@article{2836,
abstract = {We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents and the trusted third party as path formulas in linear temporal logic and prove that the satisfaction of these objectives imply fairness; a property required of fair exchange protocols. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of AGS as follows: (a) any solution of AGS is attack-free; no subset of participants can violate the objectives of the other participants; (b) the Asokan-Shoup-Waidner certified mail protocol that has known vulnerabilities is not a solution of AGS; (c) the Kremer-Markowitch non-repudiation protocol is a solution of AGS; and (d) AGS presents a new and symmetric fair non-repudiation protocol that is attack-free. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can both automatically discover vulnerabilities in protocols and generate correct protocols. The solution to AGS can be computed efficiently as the secure equilibrium solution of three-player graph games. },
author = {Chatterjee, Krishnendu and Raman, Vishwanath},
journal = {Formal Aspects of Computing},
number = {4},
pages = {825 -- 859},
publisher = {Springer},
title = {{Assume-guarantee synthesis for digital contract signing}},
doi = {10.1007/s00165-013-0283-6},
volume = {26},
year = {2013},
}
@article{2780,
abstract = {We consider a general class of random matrices whose entries are centred random variables, independent up to a symmetry constraint. We establish precise high-probability bounds on the averages of arbitrary monomials in the resolvent matrix entries. Our results generalize the previous results of Erdős et al. (Ann Probab, arXiv:1103.1919, 2013; Commun Math Phys, arXiv:1103.3869, 2013; J Combin 1(2):15-85, 2011) which constituted a key step in the proof of the local semicircle law with optimal error bound in mean-field random matrix models. Our bounds apply to random band matrices and improve previous estimates from order 2 to order 4 in the cases relevant to applications. In particular, they lead to a proof of the diffusion approximation for the magnitude of the resolvent of random band matrices. This, in turn, implies new delocalization bounds on the eigenvectors. The applications are presented in a separate paper (Erdős et al., arXiv:1205.5669, 2013).},
author = {László Erdös and Knowles, Antti and Yau, Horng-Tzer},
journal = {Annales Henri Poincare},
number = {8},
pages = {1837 -- 1926},
publisher = {Birkhäuser},
title = {{Averaging fluctuations in resolvents of random band matrices}},
doi = {10.1007/s00023-013-0235-y},
volume = {14},
year = {2013},
}
@article{2805,
abstract = {Transition in shear flows is characterized by localized turbulent regions embedded in the surrounding laminar flow. These so-called turbulent spots or puffs are observed in a variety of shear flows and in certain Reynolds-number regimes, and they are advected by the flow while keeping their characteristic length. We show here for the case of pipe flow that this seemingly passive advection of turbulent puffs involves continuous entrainment and relaminarization of laminar and turbulent fluid across strongly convoluted interfaces. Surprisingly, interface areas are almost two orders of magnitude larger than the pipe cross-section, while local entrainment velocities are much smaller than the mean speed. Even though these velocities were shown to be small and proportional to the Kolmogorov velocity scale (in agreement with a prediction by Corrsin) in a flow without mean shear before, we find that, in pipe flow, local entrainment velocities are about an order of magnitude smaller than this scale. The Lagrangian method used to study the dynamics of the laminar-turbulent interfaces allows accurate determination of the leading and trailing edge speeds. However, to resolve the highly complex interface dynamics requires much higher numerical resolutions than for ordinary turbulent flows. This method also reveals that the volume flux across the leading edge has the same radial dependence but the opposite sign as that across the trailing edge, and it is this symmetry that is responsible for the puff shape remaining constant.},
author = {Holzner, Markus and Song, Baofang and Avila, Marc and Björn Hof},
journal = {Journal of Fluid Mechanics},
pages = {140 -- 162},
publisher = {Cambridge University Press},
title = {{Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow}},
doi = {10.1017/jfm.2013.127},
volume = {723},
year = {2013},
}
@article{2850,
abstract = {Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on capturing the measured correlations among pairs of neurons. Here we suggest an alternative, constructing models that are consistent with the distribution of global network activity, i.e. the probability that K out of N cells in the network generate action potentials in the same small time bin. The inverse problem that we need to solve in constructing the model is analytically tractable, and provides a natural 'thermodynamics' for the network in the limit of large N. We analyze the responses of neurons in a small patch of the retina to naturalistic stimuli, and find that the implied thermodynamics is very close to an unusual critical point, in which the entropy (in proper units) is exactly equal to the energy. © 2013 IOP Publishing Ltd and SISSA Medialab srl.
