@article{2261, abstract = {To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.}, author = {Zhu, Fangfang and Gamboa, Matthew and Farruggio, Alfonso and Hippenmeyer, Simon and Tasic, Bosiljka and Schüle, Birgitt and Chen Tsai, Yanru and Calos, Michele}, journal = {Nucleic Acids Research}, number = {5}, publisher = {Oxford University Press}, title = {{DICE, an efficient system for iterative genomic editing in human pluripotent stem cells}}, doi = {10.1093/nar/gkt1290}, volume = {42}, year = {2014}, } @inbook{2265, abstract = {Coordinated migration of newly-born neurons to their target territories is essential for correct neuronal circuit assembly in the developing brain. Although a cohort of signaling pathways has been implicated in the regulation of cortical projection neuron migration, the precise molecular mechanisms and how a balanced interplay of cell-autonomous and non-autonomous functions of candidate signaling molecules controls the discrete steps in the migration process, are just being revealed. In this chapter, I will focally review recent advances that improved our understanding of the cell-autonomous and possible cell-nonautonomous functions of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential steps of cortical projection neuron migration. I will then elaborate on the emerging concept that the Reelin signaling pathway, acts exactly at precise stages in the course of cortical projection neuron migration. Lastly, I will discuss how finely tuned transcriptional programs and downstream effectors govern particular aspects in driving radial migration at discrete stages and how they regulate the precise positioning of cortical projection neurons in the developing cerebral cortex.}, author = {Hippenmeyer, Simon}, booktitle = { Cellular and Molecular Control of Neuronal Migration}, editor = {Nguyen, Laurent}, pages = {1 -- 24}, publisher = {Springer}, title = {{Molecular pathways controlling the sequential steps of cortical projection neuron migration}}, doi = {10.1007/978-94-007-7687-6_1}, volume = {800}, year = {2014}, } @inproceedings{2275, abstract = {Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches. This partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed. Our main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach. }, author = {Olsson, Carl and Ulen, Johannes and Boykov, Yuri and Kolmogorov, Vladimir}, location = {Sydney, Australia}, pages = {2936 -- 2943}, publisher = {IEEE}, title = {{Partial enumeration and curvature regularization}}, doi = {10.1109/ICCV.2013.365}, year = {2014}, } @article{2285, abstract = {GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity.}, author = {Hosp, Jonas and Strüber, Michael and Yanagawa, Yuchio and Obata, Kunihiko and Vida, Imre and Jonas, Peter M and Bartos, Marlene}, journal = {Hippocampus}, number = {2}, pages = {189 -- 203}, publisher = {Wiley-Blackwell}, title = {{Morpho-physiological criteria divide dentate gyrus interneurons into classes}}, doi = {10.1002/hipo.22214}, volume = {23}, year = {2014}, } @article{2407, abstract = {Two definitions of the effective mass of a particle interacting with a quantum field, such as a polaron, are considered and shown to be equal in models similar to the Fröhlich polaron model. These are: 1. the mass defined by the low momentum energy E(P)≈E(0)+P2/2 M of the translation invariant system constrained to have momentum P and 2. the mass M of a simple particle in an arbitrary slowly varying external potential, V, described by the nonrelativistic Schrödinger equation, whose ground state energy equals that of the combined particle/field system in a bound state in the same V.}, author = {Lieb, Élliott and Seiringer, Robert}, journal = {Journal of Statistical Physics}, number = {1-2}, pages = {51 -- 57}, publisher = {Springer}, title = {{Equivalence of two definitions of the effective mass of a polaron}}, doi = {10.1007/s10955-013-0791-z}, volume = {154}, year = {2014}, } @article{248, abstract = {For any pencil of conics or higher-dimensional quadrics over ℚ, with all degenerate fibres defined over ℚ, we show that the Brauer–Manin obstruction controls weak approximation. The proof is based on the Hasse principle and weak approximation for some special intersections of quadrics over ℚ, which is a consequence of recent advances in additive combinatorics.