@article{595, author = {Bernecky, Carrie A and Cramer, Patrick}, journal = {EMBO Journal}, number = {6}, pages = {771 -- 772}, publisher = {Wiley-Blackwell}, title = {{Struggling to let go: A non-coding RNA directs its own extension and destruction}}, doi = {10.1038/emboj.2013.36}, volume = {32}, year = {2013}, } @article{6128, abstract = {Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O2 and CO2. CO2 is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO2 responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing neuron URX inhibits CO2 avoidance. This inhibition can be graded according to O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to modulate CO2 responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans.}, author = {Kodama-Namba, Eiji and Fenk, Lorenz A. and Bretscher, Andrew J. and Gross, Einav and Busch, K. Emanuel and de Bono, Mario}, issn = {1553-7404}, journal = {PLoS Genetics}, number = {12}, publisher = {Public Library of Science (PLoS)}, title = {{Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans}}, doi = {10.1371/journal.pgen.1004011}, volume = {9}, year = {2013}, } @article{6130, abstract = {Cas9 is an RNA-guided double-stranded DNA nuclease that participates in clustered regularly interspaced short palindromic repeats (CRISPR)-mediated adaptive immunity in prokaryotes. CRISPR–Cas9 has recently been used to generate insertion and deletion mutations in Caenorhabditis elegans, but not to create tailored changes (knock-ins). We show that the CRISPR–CRISPR-associated (Cas) system can be adapted for efficient and precise editing of the C. elegans genome. The targeted double-strand breaks generated by CRISPR are substrates for transgene-instructed gene conversion. This allows customized changes in the C. elegans genome by homologous recombination: sequences contained in the repair template (the transgene) are copied by gene conversion into the genome. The possibility to edit the C. elegans genome at selected locations will facilitate the systematic study of gene function in this widely used model organism.}, author = {Chen, Changchun and Fenk, Lorenz A. and de Bono, Mario}, issn = {1362-4962}, journal = {Nucleic Acids Research}, number = {20}, publisher = {Oxford University Press}, title = {{Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination}}, doi = {10.1093/nar/gkt805}, volume = {41}, year = {2013}, } @inbook{6132, author = {de Bono, Mario and Schafer, W.R. and Gottschalk, A.}, booktitle = {Optogenetics}, editor = {Hegemann, Peter and Sigrist, Stephan}, isbn = {9783110270723; 9783110270716}, pages = {61--78}, publisher = {Walter de Gruyter}, title = {{Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans}}, year = {2013}, } @article{6133, abstract = {cGMP signaling is widespread in the nervous system. However, it has proved difficult to visualize and genetically probe endogenously evoked cGMP dynamics in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical O2-binding soluble guanylate cyclase and that is sustained until oxygen levels fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2) and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation following a rise in O2, apparently by keeping in check gating of cGMP channels and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible when the same neuron in an individual animal is stimulated repeatedly, suggesting that cGMP transduction has high intrinsic reliability. However, responses vary substantially across individuals, despite animals being genetically identical and similarly reared. This variability may reflect stochastic differences in expression of cGMP signaling components. Our work provides in vivo insights into the architecture of neuronal cGMP signaling.}, author = {Couto, A. and Oda, S. and Nikolaev, V. O. and Soltesz, Z. and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {35}, pages = {E3301--E3310}, publisher = {Proceedings of the National Academy of Sciences}, title = {{In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor}}, doi = {10.1073/pnas.1217428110}, volume = {110}, year = {2013}, } @article{6135, abstract = {Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery.}, author = {Rodriguez, Miriam and Snoek, L. Basten and de Bono, Mario and Kammenga, Jan E.}, issn = {0168-9525}, journal = {Trends in Genetics}, number = {6}, pages = {367--374}, publisher = {Elsevier}, title = {{Worms under stress: C. elegans stress response and its relevance to complex human disease and aging}}, doi = {10.1016/j.tig.2013.01.010}, volume = {29}, year = {2013}, } @article{6370, abstract = {The molecular and supramolecular origins of the superior nonlinear optical (NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile), are presented. The molecular charge-transfer distribution is topographically mapped, demonstrating that a uniformly delocalized passive electronic medium facilitates the charge-transfer between the phenolic electron donor and the cyano electron acceptors which lie at opposite ends of the molecule. Its ability to act as a “push–pull” π-conjugated molecule is quantified, relative to similar materials, by supporting empirical calculations; these include bond-length alternation and harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with frontier molecular orbital considerations, reveal that OH1 can exist readily in its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals a correlation between the quinoidal resonance contribution to the overall structure of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally locked polyene framework materials. Solid-state tensorial coefficients of the molecular dipole, polarizability, and the first hyperpolarizability for OH1 are derived from the first-, second-, and third-order electronic moments of the experimental charge-density distribution. The