@article{347, abstract = {A synthetic route for producing Cu 2ZnGeSe 4 nanocrystals with narrow size distributions and controlled composition is presented. These nanocrystals were used to produce densely packed nanomaterials by hot-pressing. From the characterization of the thermoelectric properties of these nanomaterials, Cu 2ZnGeSe 4 is demonstrated to show excellent thermoelectric properties. A very preliminary adjustment of the nanocrystal composition has already resulted in a figure of merit of up to 0.55 at 450°C. }, author = {Ibáñez, Maria and Zamani, Reza and Lalonde, Aaron and Cadavid, Doris and Li, Wenhua and Shavel, Alexey and Arbiol, Jordi and Morante, Joan and Gorsse, Stéphane and Snyder, G Jeffrey and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {9}, pages = {4060 -- 4063}, publisher = {ACS}, title = {{Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties}}, doi = {10.1021/ja211952z}, volume = {134}, year = {2012}, } @article{3846, abstract = {We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A}, journal = {Journal of Computer and System Sciences}, number = {2}, pages = {394 -- 413}, publisher = {Elsevier}, title = {{A survey of stochastic ω regular games}}, doi = {10.1016/j.jcss.2011.05.002}, volume = {78}, year = {2012}, } @article{387, abstract = {In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society.}, author = {Alpichshev, Zhanybek and Biswas, Rudro and Balatsky, Alexander and Analytis, James and Chu, Jiunhaw and Fisher, Ian and Kapitulnik, Aharon}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{STM imaging of impurity resonances on Bi 2Se 3}}, doi = {10.1103/PhysRevLett.108.206402}, volume = {108}, year = {2012}, } @article{492, abstract = {Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.}, author = {Galkovskyi, Taras and Mileyko, Yuriy and Bucksch, Alexander and Moore, Brad and Symonova, Olga and Price, Charles and Topp, Chrostopher and Iyer Pascuzzi, Anjali and Zurek, Paul and Fang, Suqin and Harer, John and Benfey, Philip and Weitz, Joshua}, journal = {BMC Plant Biology}, publisher = {BioMed Central}, title = {{GiA Roots: Software for the high throughput analysis of plant root system architecture}}, doi = {10.1186/1471-2229-12-116}, volume = {12}, year = {2012}, } @article{493, abstract = {The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.}, author = {Tangermann, Michael and Müller, Klaus and Aertsen, Ad and Birbaumer, Niels and Braun, Christoph and Brunner, Clemens and Leeb, Robert and Mehring, Carsten and Miller, Kai and Müller Putz, Gernot and Nolte, Guido and Pfurtscheller, Gert and Preissl, Hubert and Schalk, Gerwin and Schlögl, Alois and Vidaurre, Carmen and Waldert, Stephan and Blankertz, Benjamin}, journal = {Frontiers in Neuroscience}, publisher = {Frontiers Research Foundation}, title = {{Review of the BCI competition IV}}, doi = {10.3389/fnins.2012.00055}, volume = {6}, year = {2012}, } @inproceedings{495, abstract = {An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice.}, author = {Kruckman, Alex and Rubin, Sasha and Sheridan, John and Zax, Ben}, booktitle = {Proceedings GandALF 2012}, location = {Napoli, Italy}, pages = {238 -- 246}, publisher = {Open Publishing Association}, title = {{A Myhill Nerode theorem for automata with advice}}, doi = {10.4204/EPTCS.96.18}, volume = {96}, year = {2012}, } @inproceedings{496, abstract = {We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations.}, author = {Rabinovich, Alexander and Rubin, Sasha}, location = {Dubrovnik, Croatia}, publisher = {IEEE}, title = {{Interpretations in trees with countably many branches}}, doi = {10.1109/LICS.2012.65}, year = {2012}, } @inproceedings{497, abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.}, author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish}, location = {Fontainebleau, France}, pages = {167 -- 182}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Faster algorithms for alternating refinement relations}}, doi = {10.4230/LIPIcs.CSL.2012.167}, volume = {16}, year = {2012}, } @article{498, abstract = {Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.}, author = {Pickup, Melinda and Field, David and Rowell, David and Young, Andrew}, journal = {Evolutionary Applications}, number = {8}, pages = {913 -- 924}, publisher = {Wiley-Blackwell}, title = {{Predicting local adaptation in fragmented plant populations: Implications for restoration genetics}}, doi = {10.1111/j.1752-4571.2012.00284.x}, volume = {5}, year = {2012}, } @article{506, author = {Sixt, Michael K}, journal = {Journal of Cell Biology}, number = {3}, pages = {347 -- 349}, publisher = {Rockefeller University Press}, title = {{Cell migration: Fibroblasts find a new way to get ahead}}, doi = {10.1083/jcb.201204039}, volume = {197}, year = {2012}, } @misc{5377, 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 solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. 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, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.}, author = {Chatterjee, Krishnendu and Velner, Yaron}, issn = {2664-1690}, pages = {33}, publisher = {IST Austria}, title = {{Mean-payoff pushdown games}}, doi = {10.15479/AT:IST-2012-0002}, year = {2012}, } @misc{5378, abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.}, author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish}, issn = {2664-1690}, pages = {21}, publisher = {IST Austria}, title = {{Faster algorithms for alternating refinement relations}}, doi = {10.15479/AT:IST-2012-0001}, year = {2012}, } @article{2125, abstract = {We consider a class of stochastic PDEs of Burgers type in spatial dimension 1, driven by space–time white noise. Even though it is well known that these equations are well posed, it turns out that if one performs a spatial discretization of the nonlinearity in the “wrong” way, then the sequence of approximate equations does converge to a limit, but this limit exhibits an additional correction term. This correction term is proportional to the local quadratic cross-variation (in space) of the gradient of the conserved quantity with the solution itself. This can be understood as a consequence of the fact that for any fixed time, the law of the solution is locally equivalent to Wiener measure, where space plays the role of time. In this sense, the correction term is similar to the usual Itô–Stratonovich correction term that arises when one considers different temporal discretizations of stochastic ODEs.