@inproceedings{1325, abstract = {We study graphs and two-player games in which rewards are assigned to states, and the goal of the players is to satisfy or dissatisfy certain property of the generated outcome, given as a mean payoff property. Since the notion of mean-payoff does not reflect possible fluctuations from the mean-payoff along a run, we propose definitions and algorithms for capturing the stability of the system, and give algorithms for deciding if a given mean payoff and stability objective can be ensured in the system.}, author = {Brázdil, Tomáš and Forejt, Vojtěch and Kučera, Antonín and Novotny, Petr}, location = {Quebec City, Canada}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Stability in graphs and games}}, doi = {10.4230/LIPIcs.CONCUR.2016.10}, volume = {59}, year = {2016}, } @inproceedings{1326, abstract = {Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. }, author = {Brázdil, Tomáš and Kučera, Antonín and Novotny, Petr}, location = {Chiba, Japan}, pages = {32 -- 49}, publisher = {Springer}, title = {{Optimizing the expected mean payoff in Energy Markov Decision Processes}}, doi = {10.1007/978-3-319-46520-3_3}, volume = {9938}, year = {2016}, } @inproceedings{1327, abstract = {We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. }, author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Anchit and Novotny, Petr}, booktitle = {Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems}, location = {Singapore}, pages = {1465 -- 1466}, publisher = {ACM}, title = {{Stochastic shortest path with energy constraints in POMDPs}}, year = {2016}, } @article{1328, abstract = {Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples.}, author = {Watzinger, Hannes and Kloeffel, Christoph and Vukusic, Lada and Rossell, Marta and Sessi, Violetta and Kukucka, Josip and Kirchschlager, Raimund and Lausecker, Elisabeth and Truhlar, Alisha and Glaser, Martin and Rastelli, Armando and Fuhrer, Andreas and Loss, Daniel and Katsaros, Georgios}, journal = {Nano Letters}, number = {11}, pages = {6879 -- 6885}, publisher = {American Chemical Society}, title = {{Heavy-hole states in germanium hut wires}}, doi = {10.1021/acs.nanolett.6b02715}, volume = {16}, year = {2016}, } @article{1329, abstract = {Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.}, author = {Huylmans, Ann K and López Ezquerra, Alberto and Parsch, John and Cordellier, Mathilde}, journal = {Genome Biology and Evolution}, number = {10}, pages = {3120 -- 3139}, publisher = {Oxford University Press}, title = {{De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata}}, doi = {10.1093/gbe/evw221}, volume = {8}, year = {2016}, } @article{1330, abstract = {In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K.}, author = {Akopyan, Arseniy and Balitskiy, Alexey}, journal = {Israel Journal of Mathematics}, number = {2}, pages = {833 -- 845}, publisher = {Springer}, title = {{Billiards in convex bodies with acute angles}}, doi = {10.1007/s11856-016-1429-z}, volume = {216}, year = {2016}, } @article{1331, abstract = {Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response.}, author = {Zwack, Paul and De Clercq, Inge and Howton, Timothy and Hallmark, H Tucker and Hurny, Andrej and Keshishian, Erika and Parish, Alyssa and Benková, Eva and Mukhtar, M Shahid and Van Breusegem, Frank and Rashotte, Aaron}, issn = {1532-2548}, journal = {Plant Physiology}, number = {2}, pages = {1249 -- 1258}, publisher = {American Society of Plant Biologists}, title = {{Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress}}, doi = {10.1104/pp.16.00415}, volume = {172}, year = {2016}, } @article{1332, abstract = {Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.}, author = {Chait, Remy P and Palmer, Adam and Yelin, Idan and Kishony, Roy}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments}}, doi = {10.1038/ncomms10333}, volume = {7}, year = {2016}, } @article{1333, abstract = {Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most.}, author = {Milinski, Manfred and Hilbe, Christian and Semmann, Dirk and Sommerfeld, Ralf and Marotzke, Jochem}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Humans choose representatives who enforce cooperation in social dilemmas through extortion}}, doi = {10.1038/ncomms10915}, volume = {7}, year = {2016}, } @article{1334, abstract = {Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping.}, author = {Schönenberger, Philipp and O'Neill, Joseph and Csicsvari, Jozsef L}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Activity dependent plasticity of hippocampal place maps}}, doi = {10.1038/ncomms11824}, volume = {7}, year = {2016}, } @inproceedings{1335, abstract = {In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, location = {Edinburgh, United Kingdom}, pages = {23 -- 38}, publisher = {Springer}, title = {{Quantitative monitor automata}}, doi = {10.1007/978-3-662-53413-7_2}, volume = {9837}, year = {2016}, } @article{21099, abstract = {Quinoline‐based oligoamide foldamers have been identified as a potent class of ligands for G‐quadruplex DNA. Their helical structure is thought to target G‐quadruplex loops or grooves and not G‐tetrads. We report a co‐crystal structure of the antiparallel hairpin dimeric DNA G‐quadruplex (G4T4G4)2 with tetramer 1a helically folded oligo‐quinolinecarboxamide bearing cationic side chains—that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G4T4G4)2 in the solid state are observed.