@inproceedings{1650,
abstract = {We consider the task of deriving a key with high HILL entropy (i.e., being computationally indistinguishable from a key with high min-entropy) from an unpredictable source.
Previous to this work, the only known way to transform unpredictability into a key that was ϵ indistinguishable from having min-entropy was via pseudorandomness, for example by Goldreich-Levin (GL) hardcore bits. This approach has the inherent limitation that from a source with k bits of unpredictability entropy one can derive a key of length (and thus HILL entropy) at most k−2log(1/ϵ) bits. In many settings, e.g. when dealing with biometric data, such a 2log(1/ϵ) bit entropy loss in not an option. Our main technical contribution is a theorem that states that in the high entropy regime, unpredictability implies HILL entropy. Concretely, any variable K with |K|−d bits of unpredictability entropy has the same amount of so called metric entropy (against real-valued, deterministic distinguishers), which is known to imply the same amount of HILL entropy. The loss in circuit size in this argument is exponential in the entropy gap d, and thus this result only applies for small d (i.e., where the size of distinguishers considered is exponential in d).
To overcome the above restriction, we investigate if it’s possible to first “condense” unpredictability entropy and make the entropy gap small. We show that any source with k bits of unpredictability can be condensed into a source of length k with k−3 bits of unpredictability entropy. Our condenser simply “abuses" the GL construction and derives a k bit key from a source with k bits of unpredicatibily. The original GL theorem implies nothing when extracting that many bits, but we show that in this regime, GL still behaves like a “condenser" for unpredictability. This result comes with two caveats (1) the loss in circuit size is exponential in k and (2) we require that the source we start with has no HILL entropy (equivalently, one can efficiently check if a guess is correct). We leave it as an intriguing open problem to overcome these restrictions or to prove they’re inherent.},
author = {Skórski, Maciej and Golovnev, Alexander and Pietrzak, Krzysztof Z},
location = {Kyoto, Japan},
pages = {1046 -- 1057},
publisher = {Springer},
title = {{Condensed unpredictability }},
doi = {10.1007/978-3-662-47672-7_85},
volume = {9134},
year = {2015},
}
@inproceedings{1651,
abstract = {Cryptographic e-cash allows off-line electronic transactions between a bank, users and merchants in a secure and anonymous fashion. A plethora of e-cash constructions has been proposed in the literature; however, these traditional e-cash schemes only allow coins to be transferred once between users and merchants. Ideally, we would like users to be able to transfer coins between each other multiple times before deposit, as happens with physical cash. “Transferable” e-cash schemes are the solution to this problem. Unfortunately, the currently proposed schemes are either completely impractical or do not achieve the desirable anonymity properties without compromises, such as assuming the existence of a trusted “judge” who can trace all coins and users in the system. This paper presents the first efficient and fully anonymous transferable e-cash scheme without any trusted third parties. We start by revising the security and anonymity properties of transferable e-cash to capture issues that were previously overlooked. For our construction we use the recently proposed malleable signatures by Chase et al. to allow the secure and anonymous transfer of coins, combined with a new efficient double-spending detection mechanism. Finally, we discuss an instantiation of our construction.},
author = {Baldimtsi, Foteini and Chase, Melissa and Fuchsbauer, Georg and Kohlweiss, Markulf},
location = {Gaithersburg, MD, USA},
pages = {101 -- 124},
publisher = {Springer},
title = {{Anonymous transferable e-cash}},
doi = {10.1007/978-3-662-46447-2_5},
volume = {9020},
year = {2015},
}
@inproceedings{1652,
abstract = {We develop new theoretical tools for proving lower-bounds on the (amortized) complexity of certain functions in models of parallel computation. We apply the tools to construct a class of functions with high amortized memory complexity in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing for batches of simultaneous queries. In particular we obtain a new, more robust, type of Memory-Hard Functions (MHF); a security primitive which has recently been gaining acceptance in practice as an effective means of countering brute-force attacks on security relevant functions. Along the way we also demonstrate an important shortcoming of previous definitions of MHFs and give a new definition addressing the problem. The tools we develop represent an adaptation of the powerful pebbling paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73]) to a simple and intuitive parallel setting. We define a simple pebbling game Gp over graphs which aims to abstract parallel computation in an intuitive way. As a conceptual contribution we define a measure of pebbling complexity for graphs called cumulative complexity (CC) and show how it overcomes a crucial shortcoming (in the parallel setting) exhibited by more traditional complexity measures used in the past. As a main technical contribution we give an explicit construction of a constant in-degree family of graphs whose CC in Gp approaches maximality to within a polylogarithmic factor for any graph of equal size (analogous to the graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally, for a given graph G and related function fG, we derive a lower-bound on the amortized memory complexity of fG in the pROM in terms of the CC of G in the game Gp.},
author = {Alwen, Joel F and Serbinenko, Vladimir},
booktitle = {Proceedings of the 47th annual ACM symposium on Theory of computing},
location = {Portland, OR, United States},
pages = {595 -- 603},
publisher = {ACM},
title = {{High parallel complexity graphs and memory-hard functions}},
doi = {10.1145/2746539.2746622},
year = {2015},
}
@inproceedings{1654,
abstract = {HMAC and its variant NMAC are the most popular approaches to deriving a MAC (and more generally, a PRF) from a cryptographic hash function. Despite nearly two decades of research, their exact security still remains far from understood in many different contexts. Indeed, recent works have re-surfaced interest for {\em generic} attacks, i.e., attacks that treat the compression function of the underlying hash function as a black box.
Generic security can be proved in a model where the underlying compression function is modeled as a random function -- yet, to date, the question of proving tight, non-trivial bounds on the generic security of HMAC/NMAC even as a PRF remains a challenging open question.
In this paper, we ask the question of whether a small modification to HMAC and NMAC can allow us to exactly characterize the security of the resulting constructions, while only incurring little penalty with respect to efficiency. To this end, we present simple variants of NMAC and HMAC, for which we prove tight bounds on the generic PRF security, expressed in terms of numbers of construction and compression function queries necessary to break the construction. All of our constructions are obtained via a (near) {\em black-box} modification of NMAC and HMAC, which can be interpreted as an initial step of key-dependent message pre-processing.
