@article{9458,
  abstract     = {Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.},
  author       = {Huff, Jason T. and Zilberman, Daniel},
  issn         = {1097-4172},
  journal      = {Cell},
  number       = {6},
  pages        = {1286--1297},
  publisher    = {Elsevier},
  title        = {{Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes}},
  doi          = {10.1016/j.cell.2014.01.029},
  volume       = {156},
  year         = {2014},
}

@article{9479,
  abstract     = {Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.},
  author       = {Mérai, Zsuzsanna and Chumak, Nina and García-Aguilar, Marcelina and Hsieh, Tzung-Fu and Nishimura, Toshiro and Schoft, Vera K. and Bindics, János and Ślusarz, Lucyna and Arnoux, Stéphanie and Opravil, Susanne and Mechtler, Karl and Zilberman, Daniel and Fischer, Robert L. and Tamaru, Hisashi},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {45},
  pages        = {16166--16171},
  publisher    = {National Academy of Sciences},
  title        = {{The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes}},
  doi          = {10.1073/pnas.1418564111},
  volume       = {111},
  year         = {2014},
}

@article{9519,
  abstract     = {Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression.},
  author       = {Kim, M. Yvonne and Zilberman, Daniel},
  issn         = {1878-4372},
  journal      = {Trends in Plant Science},
  number       = {5},
  pages        = {320--326},
  publisher    = {Elsevier},
  title        = {{DNA methylation as a system of plant genomic immunity}},
  doi          = {10.1016/j.tplants.2014.01.014},
  volume       = {19},
  year         = {2014},
}

@misc{9722,
  author       = {Lovrics, Anna and Gao, Yu and Juhász, Bianka and Bock, István and Byrne, Helen M. and Dinnyés, András and Kovács, Krisztián},
  publisher    = {Public Library of Science},
  title        = {{Transition probability between TF expression states when Dbx2 inhibits Nkx2.2}},
  doi          = {10.1371/journal.pone.0111430.s006},
  year         = {2014},
}

@misc{9739,
  author       = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Adlam, Ben and Novak, Martin},
  publisher    = {Public Library of Science},
  title        = {{Detailed proofs for “The time scale of evolutionary innovation”}},
  doi          = {10.1371/journal.pcbi.1003818.s001},
  year         = {2014},
}

@misc{9740,
  abstract     = {The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.},
  author       = {Konrad, Matthias and Grasse, Anna V and Tragust, Simon and Cremer, Sylvia},
  publisher    = {Dryad},
  title        = {{Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host}},
  doi          = {10.5061/dryad.vm0vc},
  year         = {2014},
}

@misc{9747,
  abstract     = {Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.},
  author       = {Lagator, Mato and Morgan, Andrew and Neve, Paul and Colegrave, Nick},
  publisher    = {Dryad},
  title        = {{Data from: Role of sex and migration in adaptation to sink environments}},
  doi          = {10.5061/dryad.s42n1},
  year         = {2014},
}

@misc{9752,
  abstract     = {Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.},
  author       = {Simmons, Kristina and Prentice, Jason and Tkačik, Gašper and Homann, Jan and Yee, Heather and Palmer, Stephanie and Nelson, Philip and Balasubramanian, Vijay},
  publisher    = {Dryad},
  title        = {{Data from: Transformation of stimulus correlations by the retina}},
  doi          = {10.5061/dryad.246qg},
  year         = {2014},
}

@book{6853,
  abstract     = {This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.},
  author       = {Edelsbrunner, Herbert},
  isbn         = {9-783-3190-5956-3},
  issn         = {2191-5318},
  pages        = {IX, 110},
  publisher    = {Springer Nature},
  title        = {{A Short Course in Computational Geometry and Topology}},
  doi          = {10.1007/978-3-319-05957-0},
  year         = {2014},
}

@techreport{7038,
  author       = {Huszár, Kristóf and Rolinek, Michal},
  pages        = {5},
  publisher    = {IST Austria},
  title        = {{Playful Math - An introduction to mathematical games}},
  year         = {2014},
}

