@misc{9844, author = {Nikolic, Nela and Schreiber, Frank and Dal Co, Alma and Kiviet, Daniel and Bergmiller, Tobias and Littmann, Sten and Kuypers, Marcel and Ackermann, Martin}, publisher = {Public Library of Science}, title = {{Source data for figures and tables}}, doi = {10.1371/journal.pgen.1007122.s018}, year = {2017}, } @misc{9845, abstract = {Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured in single cells}, author = {Nikolic, Nela and Schreiber, Frank and Dal Co, Alma and Kiviet, Daniel and Bergmiller, Tobias and Littmann, Sten and Kuypers, Marcel and Ackermann, Martin}, publisher = {Public Library of Science}, title = {{Mathematical model}}, doi = {10.1371/journal.pgen.1007122.s017}, year = {2017}, } @misc{9846, author = {Nikolic, Nela and Schreiber, Frank and Dal Co, Alma and Kiviet, Daniel and Bergmiller, Tobias and Littmann, Sten and Kuypers, Marcel and Ackermann, Martin}, publisher = {Public Library of Science}, title = {{Supplementary methods}}, doi = {10.1371/journal.pgen.1007122.s016}, year = {2017}, } @misc{9847, abstract = {information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data}, author = {Pleska, Maros and Guet, Calin C}, publisher = {The Royal Society}, title = {{Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification}}, doi = {10.6084/m9.figshare.5633917.v1}, year = {2017}, } @misc{9849, abstract = {This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set.}, author = {Lukacisinova, Marta and Novak, Sebastian and Paixao, Tiago}, publisher = {Public Library of Science}, title = {{Modelling and simulation details}}, doi = {10.1371/journal.pcbi.1005609.s001}, year = {2017}, } @misc{9850, abstract = {In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model.}, author = {Lukacisinova, Marta and Novak, Sebastian and Paixao, Tiago}, publisher = {Public Library of Science}, title = {{Extensions of the model}}, doi = {10.1371/journal.pcbi.1005609.s002}, year = {2017}, } @misc{9851, abstract = {Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations.}, author = {Lukacisinova, Marta and Novak, Sebastian and Paixao, Tiago}, publisher = {Public Library of Science}, title = {{Heuristic prediction for multiple stresses}}, doi = {10.1371/journal.pcbi.1005609.s003}, year = {2017}, } @misc{9852, abstract = {We show how different combination strategies affect the fraction of individuals that are multi-resistant.}, author = {Lukacisinova, Marta and Novak, Sebastian and Paixao, Tiago}, publisher = {Public Library of Science}, title = {{Resistance frequencies for different combination strategies}}, doi = {10.1371/journal.pcbi.1005609.s004}, year = {2017}, } @misc{9853, abstract = {Egg laying rates and infection loads of C. obscurior queens}, author = {Giehr, Julia and Grasse, Anna V and Cremer, Sylvia and Heinze, Jürgen and Schrempf, Alexandra}, publisher = {The Royal Society}, title = {{Raw data from ant queens increase their reproductive efforts after pathogen infection}}, doi = {10.6084/m9.figshare.5117788.v1}, year = {2017}, } @misc{9855, abstract = {Includes derivation of optimal estimation algorithm, generalisation to non-poisson noise statistics, correlated input noise, and implementation of in a multi-layer neural network.}, author = {Chalk, Matthew J and Masset, Paul and Gutkin, Boris and Denève, Sophie}, publisher = {Public Library of Science}, title = {{Supplementary appendix}}, doi = {10.1371/journal.pcbi.1005582.s001}, year = {2017}, } @misc{9856, author = {Schmidt, Tom and Barton, Nicholas H and Rasic, Gordana and Turley, Andrew and Montgomery, Brian and Iturbe Ormaetxe, Inaki and Cook, Peter and Ryan, Peter and Ritchie, Scott and Hoffmann, Ary and O’Neill, Scott and Turelli, Michael}, publisher = {Public Library of Science}, title = {{Supporting Information concerning additional likelihood analyses and results}}, doi = {10.1371/journal.pbio.2001894.s014}, year = {2017}, } @misc{9857, author = {Schmidt, Tom and Barton, Nicholas H and Rasic, Gordana and Turley, Andrew and Montgomery, Brian and Iturbe Ormaetxe, Inaki and Cook, Peter and Ryan, Peter and Ritchie, Scott and Hoffmann, Ary and O’Neill, Scott and Turelli, Michael}, publisher = {Public Library of Science }, title = {{Supporting information concerning observed wMel frequencies and analyses of habitat variables}}, doi = {10.1371/journal.pbio.2001894.s015}, year = {2017}, } @misc{9858, author = {Schmidt, Tom and Barton, Nicholas H and Rasic, Gordana and Turley, Andrew and Montgomery, Brian and Iturbe