@inproceedings{962,
  abstract     = {We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance.},
  author       = {Trinh, Minh and Chu, Duc Hiep and Jaffar, Joxan},
  editor       = {Majumdar, Rupak and Kunčak, Viktor},
  issn         = {03029743},
  location     = {Heidelberg, Germany},
  pages        = {399 -- 418},
  publisher    = {Springer},
  title        = {{Model counting for recursively-defined strings}},
  doi          = {10.1007/978-3-319-63390-9_21},
  volume       = {10427},
  year         = {2017},
}

@inproceedings{963,
  abstract     = {Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. },
  author       = {Avni, Guy and Guha, Shibashis and Kupferman, Orna},
  issn         = {18688969},
  location     = {Aalborg, Denmark},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Timed network games with clocks}},
  doi          = {10.4230/LIPIcs.MFCS.2017.37},
  volume       = {83},
  year         = {2017},
}

@article{9660,
  abstract     = {In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.},
  author       = {Cheng, Bingqing and Tribello, Gareth A. and Ceriotti, Michele},
  issn         = {1089-7690},
  journal      = {The Journal of Chemical Physics},
  number       = {10},
  publisher    = {AIP Publishing},
  title        = {{The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit}},
  doi          = {10.1063/1.4997180},
  volume       = {147},
  year         = {2017},
}

@article{9661,
  abstract     = {Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this paper, we introduce a thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory.},
  author       = {Cheng, Bingqing and Ceriotti, Michele},
  issn         = {1089-7690},
  journal      = {The Journal of Chemical Physics},
  number       = {3},
  publisher    = {AIP Publishing},
  title        = {{Bridging the gap between atomistic and macroscopic models of homogeneous nucleation}},
  doi          = {10.1063/1.4973883},
  volume       = {146},
  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},
}