},
author = {Tkacik, Gasper and Marre, Olivier and Mora, Thierry and Amodei, Dario and Berry, Michael and Bialek, William},
journal = {Journal of Statistical Mechanics Theory and Experiment},
number = {3},
publisher = {IOP Publishing Ltd.},
title = {{The simplest maximum entropy model for collective behavior in a neural network}},
doi = {10.1088/1742-5468/2013/03/P03011},
volume = {2013},
year = {2013},
}
@inproceedings{2812,
abstract = {We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.},
author = {Attali, Dominique and Bauer, Ulrich and Devillers, Olivier and Glisse, Marc and Lieutier, André},
booktitle = {Proceedings of the 29th annual symposium on Computational Geometry},
location = {Rio de Janeiro, Brazil},
pages = {117 -- 125},
publisher = {ACM},
title = {{Homological reconstruction and simplification in R3}},
doi = {10.1145/2462356.2462373},
year = {2013},
}
@inproceedings{2843,
abstract = {Mathematical objects can be measured unambiguously, but not so objects from our physical world. Even the total length of tubelike shapes has its difficulties. We introduce a combination of geometric, probabilistic, and topological methods to design a stable length estimate for tube-like shapes; that is: one that is insensitive to small shape changes.},
author = {Edelsbrunner, Herbert and Pausinger, Florian},
booktitle = {17th IAPR International Conference on Discrete Geometry for Computer Imagery},
location = {Seville, Spain},
pages = {XV -- XIX},
publisher = {Springer},
title = {{Stable length estimates of tube-like shapes}},
doi = {10.1007/978-3-642-37067-0},
volume = {7749},
year = {2013},
}
@article{2817,
abstract = {The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle.},
author = {Novak, Sebastian and Chatterjee, Krishnendu and Nowak, Martin},
journal = {Journal of Theoretical Biology},
pages = {26 -- 34},
publisher = {Elsevier},
title = {{Density games}},
doi = {10.1016/j.jtbi.2013.05.029},
volume = {334},
year = {2013},
}
@article{2862,
abstract = {Motile cilia perform crucial functions during embryonic development and throughout adult life. Development of organs containing motile cilia involves regulation of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis) in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis is not yet fully understood, and it remains unclear whether these processes are coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently in ciliated organs. Lgl proteins are involved in establishing cell polarity and have been implicated in vesicle trafficking. Here, we identified a role for Lgl2 in development of ciliated epithelia in Kupffer's vesicle, which directs left-right asymmetry of the embryo; the otic vesicles, which give rise to the inner ear; and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed loss of the adherens junction component E-cadherin at lateral membranes. Genetic interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin and mediate lumen formation that is uncoupled from cilia formation. These results uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis and ciliogenesis and indicate that these processes are genetically separable in zebrafish.},
author = {Tay, Hwee and Schulze, Sabrina and Compagnon, Julien and Foley, Fiona and Heisenberg, Carl-Philipp J and Yost, H Joseph and Abdelilah Seyfried, Salim and Amack, Jeffrey},
journal = {Development},
number = {7},
pages = {1550 -- 1559},
publisher = {Company of Biologists},
title = {{Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle}},
doi = {10.1242/dev.087130},
volume = {140},
year = {2013},
}
@article{2881,
abstract = {The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated lobes and indents is a good model system to investigate the mechanisms that coordinate cell polarity and shape formation within a tissue. Auxin has been shown to coordinate the interdigitation by activating ROP GTPase-dependent signaling pathways. To identify additional components or mechanisms, we screened for mutants with abnormal PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling (such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant, and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas over-production of cytokinin and over-activation of cytokinin signaling in an ARR20 over-expression line delayed or abolished PC interdigitation throughout the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling acts upstream of ROPs to suppress the formation of interdigitated pattern. Our results provide novel mechanistic understanding of the pathways controlling PC shape and uncover a new role for cytokinin signaling in cell morphogenesis.},
author = {Hongjiang Li and Xu, Tongda and Lin, Deshu and Wen, Mingzhang and Xie, Mingtang and Duclercq, Jérôme and Bielach, Agnieszka and Kim, Jungmook and Reddy, G Venugopala and Zuo, Jianru and Eva Benková and Jirí Friml and Guo, Hongwei and Yang, Zhenbiao},