overall solid-state molecular dipole moment is compared with those from gas-phase calculations, revealing that crystal field effects are very significant in OH1. The solid-state hyperpolarizability derived from this charge-density study affords good agreement with gas-phase calculations as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced second harmonic (EFISH) generation. This lends support to the further use of charge-density studies to calculate solid-state hyperpolarizability coefficients in other organic NLO materials. Finally, this charge-density study is also employed to provide an advanced classification of hydrogen bonds in OH1, which requires more stringent criteria than those from conventional structure analysis. As a result, only the strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed, it is this electrostatic interaction that influences the molecular charge transfer: the other four, weaker, nonbonded contacts nonetheless affect the crystal packing. Overall, the establishment of these structure–property relationships lays a blueprint for designing further, more NLO efficient, materials in this industrially leading organic family of compounds.}, author = {Lin, Tze-Chia and Cole, Jacqueline M. and Higginbotham, Andrew P and Edwards, Alison J. and Piltz, Ross O. and Pérez-Moreno, Javier and Seo, Ji-Youn and Lee, Seung-Chul and Clays, Koen and Kwon, O-Pil}, issn = {1932-7447}, journal = {The Journal of Physical Chemistry C}, number = {18}, pages = {9416--9430}, publisher = {American Chemical Society (ACS)}, title = {{Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations}}, doi = {10.1021/jp400648q}, volume = {117}, year = {2013}, } @misc{6440, abstract = {In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations. We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance. In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations.}, author = {Henzinger, Thomas A and Payer, Hannes and Sezgin, Ali}, issn = {2664-1690}, pages = {23}, publisher = {IST Austria}, title = {{Replacing competition with cooperation to achieve scalable lock-free FIFO queues }}, doi = {10.15479/AT:IST-2013-124-v1-1}, year = {2013}, } @article{1442, abstract = {We give a cohomological interpretation of both the Kac polynomial and the refined Donaldson-Thomas-invariants of quivers. This interpretation yields a proof of a conjecture of Kac from 1982 and gives a new perspective on recent work of Kontsevich-Soibelman. Thisis achieved by computing, via an arithmetic Fourier transform, the dimensions of the isotypical components of the cohomology of associated Nakajima quiver varieties under the action of a Weyl group. The generating function of the corresponding Poincare polynomials is an extension of Hua's formula for Kac polynomials of quivers involving Hall-Littlewood symmetric functions. The resulting formulae contain a wide range of information on the geometry of the quiver varieties.}, author = {Tamas Hausel and Letellier, Emmanuel and Rodríguez Villegas, Fernando}, journal = {Annals of Mathematics}, number = {3}, pages = {1147 -- 1168}, publisher = {Princeton University Press}, title = {{Positivity for Kac polynomials and DT-invariants of quivers}}, doi = {10.4007/annals.2013.177.3.8}, volume = {177}, year = {2013}, } @inbook{1443, abstract = {Here we survey several results and conjectures on the cohomology of the total space of the Hitchin system: the moduli space of semi-stable rank n and degree d Higgs bundles on a complex algebraic curve C. The picture emerging is a dynamic mixture of ideas originating in theoretical physics such as gauge theory and mirror symmetry, Weil conjectures in arithmetic algebraic geometry, representation theory of finite groups of Lie type and Langlands duality in number theory.}, author = {Tamas Hausel}, booktitle = {Handbook of Moduli: Volume II}, pages = {29 -- 70}, publisher = {International Press}, title = {{Global topology of the Hitchin system}}, volume = {25}, year = {2013}, } @article{1469, abstract = {We study connections between the topology of generic character varieties of fundamental groups of punctured Riemann surfaces, Macdonald polynomials, quiver representations, Hilbert schemes on Cx × Cx, modular forms and multiplicities in tensor products of irreducible characters of finite general linear groups.}, author = {Tamas Hausel and Letellier, Emmanuel and Rodríguez Villegas, Fernando}, journal = {Advances in Mathematics}, pages = {85 -- 128}, publisher = {Academic Press}, title = {{Arithmetic harmonic analysis on character and quiver varieties II}}, doi = {10.1016/j.aim.2012.10.009}, volume = {234}, year = {2013}, } @article{1470, abstract = {We show that a natural isomorphism between the rational cohomology groups of the two zero-dimensional Hilbert schemes of n-points of two surfaces, the affine plane minus the axes and the cotangent bundle of an elliptic curve, exchanges the weight filtration on the first set of cohomology groups with the perverse Leray filtration associated with a natural fibration on the second set of cohomology groups. We discuss some associated hard Lefschetz phenomena.}, author = {De Cataldo, Mark A and Tamas Hausel and Migliorini, Luca}, journal = {Journal of Singularities}, pages = {23 -- 38}, publisher = {Worldwide Center of Mathematics}, title = {{Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces}}, doi = {10.5427/jsing.2013.7c}, volume = {7}, year = {2013}, } @article{1307, abstract = {We prove uniqueness of solutions of the DLSS equation in a class of sufficiently regular functions. The global weak solutions of the DLSS equation constructed by Jüngel and Matthes belong to this class of uniqueness. We also show uniqueness of solutions for the quantum drift-diffusion equation, which contains additional drift and second-order diffusion terms. The results hold in case of periodic or Dirichlet-Neumann boundary conditions. Our proof is based on a monotonicity property of the DLSS operator and sophisticated approximation arguments; we derive a PDE satisfied by the pointwise square root of the solution, which enables us to exploit the monotonicity property of the operator.