A Statistical View of Learning in the Centipede Game

In this article we evaluate the statistical evidence that a population of students learn about the sub-game perfect Nash equilibrium of the centipede game via repeated play of the game. This is done by formulating a model in which a player's error in assessing the utility of decisions changes as they gain experience with the game. We first estimate parameters in a statistical model where the probabilities of choices of the players are given by a Quantal Response Equilibrium (QRE) (McKelvey and Palfrey, 1995, 1996, 1998), but are allowed to change with repeated play. This model gives a better fit to the data than similar models previously considered. However, substantial correlation of outcomes of games having a common player suggests that a statistical model that captures within-subject correlation is more appropriate. Thus we then estimate parameters in a model which allows for within-player correlation of decisions and rates of learning. Through out the paper we also consider and compare the use of randomization tests and posterior predictive tests in the context of exploratory and confirmatory data analyses

Sperm storage by males causes changes in sperm phenotype and influences the reproductive fitness of males and their sons

Recent studies suggest that environmentally induced effects on sperm phenotype can influence offspring phenotype beyond the classic Mendelian inheritance mechanism. However, establishing whether such effects are conveyed purely through ejaculates, independently of maternal environmental effects, remains a significant challenge. Here, we assess whether environmentally induced effects on sperm phenotype affects male reproductive success and offspring fitness. We experimentally manipulated the duration of sperm storage by males, and thus sperm age, in the internally fertilizing fish Poecilia reticulata. We first confirm that sperm ageing influences sperm quality and consequently males reproductive success. Specifically, we show that aged sperm exhibit impaired velocity and are competitively inferior to fresh sperm when ejaculates compete to fertilize eggs. We then used homospermic (noncompetitive) artificial insemination to inseminate females with old or fresh sperm and found that male offspring arising from fertilizations by experimentally aged sperm suffered consistently impaired sperm quality when just sexually mature (four months old) and subsequently as adults (13 months old). Although we have yet to determine whether these effects have a genetic or epigenetic basis, our analyses provide evidence that environmentally induced variation in sperm phenotype constitutes an important source of variation in male reproductive fitness that has far reaching implications for offspring fitness

Scaling clearance in paediatric pharmacokinetics: All models are wrong, which are useful?

AIM: When different models for weight and age are used in paediatric pharmacokinetic studies it is difficult to compare parameters between studies or perform model-based meta-analyses. This study aimed to compare published models with the proposed standard model (allometric weight(0.75) and sigmoidal maturation function). METHODS: A systematic literature search was undertaken to identify published clearance (CL) reports for gentamicin and midazolam and all published models for scaling clearance in children. Each model was fitted to the CL values for gentamicin and midazolam, and the results compared with the standard model (allometric weight exponent of 0.75, along with a sigmoidal maturation function estimating the time in weeks of postmenstrual age to reach half the mature value and a shape parameter). For comparison, we also looked at allometric size models with no age effect, the influence of estimating the allometric exponent in the standard model and, for gentamicin, using a fixed allometric exponent of 0.632 as per a study on glomerular filtration rate maturation. Akaike information criteria (AIC) and visual predictive checks were used for evaluation. RESULTS: No model gave an improved AIC in all age groups, but one model for gentamicin and three models for midazolam gave slightly improved global AIC fits albeit using more parameters: AIC drop (number of parameters), -4.1 (5), -9.2 (4), -10.8 (5) and -10.1 (5), respectively. The 95% confidence interval of estimated CL for all top performing models overlapped. CONCLUSION: No evidence to reject the standard model was found; given the benefits of standardised parameterisation, its use should therefore be recommended

Chitin mixed in potting soil alters lettuce growth, the survival of zoonotic bacteria on the leaves and associated rhizosphere microbiology

