@article{1287, abstract = {A planar waveguide with an impedance boundary, composed of nonperfect metallic plates, and with passive or active dielectric filling, is considered. We show the possibility of selective mode guiding and amplification when a homogeneous pump is added to the dielectric and analyze differences in TE and TM mode propagation. Such a non-conservative system is also shown to feature exceptional points for specific and experimentally tunable parameters, which are described for a particular case of transparent dielectric.}, author = {Midya, Bikashkali and Konotop, Vladimir}, journal = {Optics Letters}, number = {20}, pages = {4621 -- 4624}, publisher = {Optica Publishing Group}, title = {{Modes and exceptional points in waveguides with impedance boundary conditions}}, doi = {10.1364/OL.41.004621}, volume = {41}, year = {2016}, } @article{1288, abstract = {Respiratory complex I transfers electrons from NADH to quinone, utilizing the reaction energy to translocate protons across the membrane. It is a key enzyme of the respiratory chain of many prokaryotic and most eukaryotic organisms. The reversible NADH oxidation reaction is facilitated in complex I by non-covalently bound flavin mononucleotide (FMN). Here we report that the catalytic activity of E. coli complex I with artificial electron acceptors potassium ferricyanide (FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar range in oxidized complex I to the nanomolar range in the NADH reduced enzyme, with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex I, rather than that of FMN, proved critical to the dissociation. Such dissociation is not observed with the T. thermophilus enzyme and our analysis suggests that the difference may be due to the unusually high redox potential of Fe-S cluster N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo by releasing FMN under highly reducing conditions.}, author = {Holt, Peter and Efremov, Rouslan and Nakamaru Ogiso, Eiko and Sazanov, Leonid A}, journal = {Biochimica et Biophysica Acta - Bioenergetics}, number = {11}, pages = {1777 -- 1785}, publisher = {Elsevier}, title = {{Reversible FMN dissociation from Escherichia coli respiratory complex I}}, doi = {10.1016/j.bbabio.2016.08.008}, volume = {1857}, year = {2016}, } @article{1289, abstract = {Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI) magnifying endoscopic (ME) images of the stomach, we combine methods from image processing, topology, geometry, and machine learning to classify patterns into three classes: oval, tubular and irregular. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.}, author = {Dunaeva, Olga and Edelsbrunner, Herbert and Lukyanov, Anton and Machin, Michael and Malkova, Daria and Kuvaev, Roman and Kashin, Sergey}, journal = {Pattern Recognition Letters}, number = {1}, pages = {13 -- 22}, publisher = {Elsevier}, title = {{The classification of endoscopy images with persistent homology}}, doi = {10.1016/j.patrec.2015.12.012}, volume = {83}, year = {2016}, } @article{1290, abstract = {We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.}, author = {Stone, Laura and Baym, Michael and Lieberman, Tami and Chait, Remy P and Clardy, Jon and Kishony, Roy}, journal = {Nature Chemical Biology}, number = {11}, pages = {902 -- 904}, publisher = {Nature Publishing Group}, title = {{Compounds that select against the tetracycline-resistance efflux pump}}, doi = {10.1038/nchembio.2176}, volume = {12}, year = {2016}, } @inproceedings{12903, author = {Schlögl, Alois and Stadlbauer, Stephan}, booktitle = {AHPC16 - Austrian HPC Meeting 2016}, location = {Grundlsee, Austria}, pages = {37}, publisher = {VSC - Vienna Scientific Cluster}, title = {{High performance computing at IST Austria: Modelling the human hippocampus}}, year = {2016}, } @article{1291, abstract = {We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p > 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity.}, author = {Giuliani, Alessandro and Seiringer, Robert}, journal = {Communications in Mathematical Physics}, number = {3}, pages = {983 -- 1007}, publisher = {Springer}, title = {{Periodic striped ground states in Ising models with competing interactions}}, doi = {10.1007/s00220-016-2665-0}, volume = {347}, year = {2016}, } @article{1292, abstract = {We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds.}, author = {Durst, Sebastian and Kegel, Marc and Klukas, Mirko D}, journal = {Acta Mathematica Hungarica}, number = {2}, pages = {441 -- 455}, publisher = {Springer}, title = {{Computing the Thurston–Bennequin invariant in open books}}, doi = {10.1007/s10474-016-0648-4}, volume = {150}, year = {2016}, } @article{1293, abstract = {For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.