Ormaetxe, Inaki and Cook, Peter and Ryan, Peter and Ritchie, Scott and Hoffmann, Ary and O’Neill, Scott and Turelli, Michael}, publisher = {Public Library of Science}, title = {{Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics}}, doi = {10.1371/journal.pbio.2001894.s016}, year = {2017}, } @misc{9859, abstract = {Lists of all differentially expressed genes in the different priming-challenge treatments (compared to the fully naïve control; xlsx file). Relevant columns include the following: sample_1 and sample_2 – treatment groups being compared; Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change) – log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated compared with sample 2, positive means sample 2 upregulated compared with sample 1; cuffdiff test_statistic – test statistic of differential expression test; p_value – p-value of differential expression test; q_value (FDR correction) – adjusted P-value of differential expression test. (XLSX 598 kb)}, author = {Greenwood, Jenny and Milutinovic, Barbara and Peuß, Robert and Behrens, Sarah and Essar, Daniela and Rosenstiel, Philip and Schulenburg, Hinrich and Kurtz, Joachim}, publisher = {Springer Nature}, title = {{Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae}}, doi = {10.6084/m9.figshare.c.3756974_d1.v1}, year = {2017}, } @misc{9860, author = {Greenwood, Jenny and Milutinovic, Barbara and Peuß, Robert and Behrens, Sarah and Essar, Daniela and Rosenstiel, Philip and Schulenburg, Hinrich and Kurtz, Joachim}, publisher = {Springer Nature}, title = {{Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae}}, doi = {10.6084/m9.figshare.c.3756974_d5.v1}, year = {2017}, } @misc{9861, abstract = {As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.}, author = {Argyridou, Eliza and Huylmans, Ann K and Königer, Annabella and Parsch, John}, publisher = {Dryad}, title = {{Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster}}, doi = {10.5061/dryad.02f6r}, year = {2017}, } @article{988, abstract = {The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement.}, author = {Nanda, Gaurav and Aguilera Servin, Juan L and Rakyta, Péter and Kormányos, Andor and Kleiner, Reinhold and Koelle, Dieter and Watanabe, Kazuo and Taniguchi, Takashi and Vandersypen, Lieven and Goswami, Srijit}, issn = {1530-6984}, journal = {Nano Letters}, number = {6}, pages = {3396 -- 3401}, publisher = {American Chemical Society}, title = {{Current-phase relation of ballistic graphene Josephson junctions}}, doi = {10.1021/acs.nanolett.7b00097}, volume = {17}, year = {2017}, } @article{990, abstract = {Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.}, author = {Sachdeva, Himani and Barton, Nicholas H}, issn = {0014-3820}, journal = {Evolution; International Journal of Organic Evolution}, number = {6}, pages = {1478 -- 1493 }, publisher = {Wiley-Blackwell}, title = {{Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow}}, doi = {10.1111/evo.13252}, volume = {71}, year = {2017}, } @article{993, abstract = {In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development.}, author = {Levina (Martius), Anna and Priesemann, Viola}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Subsampling scaling}}, doi = {10.1038/ncomms15140}, volume = {8}, year = {2017}, } @article{994, abstract = {The formation of vortices is usually considered to be the main mechanism of angular momentum disposal in superfluids. Recently, it was predicted that a superfluid can acquire angular momentum via an alternative, microscopic route -- namely, through interaction with rotating impurities, forming so-called `angulon quasiparticles' [Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to transfer of a small number of angular momentum quanta from the impurity to the superfluid, as opposed to vortex instabilities, where angular momentum is quantized in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules) represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically 3D as well, as opposed to a merely planar rotation which is inherent to vortices. Herein we show that the angulon theory can explain the anomalous broadening of the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities in experiment.}, author = {Cherepanov, Igor and Lemeshko, Mikhail}, journal = {Physical Review Materials}, number = {3}, publisher = {American Physical Society}, title = {{Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules}}, doi = {10.1103/PhysRevMaterials.1.035602}, volume = {1}, year = {2017}, }