2015},
}
@inproceedings{1667,
abstract = {We consider parametric version of fixed-delay continuoustime Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is to synthesize values of these parameters that, for a given cost function, minimise expected total cost incurred before reaching a given set of target states. We show that under mild assumptions, optimal values of parameters can be effectively approximated using translation to a Markov decision process (MDP) whose actions correspond to discretized values of these parameters. To this end we identify and overcome several interesting phenomena arising in systems with fixed delays.},
author = {Brázdil, Tomáš and Korenčiak, L'Uboš and Krčál, Jan and Novotny, Petr and Řehák, Vojtěch},
location = {Madrid, Spain},
pages = {141 -- 159},
publisher = {Springer},
title = {{Optimizing performance of continuous-time stochastic systems using timeout synthesis}},
doi = {10.1007/978-3-319-22264-6_10},
volume = {9259},
year = {2015},
}
@inproceedings{1668,
abstract = {We revisit the security (as a pseudorandom permutation) of cascading-based constructions for block-cipher key-length extension. Previous works typically considered the extreme case where the adversary is given the entire codebook of the construction, the only complexity measure being the number qe of queries to the underlying ideal block cipher, representing adversary’s secret-key-independent computation. Here, we initiate a systematic study of the more natural case of an adversary restricted to adaptively learning a number qc of plaintext/ciphertext pairs that is less than the entire codebook. For any such qc, we aim to determine the highest number of block-cipher queries qe the adversary can issue without being able to successfully distinguish the construction (under a secret key) from a random permutation.
More concretely, we show the following results for key-length extension schemes using a block cipher with n-bit blocks and κ-bit keys:
Plain cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ. The bound for r=1 also applies to two-key triple encryption (as used within Triple DES).
The r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching an attack by Gaži (CRYPTO 2013).
We fully characterize the security of Gaži and Tessaro’s two-call },
author = {Gazi, Peter and Lee, Jooyoung and Seurin, Yannick and Steinberger, John and Tessaro, Stefano},
location = {Istanbul, Turkey},
pages = {319 -- 341},
publisher = {Springer},
title = {{Relaxing full-codebook security: A refined analysis of key-length extension schemes}},
doi = {10.1007/978-3-662-48116-5_16},
volume = {9054},
year = {2015},
}
@inproceedings{1669,
abstract = {Computational notions of entropy (a.k.a. pseudoentropy) have found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The most important tools to argue about pseudoentropy are chain rules, which quantify by how much (in terms of quantity and quality) the pseudoentropy of a given random variable X decreases when conditioned on some other variable Z (think for example of X as a secret key and Z as information leaked by a side-channel). In this paper we give a very simple and modular proof of the chain rule for HILL pseudoentropy, improving best known parameters. Our version allows for increasing the acceptable length of leakage in applications up to a constant factor compared to the best previous bounds. As a contribution of independent interest, we provide a comprehensive study of all known versions of the chain rule, comparing their worst-case strength and limitations.},
author = {Pietrzak, Krzysztof Z and Skórski, Maciej},
location = {Guadalajara, Mexico},
pages = {81 -- 98},
publisher = {Springer},
title = {{The chain rule for HILL pseudoentropy, revisited}},
doi = {10.1007/978-3-319-22174-8_5},
volume = {9230},
year = {2015},
}
@inproceedings{1670,
abstract = {Planning in hybrid domains poses a special challenge due to the involved mixed discrete-continuous dynamics. A recent solving approach for such domains is based on applying model checking techniques on a translation of PDDL+ planning problems to hybrid automata. However, the proposed translation is limited because must behavior is only overapproximated, and hence, processes and events are not reflected exactly. In this paper, we present the theoretical foundation of an exact PDDL+ translation. We propose a schema to convert a hybrid automaton with must transitions into an equivalent hybrid automaton featuring only may transitions.},