}, author = {Timothy Browning and Matthiesen, Lilian and Skorobogatov, Alexei N}, journal = {Annals of Mathematics}, number = {1}, pages = {381 -- 402}, publisher = {John Hopkins University Press}, title = {{Rational points on pencils of conics and quadrics with many degenerate fibres}}, doi = {https://doi.org/10.4007/annals.2014.180.1.8}, volume = {180}, year = {2014}, } @article{249, abstract = {A version of the Hardy-Littlewood circle method is developed for number fields K/ℚ and is used to show that nonsingular projective cubic hypersurfaces over K always have a K-rational point when they have dimension at least 8. }, author = {Timothy Browning and Vishe, Pankaj}, journal = {Duke Mathematical Journal}, number = {10}, pages = {1825 -- 1883}, publisher = {Duke University Press}, title = {{Cubic hypersurfaces and a version of the circle method for number fields}}, doi = {10.1215/00127094-2738530}, volume = {163}, year = {2014}, } @article{252, abstract = {For any number field k, upper bounds are established for the number of k-rational points of bounded height on non-singular del Pezzo surfaces defined over k, which are equipped with suitable conic bundle structures over k.}, author = {Timothy Browning and Jones, Michael S}, journal = {Acta Arithmetica}, number = {3}, pages = {271 -- 298}, publisher = {Instytut Matematyczny}, title = {{Counting rational points on del Pezzo surfaces with a conic bundle structure}}, doi = {10.4064/aa163-3-6}, volume = {163}, year = {2014}, } @article{254, abstract = {A new "polynomial sieve" is presented and used to show that almost all integers have at most one representation as a sum of two values of a given polynomial of degree at least 3.}, author = {Timothy Browning}, journal = {International Mathematics Research Notices}, number = {7}, pages = {1987 -- 2019}, publisher = {Oxford University Press}, title = {{The polynomial sieve and equal sums of like polynomials}}, doi = {10.1093/imrn/rnt350}, volume = {2015}, year = {2014}, } @article{255, abstract = {We investigate the Hasse principle for complete intersections cut out by a quadric hypersurface and a cubic hypersurface defined over the rational numbers.}, author = {Browning, Timothy D and Dietmann, Rainer and Heath Brown, Roger}, journal = {Journal of the Institute of Mathematics of Jussieu}, number = {4}, pages = {703 -- 749}, publisher = {Cambridge University Press}, title = {{Rational points on intersections of cubic and quadric hypersurfaces}}, doi = {10.1017/S1474748014000127}, volume = {14}, year = {2014}, } @article{2699, abstract = {We prove the universality of the β-ensembles with convex analytic potentials and for any β > 0, i.e. we show that the spacing distributions of log-gases at any inverse temperature β coincide with those of the Gaussian β-ensembles.}, author = {Erdös, László and Bourgade, Paul and Yau, Horng}, journal = {Duke Mathematical Journal}, number = {6}, pages = {1127 -- 1190}, publisher = {Duke University Press}, title = {{Universality of general β-ensembles}}, doi = {10.1215/00127094-2649752}, volume = {163}, year = {2014}, } @article{2716, abstract = {Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω ω -regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on vector addition systems with states. Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts.}, author = {Chatterjee, Krishnendu and Randour, Mickael and Raskin, Jean}, journal = {Acta Informatica}, number = {3-4}, pages = {129 -- 163}, publisher = {Springer}, title = {{Strategy synthesis for multi-dimensional quantitative objectives}}, doi = {10.1007/s00236-013-0182-6}, volume = {51}, year = {2014}, } @inproceedings{2905, abstract = {Persistent homology is a recent grandchild of homology that has found use in science and engineering as well as in mathematics. This paper surveys the method as well as the applications, neglecting completeness in favor of highlighting ideas and directions.}, author = {Edelsbrunner, Herbert and Morozovy, Dmitriy}, location = {Kraków, Poland}, pages = {31 -- 50}, publisher = {European Mathematical Society Publishing House}, title = {{Persistent homology: Theory and practice}}, doi = {10.4171/120-1/3}, year = {2014}, } @article{1733, abstract = {The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces, and how to synthesize an interface from incompatible requirements. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies.