@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{2281,
  abstract     = {We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential.},
  author       = {Guo, Yujin and Seiringer, Robert},
  journal      = {Letters in Mathematical Physics},
  number       = {2},
  pages        = {141 -- 156},
  publisher    = {Springer},
  title        = {{On the mass concentration for Bose-Einstein condensates with attractive interactions}},
  doi          = {10.1007/s11005-013-0667-9},
  volume       = {104},
  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{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},
}

@article{2852,
  abstract     = {A robust combiner for hash functions takes two candidate implementations and constructs a hash function which is secure as long as at least one of the candidates is secure. So far, hash function combiners only aim at preserving a single property such as collision-resistance or pseudorandomness. However, when hash functions are used in protocols like TLS they are often required to provide several properties simultaneously. We therefore put forward the notion of robust multi-property combiners and elaborate on different definitions for such combiners. We then propose a combiner that provably preserves (target) collision-resistance, pseudorandomness, and being a secure message authentication code. This combiner satisfies the strongest notion we propose, which requires that the combined function satisfies every security property which is satisfied by at least one of the underlying hash function. If the underlying hash functions have output length n, the combiner has output length 2 n. This basically matches a known lower bound for black-box combiners for collision-resistance only, thus the other properties can be achieved without penalizing the length of the hash values. We then propose a combiner which also preserves the property of being indifferentiable from a random oracle, slightly increasing the output length to 2 n+ω(log n). Moreover, we show how to augment our constructions in order to make them also robust for the one-wayness property, but in this case require an a priory upper bound on the input length.},
  author       = {Fischlin, Marc and Lehmann, Anja and Pietrzak, Krzysztof Z},
  journal      = {Journal of Cryptology},
  number       = {3},
  pages        = {397 -- 428},
  publisher    = {Springer},
  title        = {{Robust multi-property combiners for hash functions}},
  doi          = {10.1007/s00145-013-9148-7},
  volume       = {27},
  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{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},
}

@inbook{10817,
  abstract     = {The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption.},
  author       = {Günther, David and Reininghaus, Jan and Seidel, Hans-Peter and Weinkauf, Tino},
  booktitle    = {Topological Methods in Data Analysis and Visualization III.},
  editor       = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald},
  isbn         = {9783319040981},
  issn         = {2197-666X},
  pages        = {135--150},
  publisher    = {Springer Nature},
  title        = {{Notes on the simplification of the Morse-Smale complex}},
  doi          = {10.1007/978-3-319-04099-8_9},
  year         = {2014},
}

@inproceedings{10884,
  abstract     = {We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL  ∗ \X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL  ∗ \X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \X, provided processes cannot choose the directions for sending or receiving the token.
We unify and substantially extend these results by systematically exploring fragments of indexed CTL  ∗ \X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token.},
  author       = {Aminof, Benjamin and Jacobs, Swen and Khalimov, Ayrat and Rubin, Sasha},
  booktitle    = {Verification, Model Checking, and Abstract Interpretation},
  isbn         = {9783642540127},
  issn         = {1611-3349},
  location     = {San Diego, CA, United States},
  pages        = {262--281},
  publisher    = {Springer Nature},
  title        = {{Parameterized model checking of token-passing systems}},
  doi          = {10.1007/978-3-642-54013-4_15},
  volume       = {8318},
  year         = {2014},
}

@inproceedings{10885,
  abstract     = {Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.
In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.
We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games.},
  author       = {Chatterjee, Krishnendu and Doyen, Laurent and Filiot, Emmanuel and Raskin, Jean-François},
  booktitle    = {VMCAI 2014: Verification, Model Checking, and Abstract Interpretation},
  isbn         = {9783642540127},
  issn         = {1611-3349},
  location     = {San Diego, CA, United States},
  pages        = {78--97},
  publisher    = {Springer Nature},
  title        = {{Doomsday equilibria for omega-regular games}},
  doi          = {10.1007/978-3-642-54013-4_5},
  volume       = {8318},
  year         = {2014},
}

@inproceedings{10886,
  abstract     = {We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set.},
  author       = {Zobel, Valentin and Reininghaus, Jan and Hotz, Ingrid},
  booktitle    = {Topological Methods in Data Analysis and Visualization III },
  isbn         = {9783319040981},
  issn         = {2197-666X},
  pages        = {249--262},
  publisher    = {Springer},
  title        = {{Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature}},
  doi          = {10.1007/978-3-319-04099-8_16},
  year         = {2014},
}

@inproceedings{10892,
  abstract     = {In this paper, we introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist.
Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.},
  author       = {Biedl, Therese and Huber, Stefan and Palfrader, Peter},
  booktitle    = {25th International Symposium, ISAAC 2014},
  isbn         = {9783319130743},
  issn         = {1611-3349},
  location     = {Jeonju, Korea},
  pages        = {117--127},
  publisher    = {Springer Nature},
  title        = {{Planar matchings for weighted straight skeletons}},
  doi          = {10.1007/978-3-319-13075-0_10},
  volume       = {8889},
  year         = {2014},
}

@inbook{10893,
  abstract     = {Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data.},
  author       = {Kasten, Jens and Reininghaus, Jan and Reich, Wieland and Scheuermann, Gerik},
  booktitle    = {Topological Methods in Data Analysis and Visualization III },
  editor       = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald},
  isbn         = {9783319040981},
  issn         = {2197-666X},
  pages        = {55--69},
  publisher    = {Springer},
  title        = {{Toward the extraction of saddle periodic orbits}},
  doi          = {10.1007/978-3-319-04099-8_4},
  volume       = {1},
  year         = {2014},
}

@inproceedings{10894,
  abstract     = {PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations.},
  author       = {Bauer, Ulrich and Kerber, Michael and Reininghaus, Jan and Wagner, Hubert},
  booktitle    = {ICMS 2014: International Congress on Mathematical Software},
  isbn         = {9783662441985},
  issn         = {1611-3349},
  location     = {Seoul, South Korea},
  pages        = {137--143},
  publisher    = {Springer Berlin Heidelberg},
  title        = {{PHAT – Persistent Homology Algorithms Toolbox}},
  doi          = {10.1007/978-3-662-44199-2_24},
  volume       = {8592},
  year         = {2014},
}

@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{828,
  abstract     = {The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.},
  author       = {Cuesta, Candela and Wabnik, Krzysztof T and Benková, Eva},
  journal      = {Frontiers in Plant Science},
  publisher    = {Frontiers Research Foundation},
  title        = {{Systems approaches to study root architecture dynamics}},
  doi          = {10.3389/fpls.2013.00537},
  volume       = {4},
  year         = {2013},
}

@inproceedings{2000,
  abstract     = {In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.},
  author       = {Reiter, Johannes and Božić, Ivana and Chatterjee, Krishnendu and Nowak, Martin},
  booktitle    = {Proceedings of 25th Int. Conf. on Computer Aided Verification},
  location     = {St. Petersburg, Russia},
  pages        = {101 -- 106},
  publisher    = {Springer},
  title        = {{TTP: Tool for tumor progression}},
  doi          = {10.1007/978-3-642-39799-8_6},
  volume       = {8044},
  year         = {2013},
}