@article{1294,
  abstract     = {We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints.},
  author       = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín},
  journal      = {Journal of Computer and System Sciences},
  pages        = {144 -- 170},
  publisher    = {Elsevier},
  title        = {{Trading performance for stability in Markov decision processes}},
  doi          = {10.1016/j.jcss.2016.09.009},
  volume       = {84},
  year         = {2017},
}

@misc{9707,
  abstract     = {Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.},
  author       = {Riccio, Paul and Cebrián, Christina and Zong, Hui and Hippenmeyer, Simon and Costantini, Frank},
  publisher    = {Dryad},
  title        = {{Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis}},
  doi          = {10.5061/dryad.pk16b},
  year         = {2017},
}

@misc{9709,
  abstract     = {Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.},
  author       = {Prentice, Jason and Marre, Olivier and Ioffe, Mark and Loback, Adrianna and Tkačik, Gašper and Berry, Michael},
  publisher    = {Dryad},
  title        = {{Data from: Error-robust modes of the retinal population code}},
  doi          = {10.5061/dryad.1f1rc},
  year         = {2017},
}

@misc{9842,
  abstract     = {Mathematica notebooks used to generate figures.},
  author       = {Etheridge, Alison and Barton, Nicholas H},
  publisher    = {Mendeley Data},
  title        = {{Data for: Establishment in a new habitat by polygenic adaptation}},
  doi          = {10.17632/nw68fxzjpm.1},
  year         = {2017},
}

@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},
}