}, author = {Hairer, Martin M and Jan Maas}, journal = {Annals of Probability}, number = {4}, pages = {1675 -- 1714}, publisher = {Institute of Mathematical Statistics}, title = {{A spatial version of the Itô-Stratonovich correction}}, doi = {10.1214/11-AOP662}, volume = {40}, year = {2012}, } @article{2127, abstract = {We study a new notion of Ricci curvature that applies to Markov chains on discrete spaces. This notion relies on geodesic convexity of the entropy and is analogous to the one introduced by Lott, Sturm, and Villani for geodesic measure spaces. In order to apply to the discrete setting, the role of the Wasserstein metric is taken over by a different metric, having the property that continuous time Markov chains are gradient flows of the entropy. Using this notion of Ricci curvature we prove discrete analogues of fundamental results by Bakry–Émery and Otto–Villani. Further, we show that Ricci curvature bounds are preserved under tensorisation. As a special case we obtain the sharp Ricci curvature lower bound for the discrete hypercube.}, author = {Erbar, Matthias and Jan Maas}, journal = {Archive for Rational Mechanics and Analysis}, number = {3}, pages = {997 -- 1038}, publisher = {Springer}, title = {{Ricci curvature of finite Markov chains via convexity of the entropy}}, doi = {10.1007/s00205-012-0554-z}, volume = {206}, year = {2012}, } @article{2128, abstract = {We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein.}, author = {Jan Maas and van Neerven, Jan M and Portal, Pierre}, journal = {Arkiv för Matematik}, number = {2}, pages = {379 -- 395}, publisher = {Springer}, title = {{Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure}}, doi = {10.1007/s11512-010-0143-z}, volume = {50}, year = {2012}, } @article{2201, abstract = {We study the growth dynamics of ordered structures of strongly interacting polar molecules in optical lattices. Using a dipole blockade of microwave excitations, we map the system onto an interacting spin-1/2 model possessing ground states with crystalline order, and describe a way to prepare these states by nonadiabatically driving the transitions between molecular rotational levels. The proposed technique bypasses the need to cross a phase transition and allows for the creation of ordered domains of considerably larger size compared to approaches relying on adiabatic preparation.}, author = {Lemeshko, Mikhail and Krems, Roman and Weimer, Hendrik}, journal = {Physical Review Letters}, number = {3}, publisher = {American Physical Society}, title = {{Nonadiabatic preparation of spin crystals with ultracold polar molecules}}, doi = {10.1103/PhysRevLett.109.035301}, volume = {109}, year = {2012}, } @article{2202, abstract = {We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold 87Rb atoms by Böhi, the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime.}, author = {Alyabyshev, Sergey V and Mikhail Lemeshko and Krems, Roman V}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {1}, publisher = {American Physical Society}, title = {{Sensitive imaging of electromagnetic fields with paramagnetic polar molecules}}, doi = {10.1103/PhysRevA.86.013409}, volume = {86}, year = {2012}, } @article{2203, abstract = {We show that the electric dipole-dipole interaction between a pair of polar molecules undergoes an all-out transformation when superimposed by a far-off-resonant optical field. The combined interaction potential becomes tunable by variation of wavelength, polarisation and intensity of the optical field and its dependence on the intermolecular separation exhibits a crossover from an inverse-power to an oscillating behaviour. The ability thereby offered to control molecular interactions opens up avenues toward the creation and manipulation of novel phases of ultracold polar gases among whose characteristics is a long-range entanglement of the dipoles' mutual orientation. We devised an accurate analytic model of such optical-field-dressed dipole-dipole interaction potentials, which enables a straightforward access to the optical-field parameters required for the design of intermolecular interactions in the laboratory.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Molecular Physics}, number = {15-16}, pages = {1873 -- 1881}, publisher = {Taylor & Francis}, title = {{Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other}}, doi = {10.1080/00268976.2012.689868}, volume = {110}, year = {2012}, } @article{2263, abstract = {Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.}, author = {Liang, Huixuan and Hippenmeyer, Simon and Ghashghaei, H.}, journal = {Biology open}, number = {12}, pages = {1200 -- 1203}, publisher = {The Company of Biologists}, title = {{A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors}}, doi = {10.1242/bio.20122287}, volume = {1}, year = {2012}, } @inproceedings{2267, abstract = {Capturing real-world objects with laser-scanning technology has become an everyday task. Recently, the acquisition of dynamic scenes at interactive frame rates has become feasible. A high-quality visualization of the resulting point cloud stream would require a per-frame reconstruction of object surfaces. Unfortunately, reconstruction computations are still too time-consuming to be applied interactively. In this paper we present a local surface reconstruction and visualization technique that provides interactive feedback for reasonably sized point clouds, while achieving high image quality. Our method is performed entirely on the GPU and in screen pace, exploiting the efficiency of the common rasterization pipeline. The approach is very general, as no assumption is made about point connectivity or sampling density. This naturally allows combining the outputs of multiple scanners in a single visualization, which is useful for many virtual and augmented reality applications. }, author = {Preiner, Reinhold and Jeschke, Stefan and Wimmer, Michael}, location = {Calgari, Italy}, pages = {139 -- 148}, publisher = {Eurographics Association}, title = {{Auto splats: Dynamic point cloud visualization on the GPU}}, doi = {10.2312/EGPGV/EGPGV12/139-148}, year = {2012}, }