@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},
}
@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},
}
@article{1199,
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},
journal = {Heredity},
pages = {96 -- 109},
publisher = {Nature Publishing Group},
title = {{How does epistasis influence the response to selection?}},
doi = {10.1038/hdy.2016.109},
volume = {118},
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},
}
@article{9574,
abstract = {Consider the sum X(ξ)=∑ni=1aiξi, where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x]. In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.},
author = {Bandeira, Afonso S. and Ferber, Asaf and Kwan, Matthew Alan},
issn = {1571-0653},
journal = {Electronic Notes in Discrete Mathematics},
pages = {93--99},
publisher = {Elsevier},
title = {{Resilience for the Littlewood-Offord problem}},
doi = {10.1016/j.endm.2017.06.025},
volume = {61},
year = {2017},
}
@article{9590,
abstract = {We show that for any fixed dense graph G and bounded-degree tree T on the same number of vertices, a modest random perturbation of G will typically contain a copy of T . This combines the viewpoints of the well-studied problems of embedding trees into fixed dense graphs and into random graphs, and extends a sizeable body of existing research on randomly perturbed graphs. Specifically, we show that there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn uniformly random edges to G, the resulting graph will contain T asymptotically almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of a dense graph into super-regular pairs of comparable sizes, which may be of independent interest.},
author = {Krivelevich, Michael and Kwan, Matthew Alan and Sudakov, Benny},
issn = {1095-7146},
journal = {SIAM Journal on Discrete Mathematics},
number = {1},
pages = {155--171},
publisher = {Society for Industrial & Applied Mathematics},
title = {{Bounded-degree spanning trees in randomly perturbed graphs}},
doi = {10.1137/15m1032910},
volume = {31},
year = {2017},
}
@article{9588,
abstract = {Consider the sum X(ξ)=∑ni=1aiξi , where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2 ). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x] . In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.},
author = {Bandeira, Afonso S. and Ferber, Asaf and Kwan, Matthew Alan},
issn = {0001-8708},
journal = {Advances in Mathematics},
pages = {292--312},
publisher = {Elsevier},
title = {{Resilience for the Littlewood–Offord problem}},
doi = {10.1016/j.aim.2017.08.031},
volume = {319},
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{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{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},
}
@phdthesis{202,
abstract = {Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.},
author = {Pleska, Maros},
pages = {126},
publisher = {IST Austria},
title = {{Biology of restriction-modification systems at the single-cell and population level}},
doi = {10.15479/AT:ISTA:th_916},
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{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},
}
@article{951,
abstract = {Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo},
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},
issn = {15449173},
journal = {PLoS Biology},
number = {5},
publisher = {Public Library of Science},
title = {{Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti}},
doi = {10.1371/journal.pbio.2001894},
volume = {15},
year = {2017},
}
@article{914,
abstract = {Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.},
author = {Giehr, Julia and Grasse, Anna V and Cremer, Sylvia and Heinze, Jürgen and Schrempf, Alexandra},
issn = {20545703},
journal = {Royal Society Open Science},
number = {7},
publisher = {Royal Society, The},
title = {{Ant queens increase their reproductive efforts after pathogen infection}},
doi = {10.1098/rsos.170547},
volume = {4},
year = {2017},
}
@article{680,
abstract = {In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics.},
author = {Chalk, Matthew J and Masset, Paul and Gutkin, Boris and Denève, Sophie},
issn = {1553734X},
journal = {PLoS Computational Biology},
number = {6},
publisher = {Public Library of Science},
title = {{Sensory noise predicts divisive reshaping of receptive fields}},
doi = {10.1371/journal.pcbi.1005582},
volume = {13},
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},
}