}, author = {Solus, Liam T and Uhler, Caroline and Yoshida, Ruriko}, journal = {Linear Algebra and Its Applications}, pages = {247 -- 275}, publisher = {Elsevier}, title = {{Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors}}, doi = {10.1016/j.laa.2016.07.026}, volume = {509}, year = {2016}, } @article{1295, abstract = {Voronoi diagrams and Delaunay triangulations have been extensively used to represent and compute geometric features of point configurations. We introduce a generalization to poset diagrams and poset complexes, which contain order-k and degree-k Voronoi diagrams and their duals as special cases. Extending a result of Aurenhammer from 1990, we show how to construct poset diagrams as weighted Voronoi diagrams of average balls.}, author = {Edelsbrunner, Herbert and Iglesias Ham, Mabel}, journal = {Electronic Notes in Discrete Mathematics}, pages = {169 -- 174}, publisher = {Elsevier}, title = {{Multiple covers with balls II: Weighted averages}}, doi = {10.1016/j.endm.2016.09.030}, volume = {54}, year = {2016}, } @misc{9704, abstract = {Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.}, author = {Mcmahon, Dino and Natsopoulou, Myrsini and Doublet, Vincent and Fürst, Matthias and Weging, Silvio and Brown, Mark and Gogol Döring, Andreas and Paxton, Robert}, publisher = {Dryad}, title = {{Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss}}, doi = {10.5061/dryad.cq7t1}, year = {2016}, } @misc{9710, abstract = {Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.}, author = {Barton, Nicholas H}, publisher = {Dryad}, title = {{Data from: How does epistasis influence the response to selection?}}, doi = {10.5061/dryad.s5s7r}, year = {2016}, } @misc{9720, abstract = {Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.}, author = {Mcmahon, Dino and Fürst, Matthias and Caspar, Jesicca and Theodorou, Panagiotis and Brown, Mark and Paxton, Robert}, publisher = {Dryad}, title = {{Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees}}, doi = {10.5061/dryad.4b565}, year = {2016}, } @misc{9862, author = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas}, publisher = {Public Library of Science}, title = {{Simulation study to test the robustness of ABC in face of recent times of divergence}}, doi = {10.1371/journal.pbio.2000234.s016}, year = {2016}, } @misc{9863, author = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas}, publisher = {Public Library of Science}, title = {{Accessions of surveyed individuals, geographic locations and summary statistics}}, doi = {10.1371/journal.pbio.2000234.s017}, year = {2016}, } @misc{9864, abstract = {Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.}, author = {Fernandes Redondo, Rodrigo A and de Vladar, Harold and Włodarski, Tomasz and Bollback, Jonathan P}, publisher = {The Royal Society}, title = {{Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family}}, doi = {10.6084/m9.figshare.4315652.v1}, year = {2016}, } @misc{9866, author = {Zagórski, Marcin P and Burda, Zdzisław and Wacław, Bartłomiej}, publisher = {Public Library of Science}, title = {{ZIP-archived directory containing all data and computer programs}}, doi = {10.1371/journal.pcbi.1005218.s009}, year = {2016}, } @misc{9867, abstract = {In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German.}, author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred}, publisher = {Public Library of Science}, title = {{Experimental game instructions}}, doi = {10.1371/journal.pone.0163867.s008}, year = {2016}, } @misc{9868, abstract = {The raw data file containing the experimental decisions of all our study subjects.}, author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred}, publisher = {Public Library of Science}, title = {{Experimental data}}, doi = {10.1371/journal.pone.0163867.s009}, year = {2016}, } @misc{9869, abstract = {A lower bound on the error of a positional estimator with limited positional information is derived.}, author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Error bound on an estimator of position}}, doi = {10.1371/journal.pone.0163628.s001}, year = {2016}, } @misc{9870, abstract = {The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined.}, author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Computation of positional information in an Ising model}}, doi = {10.1371/journal.pone.0163628.s002}, year = {2016}, }