journal = {Cell Research},
number = {2},
pages = {290 -- 299},
publisher = {Nature Publishing Group},
title = {{Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis}},
doi = {10.1038/cr.2012.146},
volume = {23},
year = {2013},
}
@inproceedings{2886,
abstract = {We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization.},
author = {Chmelik, Martin and Řehák, Vojtěch},
location = {Znojmo, Czech Republic},
pages = {118 -- 130},
publisher = {Springer},
title = {{Controllable-choice message sequence graphs}},
doi = {10.1007/978-3-642-36046-6_12},
volume = {7721},
year = {2013},
}
@inproceedings{2901,
abstract = { We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. },
author = {Chen, Chao and Kolmogorov, Vladimir and Yan, Zhu and Metaxas, Dimitris and Lampert, Christoph},
location = {Scottsdale, AZ, United States},
pages = {161 -- 169},
publisher = {JMLR},
title = {{Computing the M most probable modes of a graphical model}},
volume = {31},
year = {2013},
}
@inproceedings{2906,
abstract = {Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented
using CGAL, following the exact geometric computation paradigm. We report on several
techniques to accelerate the computation that turn our implementation applicable to the underlying biological
problem.},
author = {Kerber, Michael and Edelsbrunner, Herbert},
booktitle = {2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments},
location = {New Orleans, LA, United States},
pages = {70 -- 77},
publisher = {Society of Industrial and Applied Mathematics},
title = {{3D kinetic alpha complexes and their implementation}},
doi = {10.1137/1.9781611972931.6},
year = {2013},
}
@article{2913,
abstract = {The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this "neural metric" tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.},
author = {Tkacik, Gasper and Granot Atedgi, Einat and Segev, Ronen and Schneidman, Elad},
journal = {Physical Review Letters},
number = {5},
publisher = {American Physical Society},
title = {{Retinal metric: a stimulus distance measure derived from population neural responses}},
doi = {10.1103/PhysRevLett.110.058104},
volume = {110},
year = {2013},
}
@article{2920,
abstract = {Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen.},
author = {Compagnon, Julien and Heisenberg, Carl-Philipp J},
journal = {EMBO Journal},
number = {1},
pages = {1 -- 3},
publisher = {Wiley-Blackwell},
title = {{Neurulation coordinating cell polarisation and lumen formation}},
doi = {10.1038/emboj.2012.325},
volume = {32},
year = {2013},
}
@article{2918,
abstract = {Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.
},
author = {Castanon, Irinka and Abrami, Laurence and Holtzer, Laurent and Heisenberg, Carl-Philipp J and Van Der Goot, Françoise and González Gaitán, Marcos},
journal = {Nature Cell Biology},
number = {1},
pages = {28 -- 39},
publisher = {Nature Publishing Group},
title = {{Anthrax toxin receptor 2a controls mitotic spindle positioning}},
doi = {10.1038/ncb2632},
volume = {15},
year = {2013},
}
@article{353,
abstract = {We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents.},
author = {Li, Wenhua and Zamani, Reza R and Rivera Gil, Pilar and Pelaz, Beatriz and Ibanez, Maria and Cadavid, Doris and Shavel, Alexey and Alvarez-Puebla, Ramon A and Parak, Wolfgang J and Arbiol, Jordi and Cabot, Andreu},
journal = {Journal of the American Chemical Society},
number = {19},
pages = {7098 -- 7101},
publisher = {American Chemical Society},
title = {{CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents}},
doi = {10.1021/ja401428e},
volume = {135},
year = {2013},
}
@article{500,
abstract = {Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.},
author = {Ward, Melissa and Lycett, Samantha and Avila, Dorita and Bollback, Jonathan P and Leigh Brown, Andrew},
journal = {BMC Evolutionary Biology},
number = {1},
publisher = {BioMed Central},
title = {{Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza}},
doi = {10.1186/1471-2148-13-222},
volume = {13},
year = {2013},
}
@article{505,
abstract = {Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts.},
author = {Greimel, Katrin and Perz, Veronika and Koren, Klaus and Feola, Roland and Temel, Armin and Sohar, Christian and Herrero Acero, Enrique and Klimant, Ingo and Guebitz, Georg},
journal = {Green Chemistry},
number = {2},
pages = {381 -- 388},
publisher = {Royal Society of Chemistry},
title = {{Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins}},
doi = {10.1039/c2gc36666e},
volume = {15},
year = {2013},
}
@misc{5400,
abstract = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu},
issn = {2664-1690},
pages = {41},
publisher = {IST Austria},
