@misc{5390, abstract = {The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages.}, author = {Chatterjee, Krishnendu and Fijalkow, Nathanaël}, issn = {2664-1690}, pages = {21}, publisher = {IST Austria}, title = {{Topological, automata-theoretic and logical characterization of finitary languages}}, doi = {10.15479/AT:IST-2010-0002}, year = {2010}, } @inproceedings{3857, abstract = {We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs for probabilistic finite automata and present an almost complete characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems for probabilistic automata on infinite words.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A}, location = {Singapore, Singapore}, pages = {1 -- 16}, publisher = {Springer}, title = {{Probabilistic Automata on infinite words: decidability and undecidability results}}, doi = {10.1007/978-3-642-15643-4_1}, volume = {6252}, year = {2010}, } @inproceedings{3855, abstract = {We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with parity objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observations. We consider qualitative analysis problems: given a POMDP with a parity objective, decide whether there exists an observation-based strategy to achieve the objective with probability 1 (almost-sure winning), or with positive probability (positive winning). Our main results are twofold. First, we present a complete picture of the computational complexity of the qualitative analysis problem for POMDPs with parity objectives and its subclasses: safety, reachability, Büchi, and coBüchi objectives. We establish several upper and lower bounds that were not known in the literature. Second, we give optimal bounds (matching upper and lower bounds) for the memory required by pure and randomized observation-based strategies for each class of objectives.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, location = {Brno, Czech Republic}, pages = {258 -- 269}, publisher = {Springer}, title = {{Qualitative analysis of partially-observable Markov Decision Processes}}, doi = {10.1007/978-3-642-15155-2_24}, volume = {6281}, year = {2010}, } @inbook{5940, author = {Juhás, Gabriel and Kazlov, Igor and Juhásová, Ana}, booktitle = {Applications and Theory of Petri Nets}, isbn = {9783642136740}, issn = {0302-9743}, pages = {1--17}, publisher = {Springer Berlin Heidelberg}, title = {{Instance Deadlock: A Mystery behind Frozen Programs}}, doi = {10.1007/978-3-642-13675-7_1}, year = {2010}, } @article{598, abstract = {It is not well understood how the human Mediator complex, transcription factor IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription. Activator binding alters Mediator structure, yet the functional consequences of such structural shifts remain unknown. The p53 C terminus and its activation domain interact with different Mediator subunits, and we find that each interaction differentially affects Mediator structure; strikingly, distinct p53-Mediator structures differentially affect Pol II activity. Only the p53 activation domain induces the formation of a large pocket domain at the Mediator-Pol II interaction site, and this correlates with activation of stalled Pol II to a productively elongating state. Moreover, we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain phosphorylation and identify substantial differences in Pol II C-terminal domain processing that correspond to distinct p53-Mediator structural states. Our results define a fundamental mechanism by which p53 activates transcription and suggest that Mediator structural shifts trigger activation of stalled Pol II complexes.}, author = {Meyer, Krista and Lin, Shih and Bernecky, Carrie A and Gao, Yuefeng and Taatjes, Dylan}, journal = {Nature Structural and Molecular Biology}, number = {6}, pages = {753 -- 760}, publisher = {Nature Publishing Group}, title = {{P53 activates transcription by directing structural shifts in Mediator}}, doi = {10.1038/nsmb.1816}, volume = {17}, year = {2010}, } @article{6142, abstract = {Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication.}, author = {Weber, Katherine P. and De, Subhajyoti and Kozarewa, Iwanka and Turner, Daniel J. and Babu, M. Madan and de Bono, Mario}, issn = {1932-6203}, journal = {PLoS ONE}, number = {11}, publisher = {Public Library of Science}, title = {{Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans}}, doi = {10.1371/journal.pone.0013922}, volume = {5}, year = {2010}, } @inbook{619, abstract = {Sinclair Ross’s novel As for Me and My House has long since been canonized as Canadian prairie fiction. Accordingly, it has been the subject of many critical studies and academic papers. Most commentators have concentrated on such literary issues as the representation of the western landscape or the reliability of the female narrator. But so far little consideration has been given to the social and cultural implications of the novel. Few attempts have been made to analyze the text from a cultural perspective including such social markers as class, gender and ethnicity. That is all the more surprising because Sinclair Ross has often been credited for being a realistic author and As for Me and My House has often been interpreted as a regional novel characteristic of a particular time and place.