}, author = {Julian Fischer}, journal = {Communications in Partial Differential Equations}, number = {11}, pages = {2004 -- 2047}, publisher = {Taylor & Francis}, title = {{Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models}}, doi = {10.1080/03605302.2013.823548}, volume = {38}, year = {2013}, } @article{1308, abstract = {We derive sufficient conditions for advection-driven backward motion of the free boundary in a chemotaxis model with degenerate mobility. In this model, a porous-medium-type diffusive term and an advection term are in competition. The former induces forward motion, the latter may induce backward motion of the free boundary depending on the direction of advection. We deduce conditions on the growth of the initial data at the free boundary which ensure that at least initially the advection term is dominant. This implies local backward motion of the free boundary provided the advection is (locally) directed appropriately. Our result is based on a new class of moving test functions and Stampacchia's lemma. As a by-product of our estimates, we obtain quantitative bounds on the spreading of the support of solutions for the chemotaxis model and provide a proof for the finite speed of the support propagation property of solutions.}, author = {Julian Fischer}, journal = {SIAM Journal on Mathematical Analysis}, number = {3}, pages = {1585 -- 1615}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Advection-driven support shrinking in a chemotaxis model with degenerate mobility}}, doi = {10.1137/120874291}, volume = {45}, year = {2013}, } @article{1310, abstract = {We derive lower bounds on asymptotic support propagation rates for strong solutions of the Cauchy problem for the thin-film equation. The bounds coincide up to a constant factor with the previously known upper bounds and thus are sharp. Our results hold in case of at most three spatial dimensions and n∈. (1, 2.92). The result is established using weighted backward entropy inequalities with singular weight functions to yield a differential inequality; combined with some entropy production estimates, the optimal rate of propagation is obtained. To the best of our knowledge, these are the first lower bounds on asymptotic support propagation rates for higher-order nonnegativity-preserving parabolic equations.}, author = {Julian Fischer}, journal = {Journal of Differential Equations}, number = {10}, pages = {3127 -- 3149}, publisher = {Academic Press}, title = {{Optimal lower bounds on asymptotic support propagation rates for the thin-film equation}}, doi = {10.1016/j.jde.2013.07.028}, volume = {255}, year = {2013}, } @article{13405, abstract = {We report a method for preparing electrode–molecule–electrode junctions that incorporate nonsymmetrical azobenzene dithiols. Our approach is based on sequential deprotection of thiol moieties originally carrying two different protecting groups. The azobenzene derivatives retained their switching properties within monolayers and permitted the photocontrol of electrical conductance.}, author = {Ely, Tal and Das, Sanjib and Li, Wenjie and Kundu, Pintu and Tirosh, Einat and Cahen, David and Vilan, Ayelet and Klajn, Rafal}, issn = {1437-2096}, journal = {Synlett}, keywords = {Organic Chemistry}, number = {18}, pages = {2370--2374}, publisher = {Georg Thieme Verlag}, title = {{Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol}}, doi = {10.1055/s-0033-1340087}, volume = {24}, year = {2013}, } @article{13406, abstract = {Dual-responsive nanoparticles are designed by functionalizing magnetic cores with light-responsive ligands. These materials respond to both light and magnetic fields and can be assembled into various higher-order structures, depending on the relative contributions of these two stimuli.}, author = {Das, Sanjib and Ranjan, Priyadarshi and Maiti, Pradipta Sankar and Singh, Gurvinder and Leitus, Gregory and Klajn, Rafal}, issn = {0935-9648}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {3}, pages = {422--426}, publisher = {Wiley}, title = {{Dual-responsive nanoparticles and their self-assembly}}, doi = {10.1002/adma.201201734}, volume = {25}, year = {2013}, } @inproceedings{1374, abstract = {We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.}, author = {Chatterjee, Krishnendu and Fijalkow, Nathanaël}, booktitle = {22nd EACSL Annual Conference on Computer Science Logic}, location = {Torino, Italy}, pages = {181 -- 196}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Infinite-state games with finitary conditions}}, doi = {10.4230/LIPIcs.CSL.2013.181}, volume = {23}, year = {2013}, } @inproceedings{1376, abstract = {We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan and Pavlogiannis, Andreas}, booktitle = {13th International Conference on Formal Methods in Computer-Aided Design}, location = {Portland, OR, United States}, pages = {18 -- 25}, publisher = {IEEE}, title = {{Distributed synthesis for LTL fragments}}, doi = {10.1109/FMCAD.2013.6679386}, year = {2013}, } @inproceedings{1385, abstract = {It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results.}, author = {Hofferek, Georg and Gupta, Ashutosh and Könighofer, Bettina and Jiang, Jie and Bloem, Roderick}, booktitle = {2013 Formal Methods in Computer-Aided Design}, location = {Portland, OR, United States}, pages = {77 -- 84}, publisher = {IEEE}, title = {{Synthesizing multiple boolean functions using interpolation on a single proof}}, doi = {10.1109/FMCAD.2013.6679394}, year = {2013}, }