@misc{9888,
  abstract     = {Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results.},
  author       = {Wolf, Stephan and Mcmahon, Dino and Lim, Ka and Pull, Christopher and Clark, Suzanne and Paxton, Robert and Osborne, Juliet},
  publisher    = {Public Library of Science},
  title        = {{Supporting information}},
  doi          = {10.1371/journal.pone.0103989.s003},
  year         = {2014},
}

@article{9931,
  abstract     = {Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.},
  author       = {Dhar, Riddhiman and Bergmiller, Tobias and Wagner, Andreas},
  issn         = {1558-5646},
  journal      = {Evolution},
  number       = {6},
  pages        = {1775--1791},
  publisher    = {Wiley},
  title        = {{Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes}},
  doi          = {10.1111/evo.12373},
  volume       = {68},
  year         = {2014},
}

@misc{9932,
  abstract     = {Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.},
  author       = {Dhar, Riddhiman and Bergmiller, Tobias and Wagner, Andreas},
  publisher    = {Dryad},
  title        = {{Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes}},
  doi          = {10.5061/dryad.jc402},
  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{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},
}

@inbook{1806,
  abstract     = {The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants.},
  author       = {Baster, Pawel and Friml, Jiří},
  booktitle    = {Auxin and Its Role in Plant Development},
  editor       = {Zažímalová, Eva and Petrášek, Jan and Benková, Eva},
  pages        = {143 -- 170},
  publisher    = {Springer},
  title        = {{Auxin on the road navigated by cellular PIN polarity}},
  doi          = {10.1007/978-3-7091-1526-8_8},
  year         = {2014},
}

@article{1816,
  abstract     = {Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques.},
  author       = {Huber, Stefan and Held, Martin and Meerwald, Peter and Kwitt, Roland},
  journal      = {International Journal of Computational Geometry and Applications},
  number       = {1},
  pages        = {61 -- 86},
  publisher    = {World Scientific Publishing},
  title        = {{Topology-preserving watermarking of vector graphics}},
  doi          = {10.1142/S0218195914500034},
  volume       = {24},
  year         = {2014},
}

@inbook{1829,
  abstract     = {Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements.},
  author       = {Muelling, Katharina and Kroemer, Oliver and Lampert, Christoph and Schölkopf, Bernhard},
  booktitle    = {Learning Motor Skills},
  editor       = {Kober, Jens and Peters, Jan},
  pages        = {69 -- 82},
  publisher    = {Springer},
  title        = {{Movement templates for learning of hitting and batting}},
  doi          = {10.1007/978-3-319-03194-1_3},
  volume       = {97},
  year         = {2014},
}

@article{1842,
  abstract     = {We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices.},
  author       = {Cibulka, Josef and Gao, Pu and Krcál, Marek and Valla, Tomáš and Valtr, Pavel},
  journal      = {Discrete & Computational Geometry},
  number       = {1},
  pages        = {64 -- 79},
  publisher    = {Springer},
  title        = {{On the geometric ramsey number of outerplanar graphs}},
  doi          = {10.1007/s00454-014-9646-x},
  volume       = {53},
  year         = {2014},
}

@article{1844,
  abstract     = {Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.},
  author       = {Risso, Valeria and Manssour Triedo, Fadia and Delgado Delgado, Asuncion and Arco, Rocio and Barroso Deljesús, Alicia and Inglés Prieto, Álvaro and Godoy Ruiz, Raquel and Gavira, Josè and Gaucher, Eric and Ibarra Molero, Beatriz and Sánchez Ruiz, Jose},
  journal      = {Molecular Biology and Evolution},
  number       = {2},
  pages        = {440 -- 455},
  publisher    = {Oxford University Press},
  title        = {{Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history}},
  doi          = {10.1093/molbev/msu312},
  volume       = {32},
  year         = {2014},
}