title = {{What is decidable about partially observable Markov decision processes with ω-regular objectives}},
doi = {10.15479/AT:IST-2013-109-v1-1},
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},
}
@misc{5405,
abstract = {The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2-1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2-1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic) with only parity objectives, or with only mean-payoff objectives. We present an algorithm running
in time O(d · n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the objective
can be ensured with probability 1, where n is the number of states of the game, d the number of priorities
of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states
in 2-1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems
with both functional requirement (given as a qualitative objective) and performance requirement (given
as a quantitative objective).},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Gimbert, Hugo and Oualhadj, Youssouf},
issn = {2664-1690},
pages = {22},
publisher = {IST Austria},
title = {{Perfect-information stochastic mean-payoff parity games}},
doi = {10.15479/AT:IST-2013-128-v1-1},
year = {2013},
}
@article{810,
abstract = {Cryo-electron tomography combined with image processing by sub-tomogram averaging is unique in its power to resolve the structures of proteins and macromolecular complexes in situ. Limitations of the method, including the low signal to noise ratio within individual images from cryo-tomographic datasets and difficulties in determining the defocus at which the data was collected, mean that to date the very best structures obtained by sub-tomogram averaging are limited to a resolution of approximately 15. Å. Here, by optimizing data collection and defocus determination steps, we have determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution alpha-helices can be directly and clearly visualized. These data demonstrate for the first time that high-resolution structural information can be obtained from cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has the potential to allow detailed studies of unsolved and biologically relevant structures under biologically relevant conditions.},
author = {Florian Schur and Hagen, Wim J and De Marco, Alex and Briggs, John A},
journal = {Journal of Structural Biology},
number = {3},
pages = {394 -- 400},
publisher = {Academic Press},
title = {{Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging}},
doi = {10.1016/j.jsb.2013.10.015},
volume = {184},
year = {2013},
}
@article{827,
abstract = {As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.},
author = {O'Brien, José and Benková, Eva},
journal = {Frontiers in Plant Science},
publisher = {Frontiers Research Foundation},
title = {{Cytokinin cross talking during biotic and abiotic stress responses}},
doi = {10.3389/fpls.2013.00451},
volume = {4},
year = {2013},
}
@article{973,
abstract = {We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion.},
author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A},
journal = {Physical Review Letters},
number = {12},
publisher = {American Physical Society},
title = {{Local conservation laws and the structure of the many body localized states}},
doi = {10.1103/PhysRevLett.111.127201},
volume = {111},
year = {2013},
}
@article{6768,
abstract = {The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme.},
author = {Mondelli, Marco},
issn = {2105-1232},
journal = {Image Processing On Line},
pages = {68--111},
publisher = {Image Processing On Line},
title = {{A finite difference scheme for the stack filter simulating the MCM}},
doi = {10.5201/ipol.2013.53},
volume = {3},
year = {2013},
}
@inproceedings{2305,
abstract = {We study the complexity of central controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize both the expected mean-payoff performance of the system and its stability. e argue that the basic theoretical notion of expressing the stability in terms of the variance of the mean-payoff (called global variance in our paper) is not always sufficient, since it ignores possible instabilities on respective runs. For this reason we propose alernative definitions of stability, which we call local and hybrid variance, and which express how rewards on each run deviate from the run's own mean-payoff and from the expected mean-payoff, respectively. We show that a strategy ensuring both the expected mean-payoff and the variance below given bounds requires randomization and memory, under all the above semantics of variance. We then look at the problem of determining whether there is a such a strategy. For the global variance, we show that the problem is in PSPACE, and that the answer can be approximated in pseudo-polynomial time. For the hybrid variance, the analogous decision problem is in NP, and a polynomial-time approximating algorithm also exists. For local variance, we show that the decision problem is in NP. Since the overall performance can be traded for stability (and vice versa), we also present algorithms for approximating the associated Pareto curve in all the three cases. Finally, we study a special case of the decision problems, where we require a given expected mean-payoff together with zero variance. Here we show that the problems can be all solved in polynomial time.},