Chitin is a promising soil amendment for improving soil quality, plant growth, and plant resilience. The objectives of this study were twofold. First, to study the effect of chitin mixed in potting soil on lettuce growth and on the survival of two zoonotic bacterial pathogens, Escherichia colt O157:H7 and Salmonella enterica on the lettuce leaves. Second, to assess the related changes in the microbial lettuce rhizosphere, using phospholipid fatty acid (PLFA) analysis and amplicon sequencing of a bacterial 16S rRNA gene fragment and the fungal ITS2. As a result of chitin addition, lettuce fresh yield weight was significantly increased. S. enterica survival in the lettuce phyllosphere was significantly reduced. The E. coli O157:H7 survival was also lowered, but not significantly. Moreover, significant changes were observed in the bacterial and fungal community of the lettuce rhizosphere. PLFA analysis showed a significant increase in fungal and bacterial biomass. Amplicon sequencing showed no increase in fungal and bacterial biodiversity, but relative abundances of the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Proteobacteria and the fungal phyla Ascomycota, Basidiomycota, and Zygomycota were significantly changed. More specifically, a more than 10-fold increase was observed for operational taxonomic units belonging to the bacterial genera Cellvibrio, Pedobacter, Dyadobacter, and Streptomyces and to the fungal genera Lecanicillium and Mortierella. These genera include several species previously reported to be involved in biocontrol, plant growth promotion, the nitrogen cycle and chitin degradation. These results enhance the understanding of the response of the rhizosphere microbiome to chitin amendment. Moreover, this is the first study to investigate the use of soil amendments to control the survival of S. enterica on plant leaves

A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples

One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same taxonomic distribution of organisms, or the same distribution of functions? Here we provide a non-parametric statistical “triangulation test” to address this type of question. The test requires that multiple replicates are available for each of the biological samples, and it is based on three-way computational comparisons of samples. To illustrate the application of the test, we collected three biological samples taken from different locations in one piece of human stool, each represented by three replicates, and analyzed them using MEGAN. (Despite its name, the triangulation test does not require that the number of biological samples or replicates be three.) The triangulation test rejects the null hypothesis that the three biological samples exhibit the same distribution of taxa or function (error probability ≤0.05), indicating that the microbial composition of the investigated human stool is not homogenous on a macroscopic scale, suggesting that pooling material from multiple locations is a reasonable practice. We provide an implementation of the test in our open source program MEGAN Community Edition

Non-L\'evy mobility patterns of Mexican Me'Phaa peasants searching for fuelwood

We measured mobility patterns that describe walking trajectories of individual Me'Phaa peasants searching and collecting fuelwood in the forests of "La Monta\~na de Guerrero" in Mexico. These one-day excursions typically follow a mixed pattern of nearly-constant steps when individuals displace from their homes towards potential collecting sites and a mixed pattern of steps of different lengths when actually searching for fallen wood in the forest. Displacements in the searching phase seem not to be compatible with L\'evy flights described by power-laws with optimal scaling exponents. These findings however can be interpreted in the light of deterministic searching on heavily degraded landscapes where the interaction of the individuals with their scarce environment produces alternative searching strategies than the expected L\'evy flights. These results have important implications for future management and restoration of degraded forests and the improvement of the ecological services they may provide to their inhabitants.Comment: 15 pages, 4 figures. First version submitted to Human Ecology. The final publication will be available at http://www.springerlink.co

Reconciling actual and perceived rates of predation by domestic cats

© 2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.The predation of wildlife by domestic cats (Felis catus) is a complex problem: Cats are popular companion animals in modern society but are also acknowledged predators of birds, herpetofauna, invertebrates, and small mammals. A comprehensive understanding of this conservation issue demands an understanding of both the ecological consequence of owning a domestic cat and the attitudes of cat owners. Here, we determine whether cat owners are aware of the predatory behavior of their cats, using data collected from 86 cats in two UK villages. We examine whether the amount of prey their cat returns influences the attitudes of 45 cat owners toward the broader issue of domestic cat predation. We also contribute to the wider understanding of physiological, spatial, and behavioral drivers of prey returns among cats. We find an association between actual prey returns and owner predictions at the coarse scale of predatory/nonpredatory behavior, but no correlation between the observed and predicted prey-return rates among predatory cats. Cat owners generally disagreed with the statement that cats are harmful to wildlife, and disfavored all mitigation options apart from neutering. These attitudes were uncorrelated with the predatory behavior of their cats. Cat owners failed to perceive the magnitude of their cats' impacts on wildlife and were not influenced by ecological information. Management options for the mitigation of cat predation appear unlikely to work if they focus on "predation awareness" campaigns or restrictions of cat freedom. We consider both the ecological consequence of owning a domestic cat and the attitudes of cat owners. Our findings suggest cat owners fail to perceive the magnitude of their cats' impacts on wildlife, with no correlation between the observed and predicted prey return rates among predatory cats. On the basis of opinions of cat owners in this study, management options for the mitigation of cat predation appear unlikely to work if they focus on "predation awareness" campaigns, or restrictions of cat freedom.published_or_final_versio