}, author = {Zacharasiewicz, Waldemar and Kirsch, Fritz Peter}, booktitle = {Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l'Ouest canadien}, pages = {173 -- 179}, publisher = {Facultas.WUV}, title = {{“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House}}, year = {2010}, } @article{6198, abstract = {Stroke is a major public health problem leading to high rates of death and disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are crucial for neuronal injury after stroke insult. However, directly inhibiting NMDARs or nNOS can cause severe side effects because they have key physiological functions in the CNS. Here we show that cerebral ischemia induces the interaction of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95 interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS (nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction, ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively, had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke, perhaps without major side effects. }, author = {Zhou, L and Li, F and Xu, Haibing and Luo, CX and Wu, HY and Zhu, MM and Lu, W and Ji, X and Zhou, QG and Zhu, DY}, issn = {1078-8956}, journal = {Nature Medicine}, number = {12}, pages = {1439--1443}, publisher = {Nature Publishing Group}, title = {{Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95}}, doi = {10.1038/nm.2245}, volume = {16}, year = {2010}, } @article{6320, abstract = {We study the average order of the divisor function, as it ranges over the values of binary quartic forms that are reducible over ℚ.}, author = {Bretèche, Régis de la and Browning, Timothy D}, journal = {Crelles Journal}, number = {646}, pages = {1--44}, publisher = {Walter de Gruyter GmbH}, title = {{Le problème des diviseurs pour des formes binaires de degré 4}}, doi = {10.1515/crelle.2010.064}, volume = {2010}, year = {2010}, } @article{7078, abstract = {We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction, magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate that our Bridgman-grown single crystals have a p-type carrier concentration of 3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3. Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K, the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature of 294 K. For each sample type, three-terminal capacitive dilatometry measurements detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on SnTe show elastic hardening near the structural transition, pointing to co-elastic behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening, pointing to ferroelastic behavior. Effective Debye temperature, θD, values of SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In addition, a precursor softening extending over approximately 100 K anticipates this collapse at the critical temperature and quantitative analysis over three decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02, a value indicating a three-dimensional softening of phonon branches at a temperature T0∼75 K, considerably below Tc. We suggest that the differences in these two types of elastic behaviors lie in the absence of elastic domain-wall motion in the one case and their nucleation in the other.}, author = {Salje, E. K. H. and Safarik, D. J. and Modic, Kimberly A and Gubernatis, J. E. and Cooley, J. C. and Taylor, R. D. and Mihaila, B. and Saxena, A. and Lookman, T. and Smith, J. L. and Fisher, R. A. and Pasternak, M. and Opeil, C. P. and Siegrist, T. and Littlewood, P. B. and Lashley, J. C.}, issn = {1098-0121}, journal = {Physical Review B}, number = {18}, publisher = {APS}, title = {{Tin telluride: A weakly co-elastic metal}}, doi = {10.1103/physrevb.82.184112}, volume = {82}, year = {2010}, } @article{7079, abstract = {We have observed that reacting Pb:Te:Ag:Se in a 1:1:1.9:1 molar ratio gives rise to what appears to be a predominantly single-phase alloy, which crystallizes in the PbSe cF8 fcc structure. However, further investigation of the structure using energy dispersive x-ray analysis reveals the presence of two phases, PbSe and β-Ag2Te, with identical lattice parameters. The total thermal conductivity of the formed alloy is remarkably low for a crystalline material, κT<0.6W∕mK at 675K, it is reproducible, and in addition, the compound has good mechanical properties.