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín},
booktitle = {28th Annual ACM/IEEE Symposium},
location = {New Orleans, LA, United States},
pages = {331 -- 340},
publisher = {IEEE},
title = {{Trading performance for stability in Markov decision processes}},
doi = {10.1109/LICS.2013.39},
year = {2013},
}
@article{2944,
abstract = {We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.},
author = {Aeschbacher, Simon and Futschik, Andreas and Beaumont, Mark},
journal = {Molecular Ecology},
number = {4},
pages = {987 -- 1002},
publisher = {Wiley-Blackwell},
title = {{Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. }},
doi = {10.1111/mec.12165},
volume = {22},
year = {2013},
}
@article{2855,
abstract = {Genomic imprinting leads to preferred expression of either the maternal or paternal alleles of a subset of genes. Imprinting is essential for mammalian development, and its deregulation causes many diseases. However, the functional relevance of imprinting at the cellular level is poorly understood for most imprinted genes. We used mosaic analysis with double markers (MADM) in mice to create uniparental disomies (UPDs) and to visualize imprinting effects with single-cell resolution. Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7 UPD caused highly significant paternal growth dominance in the liver and lung, but not in the brain or heart. A single gene on chromosome 7, encoding the secreted insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and cell-type specificity of genomic imprinting effects.},
author = {Hippenmeyer, Simon and Johnson, Randy and Luo, Liqun},
journal = {Cell Reports},
number = {3},
pages = {960 -- 967},
publisher = {Cell Press},
title = {{Mosaic analysis with double markers reveals cell type specific paternal growth dominance}},
doi = {10.1016/j.celrep.2013.02.002},
volume = {3},
year = {2013},
}
@inproceedings{2329,
abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.},
author = {Chatterjee, Krishnendu and Velner, Yaron},
location = {Buenos Aires, Argentinia},
pages = {500 -- 515},
publisher = {Springer},
title = {{Hyperplane separation technique for multidimensional mean-payoff games}},
doi = {10.1007/978-3-642-40184-8_35},
volume = {8052},
year = {2013},
}
@article{2300,
abstract = {We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.},
author = {Giuliani, Alessandro and Lieb, Élliott and Seiringer, Robert},
journal = {Physical Review B},
number = {6},
publisher = {American Physical Society},
title = {{Realization of stripes and slabs in two and three dimensions}},
doi = {10.1103/PhysRevB.88.064401},
volume = {88},
year = {2013},
}
@inproceedings{2259,
abstract = {The learning with rounding (LWR) problem, introduced by Banerjee, Peikert and Rosen at EUROCRYPT ’12, is a variant of learning with errors (LWE), where one replaces random errors with deterministic rounding. The LWR problem was shown to be as hard as LWE for a setting of parameters where the modulus and modulus-to-error ratio are super-polynomial. In this work we resolve the main open problem and give a new reduction that works for a larger range of parameters, allowing for a polynomial modulus and modulus-to-error ratio. In particular, a smaller modulus gives us greater efficiency, and a smaller modulus-to-error ratio gives us greater security, which now follows from the worst-case hardness of GapSVP with polynomial (rather than super-polynomial) approximation factors.
As a tool in the reduction, we show that there is a “lossy mode” for the LWR problem, in which LWR samples only reveal partial information about the secret. This property gives us several interesting new applications, including a proof that LWR remains secure with weakly random secrets of sufficient min-entropy, and very simple constructions of deterministic encryption, lossy trapdoor functions and reusable extractors.
Our approach is inspired by a technique of Goldwasser et al. from ICS ’10, which implicitly showed the existence of a “lossy mode” for LWE. By refining this technique, we also improve on the parameters of that work to only requiring a polynomial (instead of super-polynomial) modulus and modulus-to-error ratio.