}, author = {Cerny, Pavol and Chmelik, Martin and Henzinger, Thomas A and Radhakrishna, Arjun}, journal = {Theoretical Computer Science}, number = {3}, pages = {348 -- 363}, publisher = {Elsevier}, title = {{Interface simulation distances}}, doi = {10.1016/j.tcs.2014.08.019}, volume = {560}, year = {2014}, } @article{2141, abstract = {The computation of the winning set for Büchi objectives in alternating games on graphs is a central problem in computer-aided verification with a large number of applications. The long-standing best known upper bound for solving the problem is Õ(n ⋅ m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n ⋅ m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2)-time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n ⋅ m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m>n4/3 an earlier bound of O(m ⋅ √m)). We then show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. Our algorithms are the first dynamic algorithms for this problem. We then consider another core graph theoretic problem in verification of probabilistic systems, namely computing the maximal end-component decomposition of a graph. We present two improved static algorithms for the maximal end-component decomposition problem. Our first algorithm is an O(m ⋅ √m)-time algorithm, and our second algorithm is an O(n2)-time algorithm which is obtained using the same technique as for alternating Büchi games. Thus, we obtain an O(min &lcu;m ⋅ √m,n2})-time algorithm improving the long-standing O(n ⋅ m) time bound. Finally, we show how to maintain the maximal end-component decomposition of a graph under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per edge deletion, and O(m) worst-case time per edge insertion. Again, our algorithms are the first dynamic algorithms for this problem.}, author = {Chatterjee, Krishnendu and Henzinger, Monika H}, journal = {Journal of the ACM}, number = {3}, publisher = {ACM}, title = {{Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition}}, doi = {10.1145/2597631}, volume = {61}, year = {2014}, } @article{3263, abstract = {Adaptation in the retina is thought to optimize the encoding of natural light signals into sequences of spikes sent to the brain. While adaptive changes in retinal processing to the variations of the mean luminance level and second-order stimulus statistics have been documented before, no such measurements have been performed when higher-order moments of the light distribution change. We therefore measured the ganglion cell responses in the tiger salamander retina to controlled changes in the second (contrast), third (skew) and fourth (kurtosis) moments of the light intensity distribution of spatially uniform temporally independent stimuli. The skew and kurtosis of the stimuli were chosen to cover the range observed in natural scenes. We quantified adaptation in ganglion cells by studying linear-nonlinear models that capture well the retinal encoding properties across all stimuli. We found that the encoding properties of retinal ganglion cells change only marginally when higher-order statistics change, compared to the changes observed in response to the variation in contrast. By analyzing optimal coding in LN-type models, we showed that neurons can maintain a high information rate without large dynamic adaptation to changes in skew or kurtosis. This is because, for uncorrelated stimuli, spatio-temporal summation within the receptive field averages away non-gaussian aspects of the light intensity distribution.}, author = {Tkacik, Gasper and Ghosh, Anandamohan and Schneidman, Elad and Segev, Ronen}, journal = {PLoS One}, number = {1}, publisher = {Public Library of Science}, title = {{Adaptation to changes in higher-order stimulus statistics in the salamander retina}}, doi = {10.1371/journal.pone.0085841}, volume = {9}, year = {2014}, } @article{332, abstract = {Cu2ZnSnS4, based on abundant and environmental friendly elements and with a direct band gap of 1.5 eV, is a main candidate material for solar energy conversion through both photovoltaics and photocatalysis. We detail here the synthesis of quasi-spherical Cu 2ZnSnS4 nanoparticles with unprecedented narrow size distributions. We further detail their use as seeds to produce CZTS-Au and CZTS-Pt heterostructured nanoparticles. Such heterostructured nanoparticles are shown to have excellent photocatalytic properties toward degradation of Rhodamine B and hydrogen generation by water splitting. }, author = {Yu, Xuelian and Shavel, Alexey and An, Xiaoqiang and Luo, Zhishan and Ibáñez, Maria and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {26}, pages = {9236 -- 9239}, publisher = {ACS}, title = {{Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation}}, doi = {10.1021/ja502076b}, volume = {136}, year = {2014}, } @inproceedings{2054, abstract = {We study two-player concurrent games on finite-state graphs played for an infinite number of rounds, where in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. The objectives are ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). While the qualitative analysis problem for concurrent parity games with infinite-memory, infinite-precision randomized strategies was studied before, we study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies. In terms of precision, strategies can be deterministic, uniform, finite-precision, or infinite-precision; and in terms of memory, strategies can be memoryless, finite-memory, or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies. We show that the winning sets can be computed in (n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. Our symbolic algorithms are based on a characterization of the winning sets as μ-calculus formulas, however, our μ-calculus formulas are crucially different from the ones for concurrent parity games (without bounded rationality); and our memoryless witness strategy constructions are significantly different from the infinite-memory witness strategy constructions for concurrent parity games.}, author = {Chatterjee, Krishnendu}, booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}, editor = {Baldan, Paolo and Gorla, Daniele}, location = {Rome, Italy}, pages = {544 -- 559}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Qualitative concurrent parity games: Bounded rationality}}, doi = {10.1007/978-3-662-44584-6_37}, volume = {8704}, year = {2014}, } @article{349, abstract = {Thermoelectricity is a key technology with the potential to improve the efficiency of energy conversion processes, which may strongly benefit from advances in the field of nanotechnology. Nanostructured materials are very appealing for thermoelectric applications, but the full development of their potential requires precise control of their properties at the nanoscale. Bottom-up assembly of nanoparticles provides access to a three-dimensional composition control at the nanoscale not attainable in any other technology. In particular, colloidal nanoheterostructures are especially interesting building blocks for the bottom-up production of functional nanomaterials. In the present work, we use PbTe@PbS core-shell nanoparticles as building blocks for the bottom-up production of PbTe-PbS nanocomposites. We used a ligand exchange strategy and a hot press process to promote the electrical conductivity of the nanocomposite and to increase its density. These two approaches allowed us to improve the performance of bottom-up assembled PbTe-PbS bulk nanostructured materials. }, author = {Ortega, Silvia and Ibáñez, Maria and Cadavid, Doris and Cabot, Andreu}, journal = {International Journal of Nanotechnology}, number = {9-11}, pages = {955 -- 970}, publisher = {Inderscience Enterprises Limited }, title = {{Bottom up processing of PbTe PbS thermoelectric nanocomposites}}, doi = {10.1504/IJNT.2014.063802}, volume = {11}, year = {2014}, } @article{355, abstract = {We report on the photocatalytic hydrogen evolution under full-arc light irradiation of CuIn1-xGaxS2 wurtzite nanocrystals in the presence of SO3 2- and S2- as sacrificial reagents. We analyzed the hydrogen generation rate as a function of the Ga content and associated it with the energy band positions. For photocatalytic water splitting, the CuInS2 bandgap is slightly too low to efficiently overcome the reaction over-potential. The presence of Ga shifts up the CuInS2 conduction band edge providing a larger driving force for photogenerated carriers to activate the water splitting reduction reaction. The larger the Ga content, the more energetically favorable the electron injection, and thus a more efficient use of the photogenerated carriers is reached. However, the band gap increase associated with the Ga incorporation reduces the concentration of photogenerated carriers available for water splitting, and consequently a lower hydrogen conversion rate is obtained for very high Ga contents. The optimum Ga concentration was experimentally found at CuIn0.3Ga0.7S2. }, author = {Yu, Xuelian and An, Xiaoqiang and Shavel, Alexey and Ibáñez, Maria and Cabot, Andreu}, journal = {Journal of Materials Chemistry A}, number = {31}, pages = {12317 -- 12322}, publisher = {Royal Society of Chemistry}, title = {{The effect of the Ga content on the photocatalytic hydrogen evolution of CuIn1-xGaxS2 nanocrystals}}, doi = {10.1039/c4ta01315h}, volume = {2}, year = {2014}, }