}, author = {Drymiotis, Fivos R. and Drye, Tyler B. and Wang, Yisha and He, Jian and Rhodes, Daniel and Modic, Kimberly A and Cawthorne, Samantha and Zhang, Qiu Run}, issn = {0021-8979}, journal = {Journal of Applied Physics}, number = {3}, publisher = {AIP}, title = {{Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures}}, doi = {10.1063/1.3284946}, volume = {107}, year = {2010}, } @article{7318, abstract = {The decomposition reaction of H2O2 aqueous solutions (H2O2 - H2O + 1/2O2) catalyzed by transition metal oxide powders has been compared with the charging voltage of nonaqueous Li-O2 cells containing the same catalyst. An inverse linear relationship between Ln k (rate constant for the H2O2 decomposition) and the charging voltage has been found, despite differences in media and possible mechanistic differences. The results suggest that the decomposition may be a reliable, useful, and fast screening tool for materials that promote the charging process of the Li-O2 battery and may ultimately give insight into the charging mechanism.}, author = {Giordani, V. and Freunberger, Stefan Alexander and Bruce, P. G. and Tarascon, J.-M. and Larcher, D.}, issn = {1099-0062}, journal = {Electrochemical and Solid-State Letters}, number = {12}, publisher = {The Electrochemical Society}, title = {{H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells}}, doi = {10.1149/1.3494045}, volume = {13}, year = {2010}, } @inproceedings{754, abstract = {Most people believe that renaming is easy: simply choose a name at random; if more than one process selects the same name, then try again. We highlight the issues that occur when trying to implement such a scheme and shed new light on the read-write complexity of randomized renaming in an asynchronous environment. At the heart of our new perspective stands an adaptive implementation of a randomized test-and-set object, that has poly-logarithmic step complexity per operation, with high probability. Interestingly, our implementation is anonymous, as it does not require process identifiers. Based on this implementation, we present two new randomized renaming algorithms. The first ensures a tight namespace of n names using O( n log4 n) total steps, with high probability. This significantly improves on the complexity of the best previously known namespace-optimal algorithms. The second algorithm achieves a namespace of size k (1 + ε) using O( k log4 k / log2 (1 + ε) ) total steps, both with high probability, where k is the total contention in the execution. It is the first adaptive randomized renaming algorithm, and it improves on existing deterministic solutions by providing a smaller namespace, and by lowering step complexity.}, author = {Alistarh, Dan-Adrian and Attiya, Hagit and Gilbert, Seth and Giurgiu, Andrei and Guerraoui, Rachid}, pages = {94 -- 108}, publisher = {Springer}, title = {{Fast randomized test-and-set and renaming}}, doi = {10.1007/978-3-642-15763-9_9}, volume = {6343 LNCS}, year = {2010}, } @inproceedings{755, abstract = {Gossip, also known as epidemic dissemination, is becoming an increasingly popular technique in distributed systems. Yet, it has remained a partially open question: how robust are such protocols? We consider a natural extension of the random phone-call model (introduced by Karp et al. [1]), and we analyze two different notions of robustness: the ability to tolerate adaptive failures, and the ability to tolerate oblivious failures. For adaptive failures, we present a new gossip protocol, TrickleGossip, which achieves near-optimal O(n log 3 n) message complexity. To the best of our knowledge, this is the first epidemic-style protocol that can tolerate adaptive failures. We also show a direct relation between resilience and message complexity, demonstrating that gossip protocols which tolerate a large number of adaptive failures need to use a super-linear number of messages with high probability. For oblivious failures, we present a new gossip protocol, CoordinatedGossip, that achieves optimal O(n) message complexity. This protocol makes novel use of the universe reduction technique to limit the message complexity.