While our focus is on PRF security, a further attractive feature of our new constructions is that they clearly defeat all recent generic attacks against properties such as state recovery and universal forgery. These exploit properties of the so-called ``functional graph'' which are not directly accessible in our new constructions. },
author = {Gazi, Peter and Pietrzak, Krzysztof Z and Tessaro, Stefano},
location = {Auckland, New Zealand},
pages = {85 -- 109},
publisher = {Springer},
title = {{Generic security of NMAC and HMAC with input whitening}},
doi = {10.1007/978-3-662-48800-3_4},
volume = {9453},
year = {2015},
}
@article{1655,
abstract = {Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration.},
author = {Martius, Georg S and Olbrich, Eckehard},
journal = {Entropy},
number = {10},
pages = {7266 -- 7297},
publisher = {Multidisciplinary Digital Publishing Institute},
title = {{Quantifying emergent behavior of autonomous robots}},
doi = {10.3390/e17107266},
volume = {17},
year = {2015},
}
@inproceedings{1656,
abstract = {Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
booktitle = {Proceedings - Symposium on Logic in Computer Science},
location = {Kyoto, Japan},
publisher = {IEEE},
title = {{Nested weighted automata}},
doi = {10.1109/LICS.2015.72},
volume = {2015-July},
year = {2015},
}
@inproceedings{1657,
abstract = {We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) ~the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) ~the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., Ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems, which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. },
author = {Chatterjee, Krishnendu and Komárková, Zuzana and Kretinsky, Jan},
location = {Kyoto, Japan},
pages = {244 -- 256},
publisher = {IEEE},
title = {{Unifying two views on multiple mean-payoff objectives in Markov decision processes}},
doi = {10.1109/LICS.2015.32},
year = {2015},
}
@inproceedings{1658,
abstract = {Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space.},
author = {Bogomolov, Sergiy and Henzinger, Thomas A and Podelski, Andreas and Ruess, Jakob and Schilling, Christian},
location = {Nantes, France},
pages = {77 -- 89},
publisher = {Springer},
title = {{Adaptive moment closure for parameter inference of biochemical reaction networks}},
doi = {10.1007/978-3-319-23401-4_8},
volume = {9308},
year = {2015},
}
@inproceedings{1659,
abstract = {The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata.},
author = {Boker, Udi and Henzinger, Thomas A and Otop, Jan},
booktitle = {LICS},
issn = {1043-6871 },
location = {Kyoto, Japan},
pages = {750 -- 761},
publisher = {IEEE},
title = {{The target discounted-sum problem}},
doi = {10.1109/LICS.2015.74},
year = {2015},
}
@inproceedings{1660,
abstract = {We study the pattern frequency vector for runs in probabilistic Vector Addition Systems with States (pVASS). Intuitively, each configuration of a given pVASS is assigned one of finitely many patterns, and every run can thus be seen as an infinite sequence of these patterns. The pattern frequency vector assigns to each run the limit of pattern frequencies computed for longer and longer prefixes of the run. If the limit does not exist, then the vector is undefined. We show that for one-counter pVASS, the pattern frequency vector is defined and takes one of finitely many values for almost all runs. Further, these values and their associated probabilities can be approximated up to an arbitrarily small relative error in polynomial time. For stable two-counter pVASS, we show the same result, but we do not provide any upper complexity bound. As a byproduct of our study, we discover counterexamples falsifying some classical results about stochastic Petri nets published in the 80s.},
author = {Brázdil, Tomáš and Kiefer, Stefan and Kučera, Antonín and Novotny, Petr},
location = {Kyoto, Japan},
pages = {44 -- 55},
publisher = {IEEE},
title = {{Long-run average behaviour of probabilistic vector addition systems}},
doi = {10.1109/LICS.2015.15},
year = {2015},
}
@inproceedings{1661,
abstract = {The computation of the winning set for one-pair Streett objectives and for k-pair Streett objectives in (standard) graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formed ness of specifications, and the synthesis of reactive systems. We give faster algorithms for the computation of the winning set for (1) one-pair Streett objectives (aka parity-3 problem) in game graphs and (2) for k-pair Streett objectives in graphs. For both problems this represents the first improvement in asymptotic running time in 15 years.},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Loitzenbauer, Veronika},
booktitle = {Proceedings - Symposium on Logic in Computer Science},
location = {Kyoto, Japan},
publisher = {IEEE},
title = {{Improved algorithms for one-pair and k-pair Streett objectives}},
doi = {10.1109/LICS.2015.34},
volume = {2015-July},
year = {2015},
}
@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},
}
@article{1684,
abstract = {Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.},
author = {Vicoso, Beatriz and Bachtrog, Doris},
journal = {PLoS Biology},
number = {4},
publisher = {Public Library of Science},
title = {{Numerous transitions of sex chromosomes in Diptera}},
doi = {10.1371/journal.pbio.1002078},
volume = {13},
year = {2015},
}
@inproceedings{1685,
abstract = {Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.
Our techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest.},
author = {Cohen Addad, Vincent and De Mesmay, Arnaud N},
location = {Patras, Greece},
pages = {386 -- 398},
publisher = {Springer},
title = {{A fixed parameter tractable approximation scheme for the optimal cut graph of a surface}},
doi = {10.1007/978-3-662-48350-3_33},
volume = {9294},
year = {2015},
}
@article{1106,
abstract = {Circumferential skin creases Kunze type (CSC-KT) is a specific congenital entity with an unknown genetic cause. The disease phenotype comprises characteristic circumferential skin creases accompanied by intellectual disability, a cleft palate, short stature, and dysmorphic features. Here, we report that mutations in either MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a member of the microtubule end-binding family of proteins that bind to the guanosine triphosphate cap at growing microtubule plus ends, and TUBB encodes a β-tubulin isotype that is expressed abundantly in the developing brain. Functional analyses of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer folding and assembly pathway that leads to a compromised yield of native heterodimers. The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we show that the mutations result in enhanced MAPRE2 binding to microtubules, implying an increased dwell time at microtubule plus ends. Further, in vivo analysis of MAPRE2 mutations in a zebrafish model of craniofacial development shows that the variants most likely perturb the patterning of branchial arches, either through excessive activity (under a recessive paradigm) or through haploinsufficiency (dominant de novo paradigm). Taken together, our data add CSC-KT to the growing list of tubulinopathies and highlight how multiple inheritance paradigms can affect dosage-sensitive biological systems so as to result in the same clinical defect.},
author = {Isrie, Mala and Breuss, Martin and Tian, Guoling and Hansen, Andi H and Cristofoli, Francesca and Morandell, Jasmin and Kupchinsky, Zachari A and Sifrim, Alejandro and Rodriguez Rodriguez, Celia and Dapena, Elena P and Doonanco, Kurston and Leonard, Norma and Tinsa, Faten and Moortgat, Stéphanie and Ulucan, Hakan and Koparir, Erkan and Karaca, Ender and Katsanis, Nicholas and Marton, Valeria and Vermeesch, Joris R and Davis, Erica E and Cowan, Nicholas J and Keays, David and Van Esch, Hilde},