},
author = {Alwen, Joel F and Krenn, Stephan and Pietrzak, Krzysztof Z and Wichs, Daniel},
location = {Santa Barbara, CA, United States},
number = {1},
pages = {57 -- 74},
publisher = {Springer},
title = {{Learning with rounding, revisited: New reduction properties and applications}},
doi = {10.1007/978-3-642-40041-4_4},
volume = {8042},
year = {2013},
}
@article{2297,
abstract = {We present an overview of mathematical results on the low temperature properties of dilute quantum gases, which have been obtained in the past few years. The presentation includes a discussion of Bose-Einstein condensation, the excitation spectrum for trapped gases and its relation to superfluidity, as well as the appearance of quantized vortices in rotating systems. All these properties are intensely being studied in current experiments on cold atomic gases. We will give a description of the mathematics involved in understanding these phenomena, starting from the underlying many-body Schrödinger equation.},
author = {Seiringer, Robert},
journal = {Japanese Journal of Mathematics},
number = {2},
pages = {185 -- 232},
publisher = {Springer},
title = {{Hot topics in cold gases: A mathematical physics perspective}},
doi = {10.1007/s11537-013-1264-5},
volume = {8},
year = {2013},
}
@article{2280,
abstract = {The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented.},
author = {Uhler, Caroline and Wright, Stephen},
journal = {SIAM Review},
number = {4},
pages = {671 -- 706},
publisher = {Society for Industrial and Applied Mathematics },
title = {{Packing ellipsoids with overlap}},
doi = {10.1137/120872309},
volume = {55},
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{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{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},
}
@article{1790,
abstract = {In the September 12, 2013 issue of Nature, the Epi4K Consortium (. Allen etal., 2013) reported sequencing 264patient trios with epileptic encephalopathies. The Consortium focused on genes exceptionally intolerant to sequence variations and found substantial interconnections with autism and intellectual disability gene networks.},
author = {Gaia Novarino and Baek, SeungTae and Gleeson, Joseph G},
journal = {Neuron},
number = {1},
pages = {9 -- 11},
publisher = {Elsevier},
title = {{The sacred disease: The puzzling genetics of epileptic disorders}},
doi = {10.1016/j.neuron.2013.09.019},
volume = {80},
year = {2013},
}
@article{1726,
abstract = {The development of a functional tissue requires coordination of the amplification of progenitors and their differentiation into specific cell types. The molecular basis for this coordination during myotome ontogeny is not well understood. Dermomytome progenitors that colonize the myotome first acquire myocyte identity and subsequently proliferate as Pax7-expressing progenitors before undergoing terminal differentiation. We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this transition in both avian and mouse embryos. Initially, Shh ligand emanating from notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation of dermomyotome cells and promotes myogenic differentiation of progenitors that colonized the myotome. Interfering with Shh signaling at this stage produces small myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter of Shh activity combined with mouse genetics revealed the existence of both activator and repressor Shh activities operating on distinct subsets of cells during the epaxial myotomal maturation. In contrast to observations in mice, in avians Shh promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently, myogenic progenitors become refractory to Shh; this is likely to occur at the level of, or upstream of, smoothened signaling. The end of responsiveness to Shh coincides with, and is thus likely to enable, the transition into the growth phase of the myotome.},
author = {Kahane, Nitza and Ribes, Vanessa and Anna Kicheva and Briscoe, James and Kalcheim, Chaya},
journal = {Development},
number = {8},
pages = {1740 -- 1750},
publisher = {Company of Biologists},
title = {{The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling}},
doi = {10.1242/dev.092726},
volume = {140},
year = {2013},
}
@article{1978,
abstract = {Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.},
author = {Baradaran, Rozbeh and Berrisford, John M and Minhas, Gurdeep S and Leonid Sazanov},
journal = {Nature},
number = {7438},
pages = {443 -- 448},
publisher = {Nature Publishing Group},
title = {{Crystal structure of the entire respiratory complex i}},
doi = {10.1038/nature11871},
volume = {494},
year = {2013},
}
@article{2010,
abstract = {Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case.},
author = {Uhler, Caroline and Raskutti, Garvesh and Bühlmann, Peter and Yu, Bin},
journal = {The Annals of Statistics},
number = {2},
pages = {436 -- 463},
publisher = {Institute of Mathematical Statistics},
title = {{Geometry of the faithfulness assumption in causal inference}},
doi = {10.1214/12-AOS1080},
volume = {41},
year = {2013},
}
@misc{2205,