author = {Bogomolov, Sergiy and Magazzeni, Daniele and Minopoli, Stefano and Wehrle, Martin},
location = {Jerusalem, Israel},
pages = {42 -- 46},
publisher = {AAAI Press},
title = {{PDDL+ planning with hybrid automata: Foundations of translating must behavior}},
year = {2015},
}
@inproceedings{1671,
abstract = {This paper studies the concrete security of PRFs and MACs obtained by keying hash functions based on the sponge paradigm. One such hash function is KECCAK, selected as NIST’s new SHA-3 standard. In contrast to other approaches like HMAC, the exact security of keyed sponges is not well understood. Indeed, recent security analyses delivered concrete security bounds which are far from existing attacks. This paper aims to close this gap. We prove (nearly) exact bounds on the concrete PRF security of keyed sponges using a random permutation. These bounds are tight for the most relevant ranges of parameters, i.e., for messages of length (roughly) l ≤ min{2n/4, 2r} blocks, where n is the state size and r is the desired output length; and for l ≤ q queries (to the construction or the underlying permutation). Moreover, we also improve standard-model bounds. As an intermediate step of independent interest, we prove tight bounds on the PRF security of the truncated CBC-MAC construction, which operates as plain CBC-MAC, but only returns a prefix of the output.},
author = {Gazi, Peter and Pietrzak, Krzysztof Z and Tessaro, Stefano},
location = {Santa Barbara, CA, United States},
pages = {368 -- 387},
publisher = {Springer},
title = {{The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC}},
doi = {10.1007/978-3-662-47989-6_18},
volume = {9215},
year = {2015},
}
@inproceedings{1672,
abstract = {Composable notions of incoercibility aim to forbid a coercer from using anything beyond the coerced parties’ inputs and outputs to catch them when they try to deceive him. Existing definitions are restricted to weak coercion types, and/or are not universally composable. Furthermore, they often make too strong assumptions on the knowledge of coerced parties—e.g., they assume they known the identities and/or the strategies of other coerced parties, or those of corrupted parties— which makes them unsuitable for applications of incoercibility such as e-voting, where colluding adversarial parties may attempt to coerce honest voters, e.g., by offering them money for a promised vote, and use their own view to check that the voter keeps his end of the bargain. In this work we put forward the first universally composable notion of incoercible multi-party computation, which satisfies the above intuition and does not assume collusions among coerced parties or knowledge of the corrupted set. We define natural notions of UC incoercibility corresponding to standard coercion-types, i.e., receipt-freeness and resistance to full-active coercion. Importantly, our suggested notion has the unique property that it builds on top of the well studied UC framework by Canetti instead of modifying it. This guarantees backwards compatibility, and allows us to inherit results from the rich UC literature. We then present MPC protocols which realize our notions of UC incoercibility given access to an arguably minimal setup—namely honestly generate tamper-proof hardware performing a very simple cryptographic operation—e.g., a smart card. This is, to our knowledge, the first proposed construction of an MPC protocol (for more than two parties) that is incoercibly secure and universally composable, and therefore the first construction of a universally composable receipt-free e-voting protocol.},
author = {Alwen, Joel F and Ostrovsky, Rafail and Zhou, Hongsheng and Zikas, Vassilis},
location = {Santa Barbara, CA, United States},
pages = {763 -- 780},
publisher = {Springer},
title = {{Incoercible multi-party computation and universally composable receipt-free voting}},
doi = {10.1007/978-3-662-48000-7_37},
volume = {9216},
year = {2015},
}
@article{1673,
abstract = {When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement-that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two. },
author = {Adlam, Ben and Chatterjee, Krishnendu and Nowak, Martin},
journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
number = {2181},
publisher = {Royal Society of London},
title = {{Amplifiers of selection}},
doi = {10.1098/rspa.2015.0114},
volume = {471},
year = {2015},
}
@article{1674,