journal = {The American Journal of Human Genetics},
number = {6},
pages = {790 -- 800},
publisher = {Cell Press},
title = {{Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type}},
doi = {10.1016/j.ajhg.2015.10.014},
volume = {97},
year = {2015},
}
@article{120,
abstract = {Clustering of fine particles is of crucial importance in settings ranging from the early stages of planet formation to the coagulation of industrial powders and airborne pollutants. Models of such clustering typically focus on inelastic deformation and cohesion. However, even in charge-neutral particle systems comprising grains of the same dielectric material, tribocharging can generate large amounts of net positive or negative charge on individual particles, resulting in long-range electrostatic forces. The effects of such forces on cluster formation are not well understood and have so far not been studied in situ. Here we report the first observations of individual collide-and-capture events between charged submillimetre particles, including Kepler-like orbits. Charged particles can become trapped in their mutual electrostatic energy well and aggregate via multiple bounces. This enables the initiation of clustering at relative velocities much larger than the upper limit for sticking after a head-on collision, a long-standing issue known from pre-planetary dust aggregation. Moreover, Coulomb interactions together with dielectric polarization are found to stabilize characteristic molecule-like configurations, providing new insights for the modelling of clustering dynamics in a wide range of microscopic dielectric systems, such as charged polarizable ions, biomolecules and colloids.},
author = {Lee, Victor and Waitukaitis, Scott R and Miskin, Marc and Jaeger, Heinrich},
journal = {Nature Physics},
number = {9},
pages = {733 -- 737},
publisher = {Nature Publishing Group},
title = {{Direct observation of particle interactions and clustering in charged granular streams}},
doi = {10.1038/nphys3396},
volume = {11},
year = {2015},
}
@article{121,
abstract = {We show that the simplest building blocks of origami-based materials - rigid, degree-four vertices - are generically multistable. The existence of two distinct branches of folding motion emerging from the flat state suggests at least bistability, but we show how nonlinearities in the folding motions allow generic vertex geometries to have as many as five stable states. In special geometries with collinear folds and symmetry, more branches emerge leading to as many as six stable states. Tuning the fold energy parameters, we show how monostability is also possible. Finally, we show how to program the stability features of a single vertex into a periodic fold tessellation. The resulting metasheets provide a previously unanticipated functionality - tunable and switchable shape and size via multistability.},
author = {Waitukaitis, Scott R and Menaut, Rémi and Chen, Bryan and Van Hecke, Martin},
journal = {APS Physics, Physical Review Letters},
number = {5},
publisher = {American Physical Society},
title = {{Origami multistability: From single vertices to metasheets}},
doi = {10.1103/PhysRevLett.114.055503},
volume = {114},
year = {2015},
}
@article{886,
abstract = {The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.},
author = {Kondrashov, Dmitry A and Fyodor Kondrashov},
journal = {Trends in Genetics},
number = {1},
pages = {24 -- 33},
publisher = {Elsevier},
title = {{Topological features of rugged fitness landscapes in sequence space}},
doi = {10.1016/j.tig.2014.09.009},
volume = {31},
year = {2015},
}
@article{9017,
abstract = {MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.},
author = {Richet, Nicolas and Liu, Danni and Legrand, Pierre and Velours, Christophe and Corpet, Armelle and Gaubert, Albane and Bakail, May M and Moal-Raisin, Gwenaelle and Guerois, Raphael and Compper, Christel and Besle, Arthur and Guichard, Berengère and Almouzni, Genevieve and Ochsenbein, Françoise},
issn = {1362-4962},
journal = {Nucleic Acids Research},
number = {3},
pages = {1905--1917},
publisher = {Oxford University Press},
title = {{Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork}},
doi = {10.1093/nar/gkv021},
volume = {43},
year = {2015},
}
@article{9057,
abstract = {Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.},
author = {Palacci, Jérémie A and Sacanna, Stefano and Abramian, Anaïs and Barral, Jérémie and Hanson, Kasey and Grosberg, Alexander Y. and Pine, David J. and Chaikin, Paul M.},
issn = {2375-2548},
journal = {Science Advances},
number = {4},
publisher = {American Association for the Advancement of Science },
title = {{Artificial rheotaxis}},
doi = {10.1126/sciadv.1400214},
volume = {1},
year = {2015},
}
@article{906,
abstract = {The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.},
author = {Arkhipova, Oksana V and Meer, Margarita V and Mikoulinskaia, Galina V and Zakharova, Marina V and Galushko, Alexander S and Akimenko, Vasilii K and Fyodor Kondrashov},
journal = {PLoS One},
number = {5},
publisher = {Public Library of Science},
title = {{Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer}},
doi = {10.1371/journal.pone.0125888},
volume = {10},
year = {2015},
}
@article{9141,
abstract = {The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere.},
author = {Lefauve, Adrien and MULLER, Caroline J and Melet, Angélique},
issn = {2169-9275},
journal = {Journal of Geophysical Research: Oceans},
number = {7},
pages = {4760--4777},
publisher = {American Geophysical Union},
title = {{A three-dimensional map of tidal dissipation over abyssal hills}},
doi = {10.1002/2014jc010598},
volume = {120},
year = {2015},
}
@article{924,
abstract = {This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper.},
author = {Boubaker, Riadh and Platel, Vincent and Bergès, Alexis and Bancelin, Mathieu and Hannezo, Edouard B},
journal = {Applied Thermal Engineering},
pages = {1 -- 8},
publisher = {Elsevier},
title = {{Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop}},
doi = {10.1016/j.applthermaleng.2014.10.009},
volume = {76},
year = {2015},
}
@article{928,
abstract = {The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events.},
author = {Sehring, Ivonne and Recho, Pierre and Denker, Elsa and Kourakis, Matthew and Mathiesen, Birthe and Hannezo, Edouard B and Dong, Bo and Jiang, Di},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Assembly and positioning of actomyosin rings by contractility and planar cell polarity}},
doi = {10.7554/eLife.09206},
volume = {4},
year = {2015},
}
@article{929,
abstract = {An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. },
author = {Hannezo, Edouard B and Dong, Bo and Recho, Pierre and Joanny, Jean and Hayashi, Shigeo},
journal = {PNAS},
number = {28},
pages = {8620 -- 8625},
publisher = {National Academy of Sciences},
title = {{Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes}},
doi = {10.1073/pnas.1504762112},
volume = {112},
year = {2015},
}
@article{933,
abstract = {Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.},
author = {García, Simón and Hannezo, Edouard B and Elgeti, Jens and Joanny, Jean and Silberzan, Pascal and Gov, Nir},
journal = {PNAS},
number = {50},
pages = {15314 -- 15319},
publisher = {National Academy of Sciences},
title = {{Physics of active jamming during collective cellular motion in a monolayer}},
doi = {10.1073/pnas.1510973112},
volume = {112},
year = {2015},
}
@article{981,
abstract = {The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials.},
author = {Zeljkovic, Ilija and Okada, Yoshinori and Maksym Serbyn and Sankar, Raman and Walkup, Daniel and Zhou, Wenwen and Liu, Junwei and Chang, Guoqing and Wang, Yungjui and Hasan, Md Z and Chou, Fangcheng and Lin, Hsin and Bansil, Arun and Fu, Liang and Madhavan, Vidya},