abstract = {The goal of the present article is to review the major developments that have led to the current understanding of molecule-field interactions and experimental methods for manipulating molecules with electromagnetic fields. Molecule-field interactions are at the core of several, seemingly distinct areas of molecular physics. This is reflected in the organisation of this article, which includes sections on field control of molecular beams, external field traps for cold molecules, control of molecular orientation and molecular alignment, manipulation of molecules by non-conservative forces, ultracold molecules and ultracold chemistry, controlled many-body phenomena, entanglement of molecules and dipole arrays, and stability of molecular systems in high-frequency super-intense laser fields. The article contains 852 references.},
author = {Mikhail Lemeshko and Krems, Roman V and Doyle, John M and Kais, Sabre},
booktitle = {Molecular Physics},
number = {12-13},
pages = {1648 -- 1682},
publisher = {Taylor & Francis},
title = {{Manipulation of molecules with electromagnetic fields}},
doi = {10.1080/00268976.2013.813595},
volume = {111},
year = {2013},
}
@article{2109,
abstract = {Most additive manufacturing technologies work by layering, i.e. slicing the shape and then generating each slice independently. This introduces an anisotropy into the process, often as different accuracies in the tangential and normal directions, but also in terms of other parameters such as build speed or tensile strength and strain. We model this as an anisotropic cubic element. Our approach then finds a compromise between modeling each part of the shape individually in the best possible direction and using one direction for the whole shape part. In particular, we compute an orthogonal basis and consider only the three basis vectors as slice normals (i.e. fabrication directions). Then we optimize a decomposition of the shape along this basis so that each part can be consistently sliced along one of the basis vectors. In simulation, we show that this approach is superior to slicing the whole shape in one direction, only. It also has clear benefits if the shape is larger than the build volume of the available equipment.},
author = {Hildebrand, Kristian and Bernd Bickel and Alexa, Marc},
journal = {Computers and Graphics (Pergamon)},
number = {6},
pages = {669 -- 675},
publisher = {Elsevier},
title = {{Orthogonal slicing for additive manufacturing}},
doi = {10.1016/j.cag.2013.05.011},
volume = {37},
year = {2013},
}
@article{2111,
abstract = {Animated animatronic figures are a unique way to give physical presence to a character. However, their movement and expressions are often limited due to mechanical constraints. In this paper, we propose a complete process for augmenting physical avatars using projector-based illumination, significantly increasing their expressiveness. Given an input animation, the system decomposes the motion into low-frequency motion that can be physically reproduced by the animatronic head and high-frequency details that are added using projected shading. At the core is a spatio-temporal optimization process that compresses the motion in gradient space, ensuring faithful motion replay while respecting the physical limitations of the system. We also propose a complete multi-camera and projection system, including a novel defocused projection and subsurface scattering compensation scheme. The result of our system is a highly expressive physical avatar that features facial details and motion otherwise unattainable due to physical constraints.},
author = {Bermano, Amit H and Bruschweiler, Philipp and Grundhöfer, Anselm and Iwai, Daisuke and Bernd Bickel and Groß, Markus S},
journal = {ACM Transactions on Graphics},
number = {6},
publisher = {ACM},
title = {{Augmenting physical avatars using projector-based illumination}},
doi = {10.1145/2508363.2508416},
volume = {32},
year = {2013},
}
@article{2130,
author = {Clément, Philippe H and Jan Maas},
journal = {Journal of Evolution Equations},
number = {1},
pages = {251 -- 252},
publisher = {Birkhäuser},
title = {{Erratum: A Trotter product formula for gradient flows in metric spaces}},
doi = {10.1007/s00028-012-0173-z},
volume = {13},
year = {2013},
}
@inproceedings{2243,
abstract = {We show that modal logic over universally first-order definable classes of transitive frames is decidable. More precisely, let K be an arbitrary class of transitive Kripke frames definable by a universal first-order sentence. We show that the global and finite global satisfiability problems of modal logic over K are decidable in NP, regardless of choice of K. We also show that the local satisfiability and the finite local satisfiability problems of modal logic over K are decidable in NEXPTIME.},
author = {Michaliszyn, Jakub and Otop, Jan},
location = {Torino, Italy},
pages = {563 -- 577},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Elementary modal logics over transitive structures}},
doi = {10.4230/LIPIcs.CSL.2013.563},
volume = {23},
year = {2013},
}
@article{2286,