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Zadimoghaddam, Morteza}, number = {PART 2}, pages = {115 -- 126}, publisher = {Springer}, title = {{How efficient can gossip be? (On the cost of resilient information exchange)}}, doi = {10.1007/978-3-642-14162-1_10}, volume = {6199 LNCS}, year = {2010}, } @inproceedings{756, abstract = {This paper studies non-cryptographic authenticated broadcast in radio networks subject to malicious failures. We introduce two protocols that address this problem. The first, NeighborWatchRB, makes use of a novel strategy in which honest devices monitor their neighbors for malicious behavior. Second, we present a more robust variant, MultiPathRB, that tolerates the maximum possible density of malicious devices per region, using an elaborate voting strategy. We also introduce a new proof technique to show that both protocols ensure asymptotically optimal running time. We demonstrate the fault tolerance of our protocols through extensive simulation. Simulations show the practical superiority of the NeighborWatchRB protocol (an advantage hidden in the constants of the asymptotic complexity). The NeighborWatchRB protocol even performs relatively well when compared to the simple, fast epidemic protocols commonly used in the radio setting, protocols that tolerate no malicious faults. We therefore believe that the overhead for ensuring authenticated broadcast is reasonable, especially in applications that use authenticated broadcast only when necessary, such as distributing an authenticated digest.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Milošević, Žarko and Newport, Calvin}, pages = {50 -- 59}, publisher = {ACM}, title = {{Securing every bit: Authenticated broadcast in radio networks}}, doi = {10.1145/1810479.1810489}, year = {2010}, } @inproceedings{758, abstract = {Set agreement [4] is a fundamental problem in distributed computing, in which processes collectively choose a small subset of values from a larger set of proposals. Set agreement has been extensively studied in both synchronous and asynchronous systems [10,11,3,5,8,9]. Real world distributed systems, however, are neither purely synchronous nor purely asynchronous. To describe such a system, Dwork et al. [6] introduced the idea of partial synchrony. They assume for every execution some (unknown) time GST (global stabilization time), after which the system is synchronous. In a recent paper [1,2], we study the complexity of set agreement in the context of partially synchronous systems, determining the minimum-sized window of synchrony in which set agreement can be solved. We show that at least ⌊t/k⌋ + 2 synchronous rounds are required for k-set agreement, where t < n is the number of crashes, and k is the agreement parameter of the set agreement task. We then introduce an algorithm that terminates in any window of synchrony of size at least ⌊t/k⌋ + 4 rounds. Together, these results tightly bound the inherent price of tolerating some asynchrony.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Travers, Corentin}, pages = {404 -- 405}, publisher = {Springer}, title = {{Brief announcement: New bounds for partially synchronous set agreement}}, doi = {10.1007/978-3-642-15763-9_40}, volume = {6343 LNCS}, year = {2010}, } @article{89, abstract = {We demonstrate the operation of a device that can produce chitosan nanoparticles in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric oscillator operated at megahertz frequencies is used to aerosolize a solution containing dissolved chitosan. The solvent is then evaporated from the aerosolized droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The nanoparticle size is controlled both by the concentration of the dissolved polymer and by the size of the aerosol droplets that are created. Our device can be used with any polymer or polymer/therapeutic combination that can be prepared in a homogeneous solution and vaporized.}, author = {Wright, Ian and Higginbotham, Andrew P and Baker, Shenda and Donnelly, Tom}, journal = {ACS Applied Materials and Interfaces}, number = {8}, pages = {2360 -- 2364}, publisher = {American Chemical Society}, title = {{Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution}}, doi = {10.1021/am100375w}, volume = {2}, year = {2010}, } @article{891, abstract = {Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.}, author = {Innan, Hideki and Fyodor Kondrashov}, journal = {Nature Reviews Genetics}, number = {2}, pages = {97 -- 108}, publisher = {Nature Publishing Group}, title = {{The evolution of gene duplications: Classifying and distinguishing between models}}, doi = {10.1038/nrg2689}, volume = {11}, year = {2010}, } @article{9012, abstract = {In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.}, author = {Palacci, Jérémie A and Abécassis, Benjamin and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {13}, publisher = {American Physical Society}, title = {{Colloidal motility and pattern formation under rectified diffusiophoresis}}, doi = {10.1103/physrevlett.104.138302}, volume = {104}, year = {2010}, } @article{9013, abstract = {In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.}, author = {Palacci, Jérémie A and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society }, title = {{Sedimentation and effective temperature of active colloidal suspensions}}, doi = {10.1103/physrevlett.105.088304}, volume = {105}, year = {2010}, }