}, author = {Mandal, Pradeep K and Baptiste, Benoît and Langlois d'Estaintot, Béatrice and Kauffmann, Brice and Huc, Ivan}, issn = {1439-7633}, journal = {ChemBioChem}, number = {20}, pages = {1911--1914}, publisher = {Wiley}, title = {{Multivalent interactions between an aromatic helical foldamer and a DNA G‐quadruplex in the solid state}}, doi = {10.1002/cbic.201600281}, volume = {17}, year = {2016}, } @article{21100, abstract = {Using commercial screens for crystallization of biomolecules and taking advantage of the use of racemic crystallography allowed the production of X-ray quality single crystals and the elucidation at 1.08 Å resolution of the solid state structure of a difficult target: the complex between glucopyranose and a water soluble macrocyclic receptor equipped with dendritic multianionic solubilizing chains.}, author = {Mandal, Pradeep K and Kauffmann, Brice and Destecroix, Harry and Ferrand, Yann and Davis, Anthony P. and Huc, Ivan}, issn = {1364-548X}, journal = {Chemical Communications}, number = {60}, pages = {9355--9358}, publisher = {Royal Society of Chemistry}, title = {{Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains}}, doi = {10.1039/c6cc04466b}, volume = {52}, year = {2016}, } @article{21101, abstract = {It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods—that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence ‘TATAAT’. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65–2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence.}, author = {Mandal, Pradeep K and Collie, Gavin W. and Srivastava, Suresh C. and Kauffmann, Brice and Huc, Ivan}, issn = {1362-4962}, journal = {Nucleic Acids Research}, number = {12}, pages = {5936--5943}, publisher = {Oxford University Press}, title = {{Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography}}, doi = {10.1093/nar/gkw367}, volume = {44}, year = {2016}, } @article{21522, abstract = {In this Letter, we demonstrate highly efficient, polarization-insensitive planar lenses (metalenses) at red, green, and blue wavelengths (λ = 660, 532, and 405 nm). Metalenses with numerical apertures (NA) of 0.85 and 0.6 and corresponding efficiencies as high as 60% and 90% are achieved. These metalenses are less than 600 nm-thick and can focus incident light down to diffraction-limited spots as small as ∼0.64λ and provide high-resolution imaging. In addition, the focal spots are very symmetric with high Strehl ratios. The single step lithography and compatibility with large-scale fabrication processes make metalenses highly promising for widespread applications in imaging and spectroscopy.}, author = {Khorasaninejad, M. and Zhu, A. Y. and Roques-Carmes, Charles and Chen, W. T. and Oh, J. and Mishra, I. and Devlin, R. C. and Capasso, F.}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Metasurface, polarization-insensitive metalenses, visible wavelength, titanium dioxide}, number = {11}, pages = {7229--7234}, publisher = {American Chemical Society}, title = {{Polarization-insensitive metalenses at visible wavelengths}}, doi = {10.1021/acs.nanolett.6b03626}, volume = {16}, year = {2016}, } @inproceedings{21635, abstract = {We report high numerical aperture meta-lenses in the visible spectrum with focal spots as small as 0.65λ. Meta-lenses are based on ultra-thin titanium dioxide metasurface phase masks. They operate in transmission mode and are polarization-insensitive.}, author = {Khorasaninejad, M. and Chen, W. T. and Zhu, A. and Oh, J. and Roques-Carmes, Charles and Mishra, I. and Devlin, R. C. and Capasso, F.}, booktitle = {Frontiers in Optics 2016}, location = {Rochester, NY, United States}, publisher = {Optica Publishing Group}, title = {{High numerical aperture meta-lenses at visible wavelengths}}, doi = {10.1364/fio.2016.jw4a.63}, year = {2016}, } @article{21812, abstract = {We report a facile strategy to grow supramolecular copolymers on Au surfaces by successively exposing a surface‐anchored monomer to solutions of oppositely charged peptide comonomers. Charge regulation on the active chain end of the polymer sufficiently slows down the kinetics of the self‐assembly process to produce kinetically trapped copolymers at near‐neutral pH. We thereby achieve architectural control at three levels: The β‐sheet sequences direct the polymerization away from the surface, the height of the supramolecular copolymer brushes is well‐controlled by the stepwise nature of the alternating copolymer growth, and 2D spatial resolution is realized by using micropatterned initiating monomers. The programmable nature of the resulting architectures renders this concept attractive for the development of customized biomaterials or chiral interfaces for optoelectronics and sensor applications.