abstract = {The spatiotemporal control of cell divisions is a key factor in epithelial morphogenesis and patterning. Mao et al (2013) now describe how differential rates of proliferation within the Drosophila wing disc epithelium give rise to anisotropic tissue tension in peripheral/proximal regions of the disc. Such global tissue tension anisotropy in turn determines the orientation of cell divisions by controlling epithelial cell elongation.},
author = {Campinho, Pedro and Heisenberg, Carl-Philipp J},
journal = {EMBO Journal},
number = {21},
pages = {2783 -- 2784},
publisher = {Wiley-Blackwell},
title = {{The force and effect of cell proliferation}},
doi = {10.1038/emboj.2013.225},
volume = {32},
year = {2013},
}
@inproceedings{2293,
abstract = {Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results.},
author = {Sharmanska, Viktoriia and Quadrianto, Novi and Lampert, Christoph},
location = {Sydney, Australia},
pages = {825 -- 832},
publisher = {IEEE},
title = {{Learning to rank using privileged information}},
doi = {10.1109/ICCV.2013.107},
year = {2013},
}
@article{2692,
abstract = {The group III metabotropic glutamate (mGlu) receptors mGlu7 and mGlu8 are receiving increased attention as potential novel therapeutic targets for anxiety disorders. The effects mediated by these receptors appear to result from a complex interplay of facilitatory and inhibitory actions at different brain sites in the anxiety/fear circuits. To better understand the effect of mGlu7 and mGlu8 receptors on extinction of contextual fear and their critical sites of action in the fear networks, we focused on the amygdala. Direct injection into the basolateral complex of the amygdala of the mGlu7 receptor agonist AMN082 facilitated extinction, whereas the mGlu8 receptor agonist (S)-3,4-DCPG sustained freezing during the extinction acquisition trial. We also determined at the ultrastructural level the synaptic distribution of these receptors in the basal nucleus (BA) and intercalated cell clusters (ITCs) of the amygdala. Both areas are thought to exert key roles in fear extinction. We demonstrate that mGlu7 and mGlu8 receptors are located in different presynaptic terminals forming both asymmetric and symmetric synapses, and that they preferentially target neurons expressing mGlu1α receptors mostly located around ITCs. In addition we show that mGlu7 and mGlu8 receptors were segregated to different inputs to a significant extent. In particular, mGlu7a receptors were primarily onto glutamatergic afferents arising from the BA or midline thalamic nuclei, but not the medial prefrontal cortex (mPFC), as revealed by combined anterograde tracing and pre-embedding electron microscopy. On the other hand, mGlu8a showed a more restricted distribution in the BA and appeared absent from thalamic, mPFC and intrinsic inputs. This segregation of mGlu7 and mGlu8 receptors in different neuronal pathways of the fear circuit might explain the distinct effects on fear extinction training observed with mGlu7 and mGlu8 receptor agonists.},
author = {Dobi, Alice and Sartori, Simone B and Busti, Daniela and Van Der Putten, Herman V and Singewald, Nicolas and Ryuichi Shigemoto and Ferraguti, Francesco},
journal = {Neuropharmacology},
pages = {274 -- 289},
publisher = {Elsevier},
title = {{Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice}},
doi = {10.1016/j.neuropharm.2012.05.025},
volume = {66},
year = {2013},
}
@article{2697,
abstract = {We consider Hermitian and symmetric random band matrices H = (h xy ) in d⩾1 d ⩾ 1 dimensions. The matrix entries h xy , indexed by x,y∈(Z/LZ)d x , y ∈ ( Z / L Z ) d , are independent, centred random variables with variances sxy=E|hxy|2 s x y = E | h x y | 2 . We assume that s xy is negligible if |x − y| exceeds the band width W. In one dimension we prove that the eigenvectors of H are delocalized if W≫L4/5 W ≫ L 4 / 5 . We also show that the magnitude of the matrix entries |Gxy|2 | G x y | 2 of the resolvent G=G(z)=(H−z)−1 G = G ( z ) = ( H - z ) - 1 is self-averaging and we compute E|Gxy|2 E | G x y | 2 . We show that, as L→∞ L → ∞ and W≫L4/5 W ≫ L 4 / 5 , the behaviour of E|Gxy|2 E | G x y | 2 is governed by a diffusion operator whose diffusion constant we compute. Similar results are obtained in higher dimensions.},
author = {László Erdös and Knowles, Antti and Yau, Horng-Tzer and Yin, Jun},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {367 -- 416},
publisher = {Springer},
title = {{Delocalization and diffusion profile for random band matrices}},
doi = {10.1007/s00220-013-1773-3},
volume = {323},
year = {2013},
}
@article{2452,
abstract = {Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.},
author = {Barbez, Elke and Laňková, Martina and Pařezová, Markéta and Maizel, Alexis and Zažímalová, Eva and Petrášek, Jan and Jirí Friml and Kleine-Vehn, Jürgen},
journal = {BMC Plant Biology},
number = {1},
publisher = {BioMed Central},
title = {{Single-cell-based system to monitor carrier driven cellular auxin homeostasis}},
doi = {10.1186/1471-2229-13-20},
volume = {13},
year = {2013},
}