journal = {Nature Materials},
number = {3},
pages = {318 -- 324},
publisher = {Nature Publishing Group},
title = {{Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators}},
doi = {10.1038/nmat4215},
volume = {14},
year = {2015},
}
@article{982,
abstract = {We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.},
author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A},
journal = {Physical Review X},
number = {4},
publisher = {American Physical Society},
title = {{Criterion for many-body localization-delocalization phase transition}},
doi = {10.1103/PhysRevX.5.041047},
volume = {5},
year = {2015},
}
@article{99,
abstract = {Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms.},
author = {Higginbotham, Andrew P and Albrecht, S M and Kiršanskas, Gediminas and Chang, W and Kuemmeth, Ferdinand and Krogstrup, Peter and Jespersen, Thomas and Nygård, Jesper and Flensberg, Karsten and Marcus, Charles},
journal = {Nature Physics},
number = {12},
pages = {1017 -- 1021},
publisher = {Nature Publishing Group},
title = {{Parity lifetime of bound states in a proximitized semiconductor nanowire}},
doi = {10.1038/nphys3461},
volume = {11},
year = {2015},
}
@article{388,
abstract = {We use ultrafast optical spectroscopy to observe binding of charged single-particle excitations (SE) in the magnetically frustrated Mott insulator Na2IrO3. Above the antiferromagnetic ordering temperature (TN) the system response is due to both Hubbard excitons (HE) and their constituent unpaired SE. The SE response becomes strongly suppressed immediately below TN. We argue that this increase in binding energy is due to a unique interplay between the frustrated Kitaev and the weak Heisenberg-type ordering term in the Hamiltonian, mediating an effective interaction between the spin-singlet SE. This interaction grows with distance causing the SE to become trapped in the HE, similar to quark confinement inside hadrons. This binding of charged particles, induced by magnetic ordering, is a result of a confinement-deconfinement transition of spin excitations. This observation provides evidence for spin liquid type behavior which is expected in Na2IrO3.},
author = {Alpichshev, Zhanybek and Mahmood, Fahad and Cao, Gang and Gedik, Nuh},
journal = {Physical Review Letters},
number = {1},
publisher = {American Physical Society},
title = {{Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3}},
doi = {10.1103/PhysRevLett.114.017203},
volume = {114},
year = {2015},
}
@article{333,
abstract = {We present a hybrid intercalation battery based on a sodium/magnesium (Na/Mg) dual salt electrolyte, metallic magnesium anode, and a cathode based on FeS2 nanocrystals (NCs). Compared to lithium or sodium, metallic magnesium anode is safer due to dendrite-free electroplating and offers extremely high volumetric (3833 mAh cm-3) and gravimetric capacities (2205 mAh g-1). Na-ion cathodes, FeS2 NCs in the present study, may serve as attractive alternatives to Mg-ion cathodes due to the higher voltage of operation and fast, highly reversible insertion of Na-ions. In this proof-of-concept study, electrochemical cycling of the Na/Mg hybrid battery was characterized by high rate capability, high Coulombic efficiency of 99.8%, and high energy density. In particular, with an average discharge voltage of ∼1.1 V and a cathodic capacity of 189 mAh g-1 at a current of 200 mA g-1, the presented Mg/FeS2 hybrid battery delivers energy densities of up to 210 Wh kg-1, comparable to commercial Li-ion batteries and approximately twice as high as state-of-the-art Mg-ion batteries based on Mo6S8 cathodes. Further significant gains in the energy density are expected from the development of Na/Mg electrolytes with a broader electrochemical stability window. Fully based on Earth-abundant elements, hybrid Na-Mg batteries are highly promising for large-scale stationary energy storage. },
author = {Walter, Marc and Kravchyk, Kostiantyn and Ibáñez, Maria and Kovalenko, Maksym},
journal = {Chemistry of Materials},
number = {21},
pages = {7452 -- 7458},
publisher = {ACS},
title = {{Efficient and inexpensive sodium magnesium hybrid battery}},
doi = {10.1021/acs.chemmater.5b03531},
volume = {27},
year = {2015},
}
@article{334,
abstract = {A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles with controlled composition. We report a detailed study of the formation of such CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for photocatalytic water splitting provides superior photocurrents. We associate this experimental fact to a higher separation efficiency of the photogenerated electron-hole pairs. We believe this and other type-II nanoheterostructures will open the door to the use of CZTS, with excellent light absorption properties and made of abundant and environmental friendly elements, to the field of photocatalysis.},
author = {Yu, Xuelian and Liu, Jingjing and Genç, Aziz and Ibáñez, Maria and Luo, Zhishan and Shavel, Alexey and Arbiol, Jordi and Zhang, Guangjin and Zhang, Yihe and Cabot, Andreu},
journal = {Langmuir},
number = {38},
pages = {10555 -- 10561},
publisher = {American Chemical Society},
title = {{Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting}},
doi = {10.1021/acs.langmuir.5b02490},
volume = {31},
year = {2015},
}
@article{354,
abstract = {A simple and effective method to introduce precise amounts of doping in nanomaterials produced from the bottom-up assembly of colloidal nanoparticles (NPs) is described. The procedure takes advantage of a ligand displacement step to incorporate controlled concentrations of halide ions while removing carboxylic acids from the NP surface. Upon consolidation of the NPs into dense pellets, halide ions diffuse within the crystal structure, doping the anion sublattice and achieving n-type electrical doping. Through the characterization of the thermoelectric properties of nanocrystalline PbS, we demonstrate this strategy to be effective to control charge transport properties on thermoelectric nanomaterials assembled from NP building blocks. This approach is subsequently extended to PbTexSe1-x@PbS core-shell NPs, where a significant enhancement of the thermoelectric figure of merit is achieved. },
author = {Ibáñez, Maria and Korkosz, Rachel and Luo, Zhishan and Riba, Pau and Cadavid, Doris and Ortega, Silvia and Cabot, Andreu and Kanatzidis, Mercouri},
journal = {Journal of the American Chemical Society},
number = {12},
pages = {4046 -- 4049},
publisher = {American Chemical Society},
title = {{Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement}},
doi = {10.1021/jacs.5b00091},
volume = {137},
year = {2015},
}
@article{360,
abstract = {A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles with controlled composition. We report a detailed study of the formation of such CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for photocatalytic water splitting provides superior photocurrents. We associate this experimental fact to a higher separation efficiency of the photogenerated electron-hole pairs. We believe this and other type-II nanoheterostructures will open the door to the use of CZTS, with excellent light absorption properties and made of abundant and environmental friendly elements, to the field of photocatalysis. },
author = {Yu, Xuelian and Liu, Jingjing and Genç, Aziz and Ibáñez, Maria and Luo, Zhishan and Shavel, Alexey and Arbiol, Jordi and Zhang, Guangjin and Zhang, Yihe and Cabot, Andreu},
journal = {Langmuir},
number = {38},
pages = {10555 -- 10561},
publisher = {American Chemical Society},
title = {{Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting}},
doi = {10.1021/acs.langmuir.5b02490},
volume = {31},
year = {2015},
}
@article{361,