abstract = {We consider N × N random matrices of the form H = W + V where W is a real symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W and we choose V so that the eigenvalues of W and V are typically of the same order. For a large class of diagonal matrices V, we show that the rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom distribution F1 in the limit of large N. Our proofs also apply to the complex Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix.},
author = {Lee, Jioon and Schnelli, Kevin},
journal = {Reviews in Mathematical Physics},
number = {8},
publisher = {World Scientific Publishing},
title = {{Edge universality for deformed Wigner matrices}},
doi = {10.1142/S0129055X1550018X},
volume = {27},
year = {2015},
}
@inproceedings{1675,
abstract = {Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble).},
author = {Dziembowski, Stefan and Faust, Sebastian and Kolmogorov, Vladimir and Pietrzak, Krzysztof Z},
location = {Santa Barbara, CA, United States},
pages = {585 -- 605},
publisher = {Springer},
title = {{Proofs of space}},
doi = {10.1007/978-3-662-48000-7_29},
volume = {9216},
year = {2015},
}
@article{1676,
author = {Sixt, Michael K and Raz, Erez},
journal = {Current Opinion in Cell Biology},
number = {10},
pages = {4 -- 6},
publisher = {Elsevier},
title = {{Editorial overview: Cell adhesion and migration}},
doi = {10.1016/j.ceb.2015.09.004},
volume = {36},
year = {2015},
}
@article{1677,
abstract = {We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale.},
author = {Alt, Johannes},
journal = {Journal of Mathematical Physics},
number = {10},
publisher = {American Institute of Physics},
title = {{The local semicircle law for random matrices with a fourfold symmetry}},
doi = {10.1063/1.4932606},
volume = {56},
year = {2015},
}
@article{1678,
abstract = {High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that avoids the need for chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small-molecule screen against human protein kinases, including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes.},
author = {Inglés Prieto, Álvaro and Gschaider-Reichhart, Eva and Muellner, Markus and Nowak, Matthias and Nijman, Sebastian and Grusch, Michael and Janovjak, Harald L},
journal = {Nature Chemical Biology},
number = {12},
pages = {952 -- 954},
publisher = {Nature Publishing Group},
title = {{Light-assisted small-molecule screening against protein kinases}},
doi = {10.1038/nchembio.1933},
volume = {11},
year = {2015},
}
@article{1679,
author = {Lemoult, Grégoire M and Maier, Philipp and Hof, Björn},
journal = {Physics of Fluids},
number = {9},
publisher = {American Institute of Physics},
title = {{Taylor's Forest}},
doi = {10.1063/1.4930850},
volume = {27},
year = {2015},
}
@article{1680,
abstract = {We consider the satisfiability problem for modal logic over first-order definable classes of frames.We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is eitherNP-complete or PSPACE-complete, and global satisfiability is NP-complete, PSPACE-complete, or ExpTime-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability.},
author = {Michaliszyn, Jakub and Otop, Jan and Kieroňski, Emanuel},
journal = {ACM Transactions on Computational Logic},
number = {1},
publisher = {ACM},
title = {{On the decidability of elementary modal logics}},
doi = {10.1145/2817825},
volume = {17},
year = {2015},
}
@article{1681,
abstract = {In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game.},
author = {Priklopil, Tadeas and Chatterjee, Krishnendu},
journal = {Games},
number = {4},
pages = {413 -- 437},
publisher = {Multidisciplinary Digital Publishing Institute},
title = {{Evolution of decisions in population games with sequentially searching individuals}},
doi = {10.3390/g6040413},
volume = {6},
year = {2015},
}
@article{1682,
abstract = {We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings.},
author = {Franek, Peter and Krcál, Marek},
journal = {Journal of the ACM},
number = {4},
publisher = {ACM},
title = {{Robust satisfiability of systems of equations}},
doi = {10.1145/2751524},
volume = {62},
year = {2015},
}
@article{1683,
abstract = {The 1 MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5 Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8 Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated.},
author = {Letts, Jame A and Sazanov, Leonid A},
journal = {Current Opinion in Structural Biology},
number = {8},
pages = {135 -- 145},
publisher = {Elsevier},
title = {{Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions}},
doi = {10.1016/j.sbi.2015.08.008},
volume = {33},
year = {2015},
}