}, author = {Frisch, Hendrik and Fritz, Eva‐Corinna and Stricker, Friedrich J and Schmüser, Lars and Spitzer, Daniel and Weidner, Tobias and Ravoo, Bart Jan and Besenius, Pol}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, number = {25}, pages = {7242--7246}, publisher = {Wiley}, title = {{Kinetically controlled sequential growth of surface‐grafted chiral supramolecular copolymers}}, doi = {10.1002/anie.201601048}, volume = {55}, year = {2016}, } @misc{21815, abstract = {A modular strategy for the synthesis of surface-confined supramolecular copolymers is reported by P. Besenius, B. J. Ravoo, and co-workers in their Communication on page 7242 ff. The sequential addition of aqueous solutions containing the anionic or cationic comonomer enables the stepwise growth of alternating copolymers from gold surfaces. Charge regulation passivates the growing chain end and yields kinetically trapped chiral copolymers with a tunable height of 5–19 nm.}, author = {Frisch, Hendrik and Fritz, Eva‐Corinna and Stricker, Friedrich J and Schmüser, Lars and Spitzer, Daniel and Weidner, Tobias and Ravoo, Bart Jan and Besenius, Pol}, booktitle = {Angewandte Chemie International Edition}, issn = {1521-3773}, number = {25}, pages = {7009--7264}, publisher = {Wiley}, title = {{Inside back cover: Kinetically controlled sequential growth of surface‐grafted chiral supramolecular Copolymers (Angew. Chem. Int. Ed. 25/2016)}}, doi = {10.1002/anie.201604416}, volume = {55}, year = {2016}, } @article{13385, abstract = {Novel light-responsive nanoparticles were synthesized by decorating the surfaces of gold and silver nanoparticles with a nitrospiropyran molecular photoswitch. Upon exposure to UV light in nonpolar solvents, these nanoparticles self-assembled to afford spherical aggregates, which disassembled rapidly when the UV stimulus was turned off. The sizes of these aggregates depended on the nanoparticle concentration, and their lifetimes could be controlled by adjusting the surface concentration of nitrospiropyran on the nanoparticles. The conformational flexibility of nitrospiropyran, which was altered by modifying the structure of the background ligand, had a profound impact on the self-assembly process. By coating the nanoparticles with a spiropyran lacking the nitro group, a conceptually different self-assembly system, relying on a reversible proton transfer, was realized. The resulting particles spontaneously (in the dark) assembled into aggregates that could be readily disassembled upon exposure to blue light.}, author = {Kundu, Pintu K. and Das, Sanjib and Ahrens, Johannes and Klajn, Rafal}, issn = {2040-3372}, journal = {Nanoscale}, keywords = {General Materials Science}, number = {46}, pages = {19280--19286}, publisher = {Royal Society of Chemistry}, title = {{Controlling the lifetimes of dynamic nanoparticle aggregates by spiropyran functionalization}}, doi = {10.1039/c6nr05959g}, volume = {8}, year = {2016}, } @article{13386, abstract = {Azobenzenealkanethiols in self-assembled monolayers (SAMs) on Au(111) exhibit reversible trans–cis photoisomerization when diluted with alkanethiol spacers. Using these mixed SAMs, we show switching of the linear optical and second-harmonic response. The effective switching of these surface optical properties relies on a reasonably large cross section and a high photoisomerization yield as well as a long lifetime of the metastable cis isomer. We quantified the switching process by X-ray absorption spectroscopy. The cross sections for the trans–cis and cis–trans photoisomerization with 365 and 455 nm light, respectively, are 1 order of magnitude smaller than in solution. In vacuum, the 365 nm photostationary state comprises 50–74% of the molecules in the cis form, limited by their rapid thermal isomerization back to the trans state. In contrast, the 455 nm photostationary state contains nearly 100% trans-azobenzene. We determined time constants for the thermal cis–trans isomerization of only a few minutes in vacuum and in a dry nitrogen atmosphere but of more than 1 day in ambient air. Our results suggest that adventitious water adsorbed on the surface of the SAM stabilizes the polar cis configuration of azobenzene under ambient conditions. The back reaction rate constants differing by 2 orders of magnitude underline the huge influence of the environment and, accordingly, its importance when comparing various experiments.}, author = {Moldt, Thomas and Przyrembel, Daniel and Schulze, Michael and Bronsch, Wibke and Boie, Larissa and Brete, Daniel and Gahl, Cornelius and Klajn, Rafal and Tegeder, Petra and Weinelt, Martin}, issn = {1520-5827}, journal = {Langmuir}, keywords = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science}, number = {42}, pages = {10795--10801}, publisher = {American Chemical Society}, title = {{Differing isomerization kinetics of azobenzene-functionalized self-assembled monolayers in ambient air and in vacuum}}, doi = {10.1021/acs.langmuir.6b01690}, volume = {32}, year = {2016}, }