abstract = {We report the synthesis and photocatalytic and magnetic characterization of colloidal nanoheterostructures formed by combining a Pt-based magnetic metal alloy (PtCo, PtNi) with Cu2ZnSnS4 (CZTS). While CZTS is one of the main candidate materials for solar energy conversion, the introduction of a Pt-based alloy on its surface strongly influences its chemical and electronic properties, ultimately determining its functionality. In this regard, up to a 15-fold increase of the photocatalytic hydrogen evolution activity was obtained with CZTS–PtCo when compared with CZTS. Furthermore, two times higher hydrogen evolution rates were obtained for CZTS–PtCo when compared with CZTS–Pt, in spite of the lower precious metal loading of the former. Besides, the magnetic properties of the PtCo nanoparticles attached to the CZTS nanocrystals were retained in the heterostructures, which could facilitate catalyst purification and recovery for its posterior recycling and/or reutilization.},
author = {Yu, Xuelian and An, Xiaoqiang and Genç, Aziz and Ibáñez, Maria and Arbiol, Jordi and Zhang, Yihe and Cabot, Andreu},
journal = {Journal of Physical Chemistry C},
number = {38},
pages = {21882 -- 21888},
publisher = {American Chemical Society},
title = {{Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution}},
doi = {10.1021/acs.jpcc.5b06199},
volume = {119},
year = {2015},
}
@article{362,
abstract = {Monodisperse Pd2Sn nanorods with tuned size and aspect ratio were prepared by co-reduction of metal salts in the presence of trioctylphosphine, amine, and chloride ions. Asymmetric Pd2Sn nanostructures were achieved by the selective desorption of a surfactant mediated by chlorine ions. A preliminary evaluation of the geometry influence on catalytic properties evidenced Pd2Sn nanorods to have improved catalytic performance. In view of these results, Pd2Sn nanorods were also evaluated for water denitration. },
author = {Lu, Zhishan and Ibáñez, Maria and Antolín, Ana and Genç, Aziz and Shavel, Alexey and Contreras, Sandra and Medina, Francesc and Arbiol, Jordi and Cabot, Andreu},
journal = {Langmuir},
number = {13},
pages = {3952 -- 3957},
publisher = {American Chemical Society},
title = {{Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties}},
doi = {10.1021/la504906q},
volume = {31},
year = {2015},
}
@phdthesis{1401,
abstract = {The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent succesful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views.},
author = {Sharmanska, Viktoriia},
pages = {144},
publisher = {IST Austria},
title = {{Learning with attributes for object recognition: Parametric and non-parametrics views}},
year = {2015},
}
@inproceedings{1729,
abstract = {We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions.},
author = {Cerny, Pavol and Clarke, Edmund and Henzinger, Thomas A and Radhakrishna, Arjun and Ryzhyk, Leonid and Samanta, Roopsha and Tarrach, Thorsten},
location = {San Francisco, CA, United States},
pages = {180 -- 197},
publisher = {Springer},
title = {{From non-preemptive to preemptive scheduling using synchronization synthesis}},
doi = {10.1007/978-3-319-21668-3_11},
volume = {9207},
year = {2015},
}
@unpublished{8183,
abstract = {We study conditions under which a finite simplicial complex $K$ can be mapped to $\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\to \mathbb R^d$ such that the images of any $r$
pairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of
the $(d+1)(r-1)$-simplex in $\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\geq 3r$) based on a series of papers by M. \"Ozaydin, M. Gromov, P. Blagojevi\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\to \mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\to \mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \sqcup S^3\sqcup S^3\to \mathbb R^5$ up to ornament
concordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.},
author = {Avvakumov, Sergey and Mabillard, Isaac and Skopenkov, A. and Wagner, Uli},
booktitle = {arXiv},
title = {{Eliminating higher-multiplicity intersections, III. Codimension 2}},
year = {2015},
}
@article{5749,
abstract = {Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.},
author = {Wielgoss, Sébastien and Bergmiller, Tobias and Bischofberger, Anna M. and Hall, Alex R.},
issn = {0737-4038},
journal = {Molecular Biology and Evolution},
number = {3},
pages = {770--782},
publisher = {Oxford University Press},
title = {{Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria}},
doi = {10.1093/molbev/msv270},
volume = {33},
year = {2015},
}
@inproceedings{1607,
abstract = {We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
location = {San Francisco, CA, USA},
pages = {140 -- 157},
publisher = {Springer},
title = {{Faster algorithms for quantitative verification in constant treewidth graphs}},
doi = {10.1007/978-3-319-21690-4_9},
volume = {9206},
year = {2015},
}
@article{9532,
abstract = {Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.},
author = {Rodrigues, Jessica A. and ZILBERMAN, Daniel},
issn = {1549-5477},
journal = {Genes and Development},
number = {24},
pages = {2517–2531},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Evolution and function of genomic imprinting in plants}},
doi = {10.1101/gad.269902.115},
volume = {29},
year = {2015},
}
@article{9575,
abstract = {We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.},
author = {Krivelevich, Michael and Kwan, Matthew Alan and Sudakov, Benny},
issn = {1571-0653},
journal = {Electronic Notes in Discrete Mathematics},
pages = {181--187},
publisher = {Elsevier},
title = {{Cycles and matchings in randomly perturbed digraphs and hypergraphs}},
doi = {10.1016/j.endm.2015.06.027},
volume = {49},
year = {2015},
}
@article{9673,
abstract = {Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation.},
author = {Leung, H.S. and Leung, P.S.S. and Cheng, Bingqing and Ngan, A.H.W.},
issn = {0749-6419},
journal = {International Journal of Plasticity},
pages = {1--25},
publisher = {Elsevier},
title = {{A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions}},
doi = {10.1016/j.ijplas.2014.09.009},
volume = {67},
year = {2015},
}
@article{9688,
abstract = {The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.},
author = {Cheng, Bingqing and Tribello, Gareth A. and Ceriotti, Michele},
issn = {1550-235X},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {18},
publisher = {American Physical Society},
title = {{Solid-liquid interfacial free energy out of equilibrium}},
doi = {10.1103/physrevb.92.180102},
volume = {92},
year = {2015},
}
@article{9684,
abstract = {The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.},
author = {Leung, P S S and Leung, H S and Cheng, Bingqing and Ngan, A H W},
issn = {1361-651X},
journal = {Modelling and Simulation in Materials Science and Engineering},
number = {3},
publisher = {IOP Publishing},
title = {{Size dependence of yield strength simulated by a dislocation-density function dynamics approach}},
doi = {10.1088/0965-0393/23/3/035001},
volume = {23},
year = {2015},
}
@article{1666,
abstract = {Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.},
author = {Tugrul, Murat and Paixao, Tiago and Barton, Nicholas H and Tkacik, Gasper},
journal = {PLoS Genetics},
number = {11},
publisher = {Public Library of Science},
title = {{Dynamics of transcription factor binding site evolution}},
doi = {10.1371/journal.pgen.1005639},
volume = {11},
year = {2015},
}
@article{1566,
abstract = {Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease.},
author = {Gómez Sicilia, Àngel and Sikora, Mateusz K and Cieplak, Marek and Carrión Vázquez, Mariano},
journal = {PLoS Computational Biology},
number = {10},
publisher = {Public Library of Science},
title = {{An exploration of the universe of polyglutamine structures}},
doi = {10.1371/journal.pcbi.1004541},
volume = {11},
year = {2015},
}
@article{1809,
abstract = {Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.},
author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar},
journal = {PLoS One},
number = {5},
publisher = {Public Library of Science},
title = {{Indirect genetic effects and the dynamics of social interactions}},
doi = {10.1371/journal.pone.0126907},
volume = {10},
year = {2015},
}
@article{1619,
abstract = {The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.},
author = {Chevereau, Guillaume and Dravecka, Marta and Batur, Tugce and Guvenek, Aysegul and Ayhan, Dilay and Toprak, Erdal and Bollenbach, Mark Tobias},
journal = {PLoS Biology},
number = {11},
publisher = {Public Library of Science},
title = {{Quantifying the determinants of evolutionary dynamics leading to drug resistance}},
doi = {10.1371/journal.pbio.1002299},
volume = {13},
year = {2015},
}
@article{2261,
abstract = {To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.},
author = {Zhu, Fangfang and Gamboa, Matthew and Farruggio, Alfonso and Hippenmeyer, Simon and Tasic, Bosiljka and Schüle, Birgitt and Chen Tsai, Yanru and Calos, Michele},
journal = {Nucleic Acids Research},
number = {5},
publisher = {Oxford University Press},
title = {{DICE, an efficient system for iterative genomic editing in human pluripotent stem cells}},
doi = {10.1093/nar/gkt1290},
volume = {42},
year = {2014},
}
@inbook{2265,
abstract = {Coordinated migration of newly-born neurons to their target territories is essential for correct neuronal circuit assembly in the developing brain. Although a cohort of signaling pathways has been implicated in the regulation of cortical projection neuron migration, the precise molecular mechanisms and how a balanced interplay of cell-autonomous and non-autonomous functions of candidate signaling molecules controls the discrete steps in the migration process, are just being revealed. In this chapter, I will focally review recent advances that improved our understanding of the cell-autonomous and possible cell-nonautonomous functions of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential steps of cortical projection neuron migration. I will then elaborate on the emerging concept that the Reelin signaling pathway, acts exactly at precise stages in the course of cortical projection neuron migration. Lastly, I will discuss how finely tuned transcriptional programs and downstream effectors govern particular aspects in driving radial migration at discrete stages and how they regulate the precise positioning of cortical projection neurons in the developing cerebral cortex.},
author = {Hippenmeyer, Simon},
booktitle = { Cellular and Molecular Control of Neuronal Migration},
editor = {Nguyen, Laurent},
pages = {1 -- 24},
publisher = {Springer},
title = {{Molecular pathways controlling the sequential steps of cortical projection neuron migration}},
doi = {10.1007/978-94-007-7687-6_1},
volume = {800},
year = {2014},
}
@inproceedings{2275,
abstract = {Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches.
This partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed.
Our main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach.
},
author = {Olsson, Carl and Ulen, Johannes and Boykov, Yuri and Kolmogorov, Vladimir},
location = {Sydney, Australia},
pages = {2936 -- 2943},
publisher = {IEEE},
title = {{Partial enumeration and curvature regularization}},
doi = {10.1109/ICCV.2013.365},
year = {2014},
}
@article{2281,
abstract = {We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential.},
author = {Guo, Yujin and Seiringer, Robert},
journal = {Letters in Mathematical Physics},
number = {2},
pages = {141 -- 156},
publisher = {Springer},
title = {{On the mass concentration for Bose-Einstein condensates with attractive interactions}},
doi = {10.1007/s11005-013-0667-9},
volume = {104},
year = {2014},
}
@article{2285,
abstract = {GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity.},
author = {Hosp, Jonas and Strüber, Michael and Yanagawa, Yuchio and Obata, Kunihiko and Vida, Imre and Jonas, Peter M and Bartos, Marlene},
journal = {Hippocampus},
number = {2},
pages = {189 -- 203},
publisher = {Wiley-Blackwell},
title = {{Morpho-physiological criteria divide dentate gyrus interneurons into classes}},
doi = {10.1002/hipo.22214},
volume = {23},
year = {2014},
}
@article{2407,
abstract = {Two definitions of the effective mass of a particle interacting with a quantum field, such as a polaron, are considered and shown to be equal in models similar to the Fröhlich polaron model. These are: 1. the mass defined by the low momentum energy E(P)≈E(0)+P2/2 M of the translation invariant system constrained to have momentum P and 2. the mass M of a simple particle in an arbitrary slowly varying external potential, V, described by the nonrelativistic Schrödinger equation, whose ground state energy equals that of the combined particle/field system in a bound state in the same V.},
author = {Lieb, Élliott and Seiringer, Robert},
journal = {Journal of Statistical Physics},
number = {1-2},
pages = {51 -- 57},
publisher = {Springer},
title = {{Equivalence of two definitions of the effective mass of a polaron}},
doi = {10.1007/s10955-013-0791-z},
volume = {154},
year = {2014},
}
@article{248,
abstract = {For any pencil of conics or higher-dimensional quadrics over ℚ, with all degenerate fibres defined over ℚ, we show that the Brauer–Manin obstruction controls weak approximation. The proof is based on the Hasse principle and weak approximation for some special intersections of quadrics over ℚ, which is a consequence of recent advances in additive combinatorics.},
author = {Timothy Browning and Matthiesen, Lilian and Skorobogatov, Alexei N},
journal = {Annals of Mathematics},
number = {1},
pages = {381 -- 402},
publisher = {John Hopkins University Press},
title = {{Rational points on pencils of conics and quadrics with many degenerate fibres}},
doi = {https://doi.org/10.4007/annals.2014.180.1.8},
volume = {180},
year = {2014},
}
@article{249,
abstract = {A version of the Hardy-Littlewood circle method is developed for number fields K/ℚ and is used to show that nonsingular projective cubic hypersurfaces over K always have a K-rational point when they have dimension at least 8. },
author = {Timothy Browning and Vishe, Pankaj},
journal = {Duke Mathematical Journal},
number = {10},
pages = {1825 -- 1883},
publisher = {Duke University Press},
title = {{Cubic hypersurfaces and a version of the circle method for number fields}},
doi = {10.1215/00127094-2738530},
volume = {163},
year = {2014},
}
@article{252,
abstract = {For any number field k, upper bounds are established for the number of k-rational points of bounded height on non-singular del Pezzo surfaces defined over k, which are equipped with suitable conic bundle structures over k.},
author = {Timothy Browning and Jones, Michael S},
journal = {Acta Arithmetica},
number = {3},
pages = {271 -- 298},
publisher = {Instytut Matematyczny},
title = {{Counting rational points on del Pezzo surfaces with a conic bundle structure}},
doi = {10.4064/aa163-3-6},
volume = {163},
year = {2014},
}
@article{254,
abstract = {A new "polynomial sieve" is presented and used to show that almost all integers have at most one representation as a sum of two values of a given polynomial of degree at least 3.},
author = {Timothy Browning},
journal = {International Mathematics Research Notices},
number = {7},
pages = {1987 -- 2019},
publisher = {Oxford University Press},
title = {{The polynomial sieve and equal sums of like polynomials}},
doi = {10.1093/imrn/rnt350},
volume = {2015},
year = {2014},
}
@article{255,
abstract = {We investigate the Hasse principle for complete intersections cut out by a quadric hypersurface and a cubic hypersurface defined over the rational numbers.},
author = {Timothy Browning and Dietmann, Rainer and Heath-Brown, Roger},
journal = {Journal of the Institute of Mathematics of Jussieu},
number = {4},
pages = {703 -- 749},
publisher = {Cambridge University Press},
title = {{Rational points on intersections of cubic and quadric hypersurfaces}},
doi = {10.1017/S1474748014000127},
volume = {14},
year = {2014},
}
@article{2699,
abstract = {We prove the universality of the β-ensembles with convex analytic potentials and for any β >
0, i.e. we show that the spacing distributions of log-gases at any inverse temperature β coincide with those of the Gaussian β-ensembles.},
author = {Erdös, László and Bourgade, Paul and Yau, Horng},
journal = {Duke Mathematical Journal},
number = {6},
pages = {1127 -- 1190},
publisher = {Duke University Press},
title = {{Universality of general β-ensembles}},
doi = {10.1215/00127094-2649752},
volume = {163},
year = {2014},
}
@article{2716,
abstract = {Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω ω -regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on vector addition systems with states. Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts.},
author = {Chatterjee, Krishnendu and Randour, Mickael and Raskin, Jean},
journal = {Acta Informatica},
number = {3-4},
pages = {129 -- 163},
publisher = {Springer},
title = {{Strategy synthesis for multi-dimensional quantitative objectives}},
doi = {10.1007/s00236-013-0182-6},
volume = {51},
year = {2014},
}
@article{2852,
abstract = {A robust combiner for hash functions takes two candidate implementations and constructs a hash function which is secure as long as at least one of the candidates is secure. So far, hash function combiners only aim at preserving a single property such as collision-resistance or pseudorandomness. However, when hash functions are used in protocols like TLS they are often required to provide several properties simultaneously. We therefore put forward the notion of robust multi-property combiners and elaborate on different definitions for such combiners. We then propose a combiner that provably preserves (target) collision-resistance, pseudorandomness, and being a secure message authentication code. This combiner satisfies the strongest notion we propose, which requires that the combined function satisfies every security property which is satisfied by at least one of the underlying hash function. If the underlying hash functions have output length n, the combiner has output length 2 n. This basically matches a known lower bound for black-box combiners for collision-resistance only, thus the other properties can be achieved without penalizing the length of the hash values. We then propose a combiner which also preserves the property of being indifferentiable from a random oracle, slightly increasing the output length to 2 n+ω(log n). Moreover, we show how to augment our constructions in order to make them also robust for the one-wayness property, but in this case require an a priory upper bound on the input length.},
author = {Fischlin, Marc and Lehmann, Anja and Pietrzak, Krzysztof Z},
journal = {Journal of Cryptology},
number = {3},
pages = {397 -- 428},
publisher = {Springer},
title = {{Robust multi-property combiners for hash functions}},
doi = {10.1007/s00145-013-9148-7},
volume = {27},
year = {2014},
}
@inproceedings{2905,
abstract = {Persistent homology is a recent grandchild of homology that has found use in
science and engineering as well as in mathematics. This paper surveys the method as well
as the applications, neglecting completeness in favor of highlighting ideas and directions.},
author = {Edelsbrunner, Herbert and Morozovy, Dmitriy},
location = {Kraków, Poland},
pages = {31 -- 50},
publisher = {European Mathematical Society Publishing House},
title = {{Persistent homology: Theory and practice}},
doi = {10.4171/120-1/3},
year = {2014},
}
@article{8021,
abstract = {Most excitatory inputs in the mammalian brain are made on dendritic spines, rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical isolation can underlie input-specific synaptic plasticity, providing a raison d'etre for spines. However, recent results indicate that the spine can experience a membrane potential different from that in the parent dendrite, as though the spine neck electrically isolated the spine. Here we use two-photon calcium imaging of mouse neocortical pyramidal neurons to analyze the correlation between the morphologies of spines activated under minimal synaptic stimulation and the excitatory postsynaptic potentials they generate. We find that excitatory postsynaptic potential amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike timing-dependent plasticity protocol, in which two-photon glutamate uncaging over a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine neck and concomitant increases in the amplitude of the evoked spine potentials. Using numerical simulations, we explore the parameter regimes for the spine neck resistance and synaptic conductance changes necessary to explain our observations. Our data, directly correlating synaptic and morphological plasticity, imply that long-necked spines have small or negligible somatic voltage contributions, but that, upon synaptic stimulation paired with postsynaptic activity, they can shorten their necks and increase synaptic efficacy, thus changing the input/output gain of pyramidal neurons. },
author = {Araya, R. and Vogels, Tim P and Yuste, R.},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences},
number = {28},
pages = {E2895--E2904},
publisher = {Proceedings of the National Academy of Sciences},
title = {{Activity-dependent dendritic spine neck changes are correlated with synaptic strength}},
doi = {10.1073/pnas.1321869111},
volume = {111},
year = {2014},
}
@article{8022,
abstract = {Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex.},
author = {Hennequin, Guillaume and Vogels, Tim P and Gerstner, Wulfram},
issn = {0896-6273},
journal = {Neuron},
number = {6},
pages = {1394--1406},
publisher = {Elsevier},
title = {{Optimal control of transient dynamics in balanced networks supports generation of complex movements}},
doi = {10.1016/j.neuron.2014.04.045},
volume = {82},
year = {2014},
}
@article{8023,
abstract = {Uniform random sparse network architectures are ubiquitous in computational neuroscience, but the implicit hypothesis that they are a good representation of real neuronal networks has been met with skepticism. Here we used two experimental data sets, a study of triplet connectivity statistics and a data set measuring neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands of model networks. Network architectures comprised three neuron types (excitatory, fast spiking, and nonfast spiking inhibitory) and were created from a set of rules that govern the statistics of the resulting connection types. In a high-dimensional parameter scan, we varied the degree distributions (i.e., how many cells each neuron connects with) and the synaptic weight correlations of synapses from or onto the same neuron. These variations converted initially uniform random and homogeneously connected networks, in which every neuron sent and received equal numbers of synapses with equal synaptic strength distributions, to highly heterogeneous networks in which the number of synapses per neuron, as well as average synaptic strength of synapses from or to a neuron were variable. By evaluating the impact of each variable on the network structure and dynamics, and their similarity to the experimental data, we could falsify the uniform random sparse connectivity hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis in 8 cases. Twenty-one parameters had no substantial impact on the results of the test protocols we used.},
author = {Tomm, Christian and Avermann, Michael and Petersen, Carl and Gerstner, Wulfram and Vogels, Tim P},
issn = {1522-1598},
journal = {Journal of Neurophysiology},
number = {8},
pages = {1801--1814},
publisher = {American Physiological Society},
title = {{Connection-type-specific biases make uniform random network models consistent with cortical recordings}},
doi = {10.1152/jn.00629.2013},
volume = {112},
year = {2014},
}
@inproceedings{8044,
abstract = {Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.},
author = {Seiringer, Robert},
booktitle = {Proceeding of the International Congress of Mathematicans},
isbn = {9788961058063},
location = {Seoul, South Korea},
pages = {1175--1194},
publisher = {Kyung Moon SA},
title = {{Structure of the excitation spectrum for many-body quantum systems}},
volume = {3},
year = {2014},
}
@article{809,
abstract = {The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position.},
author = {Bharata, Tanmay A and Menendez, Luis R and Hagena, Wim J and Luxd, Vanda and Igonete, Sebastien and Schorba, Martin and Florian Schur and Kraüsslich, Hans Georg and Briggsa, John A},
journal = {PNAS},
number = {22},
pages = {8233 -- 8238},
publisher = {National Academy of Sciences},
title = {{Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly}},
doi = {10.1073/pnas.1401455111},
volume = {111},
year = {2014},
}
@article{8244,
abstract = {Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer.},
author = {Singer, J. and Fazekas, Judit and Wang, W. and Weichselbaumer, M. and Matz, M. and Mader, A. and Steinfellner, W. and Meitz, S. and Mechtcheriakova, D. and Sobanov, Y. and Willmann, M. and Stockner, T. and Spillner, E. and Kunert, R. and Jensen-Jarolim, E.},
issn = {1535-7163},
journal = {Molecular Cancer Therapeutics},
number = {7},
pages = {1777--1790},
publisher = {American Association for Cancer Research},
title = {{Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients}},
doi = {10.1158/1535-7163.mct-13-0288},
volume = {13},
year = {2014},
}
@article{845,
abstract = {Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.},
author = {Seplyarskiy, Vladimir B and Logacheva, Maria D and Penin, Aleksey A and Baranová, Maria A and Leushkin, Evgeny V and Demidenko, Natalia V and Klepikova, Anna V and Fyodor Kondrashov and Kondrashov, Alexey S and James, Timothy Y},
journal = {Molecular Biology and Evolution},
number = {11},
pages = {3016 -- 3025},
publisher = {Oxford University Press},
title = {{Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity}},
doi = {10.1093/molbev/msu242},
volume = {31},
year = {2014},
}
@article{8458,
abstract = {The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.},
author = {Schanda, Paul and Triboulet, Sébastien and Laguri, Cédric and Bougault, Catherine M. and Ayala, Isabel and Callon, Morgane and Arthur, Michel and Simorre, Jean-Pierre},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
number = {51},
pages = {17852--17860},
publisher = {American Chemical Society},
title = {{Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan}},
doi = {10.1021/ja5105987},
volume = {136},
year = {2014},
}
@article{8459,
abstract = {Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.},
author = {Morin, Sébastien and Linnet, Troels E and Lescanne, Mathilde and Schanda, Paul and Thompson, Gary S and Tollinger, Martin and Teilum, Kaare and Gagné, Stéphane and Marion, Dominique and Griesinger, Christian and Blackledge, Martin and d’Auvergne, Edward J},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications},
number = {15},
pages = {2219--2220},
publisher = {Oxford University Press},
title = {{Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data}},
doi = {10.1093/bioinformatics/btu166},
volume = {30},
year = {2014},
}
@article{8460,
abstract = {The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states.},
author = {Ma, Peixiang and Haller, Jens D. and Zajakala, Jérémy and Macek, Pavel and Sivertsen, Astrid C. and Willbold, Dieter and Boisbouvier, Jérôme and Schanda, Paul},
issn = {1433-7851},
journal = {Angewandte Chemie International Edition},
number = {17},
pages = {4312--4317},
publisher = {Wiley},
title = {{Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy}},
doi = {10.1002/anie.201311275},
volume = {53},
year = {2014},
}
@article{8500,
abstract = {The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way.},
author = {Kaloshin, Vadim and Levi, Mark and Saprykina, Maria},
issn = {0010-3640},
journal = {Communications on Pure and Applied Mathematics},
keywords = {Applied Mathematics, General Mathematics},
number = {5},
pages = {748--775},
publisher = {Wiley},
title = {{Arnol′d diffusion in a pendulum lattice}},
doi = {10.1002/cpa.21509},
volume = {67},
year = {2014},
}
@article{8501,
abstract = {In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation.},
author = {Bounemoura, Abed and Kaloshin, Vadim},
issn = {1609-3321},
journal = {Moscow Mathematical Journal},
keywords = {General Mathematics},
number = {2},
pages = {181--203},
publisher = {Independent University of Moscow},
title = {{Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom}},
doi = {10.17323/1609-4514-2014-14-2-181-203},
volume = {14},
year = {2014},
}
@article{852,
abstract = {Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. },
author = {Rosello, Oriol P and Fyodor Kondrashov},
journal = {Genome Biology and Evolution},
number = {8},
pages = {1949 -- 1955},
publisher = {Oxford University Press},
title = {{Long-Term asymmetrical acceleration of protein evolution after gene duplication}},
doi = {10.1093/gbe/evu159},
volume = {6},
year = {2014},
}
@article{856,
abstract = {The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.},
author = {Pougach, Ksenia S and Voet, Arnout R and Fyodor Kondrashov and Voordeckers, Karin and Christiaens, Joaquin F and Baying, Bianka and Bénès, Vladimı́r and Sakai, Ryo and Aerts, Jan A and Zhu, Bo and Van Dijck, Patrick and Verstrepen, Kevin J},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network}},
doi = {10.1038/ncomms5868},
volume = {5},
year = {2014},
}
@article{863,
abstract = {The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.},
author = {Moroz, Leonid L and Kocot, Kevin M and Citarella, Mathew R and Dosung, Sohn and Norekian, Tigran P and Povolotskaya, Inna and Grigorenko, Anastasia P and Dailey, Christopher A and Berezikov, Eugene and Buckley, Katherine M and Ptitsyn, Andrey A and Reshetov, Denis A and Mukherjee, Krishanu and Moroz, Tatiana P and Bobkova, Yelena V and Yu, Fahong and Kapitonov, Vladimir V and Jurka, Jerzy W and Bobkov, Yuriy V and Swore, Joshua J and Girardo, David O and Fodor, Alexander and Gusev, Fedor E and Sanford, Rachel S and Bruders, Rebecca and Kittler, Ellen L and Mills, Claudia E and Rast, Jonathan P and Derelle, Romain and Solovyev, Victor and Fyodor Kondrashov and Swalla, Billie J and Sweedler, Jonathan V and Rogaev, Evgeny I and Halanych, Kenneth M and Kohn, Andrea B},
journal = {Nature},
number = {7503},
pages = {109 -- 114},
publisher = {Nature Publishing Group},
title = {{The ctenophore genome and the evolutionary origins of neural systems}},
doi = {10.1038/nature13400},
volume = {510},
year = {2014},
}
@article{865,
abstract = {Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers.},
author = {Koval, Alexey V and Vlasov, Peter K and Shichkova, Polina and Khunderyakova, S and Markov, Yury and Panchenko, J and Volodina, A and Fyodor Kondrashov and Katanaev, Vladimir L},
journal = {Biochemical Pharmacology},
number = {4},
pages = {571 -- 578},
publisher = {Elsevier},
title = {{Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling}},
doi = {10.1016/j.bcp.2013.12.007},
volume = {87},
year = {2014},
}