Computationally Efficient Simulation of Queues: The R Package queuecomputer

Large networks of queueing systems model important real-world systems such as MapReduce clusters, web-servers, hospitals, call centers and airport passenger terminals. To model such systems accurately, we must infer queueing parameters from data. Unfortunately, for many queueing networks there is no clear way to proceed with parameter inference from data. Approximate Bayesian computation could offer a straightforward way to infer parameters for such networks if we could simulate data quickly enough. We present a computationally efficient method for simulating from a very general set of queueing networks with the R package queuecomputer. Remarkable speedups of more than 2 orders of magnitude are observed relative to the popular DES packages simmer and simpy. We replicate output from these packages to validate the package. The package is modular and integrates well with the popular R package dplyr. Complex queueing networks with tandem, parallel and fork/join topologies can easily be built with these two packages together. We show how to use this package with two examples: a call center and an airport terminal.Comment: Updated for queuecomputer_0.8.

Mistaking Randomness for Free Will

Belief in free will is widespread. The present research considered one reason why people may believe that actions are freely chosen rather than determined: they attribute randomness in behavior to free will. Experiment 1 found that participants who were prompted to perform a random sequence of actions experienced their behavior as more freely chosen than those who were prompted to perform a deterministic sequence. Likewise, Experiment 2 found that, all else equal, the behavior of animated agents was perceived to be more freely chosen if it consisted of a random sequence of actions than if it consisted of a deterministic sequence; this was true even when the degree of randomness in agents’ behavior was largely a product of their environments. Together, these findings suggest that randomness in behavior—one’s own or another’s—can be mistaken for free will.Psycholog

Dungeness crab research program: Report for the Year 1976

All larval stages of the 1976 year class, with the exception of the 5th zoeal stage, were found in Gu1f waters January through March. The first post-larval stage was collected in San Pablo Bay in May. Fifty percent of 1976 year class crabs entered the Bay complex as compared to nearly 80% in 1975. The 1976 year class appears relatively weak. No electrophoretic polymorphism was found in Cancer magister to be of value in Dungeness crab population determinations. Multi-variate correlations comparing crab landings with an array of oceanographic parameters and the crab density dependent factor were computer-run for both northern and central California. The most significant correlating factors at the time late stage larvae prevail were sea level and atmospheric pressure for central California and, for northern California, the density dependent factor and sea surface temperature. Female crabs held at controlled temperatures indicated gonad maturation and spawning may be induced by increased temperature. Analyses of crab tissues revealed burdens of petroleum hydrocarbons, silver, selenium, cadmium, and PCB's higher in central California crabs, while DDE was found in higher amounts in northern California crab tissue. Thru-flow culture systems were developed which should yield about 163 megalopae of Dungeness crabs in 63 days from 1,200 laboratory hatched zoeae.(46pp.

Weighted averages in population annealing: analysis and general framework

Population annealing is a powerful sequential Monte Carlo algorithm designed to study the equilibrium behavior of general systems in statistical physics through massive parallelism. In addition to the remarkable scaling capabilities of the method, it allows for measurements to be enhanced by weighted averaging, admitting to reduce both systematic and statistical errors based on independently repeated simulations. We give a self-contained introduction to population annealing with weighted averaging, generalize the method to a wide range of observables such as the specific heat and magnetic susceptibility and rigorously prove that the resulting estimators for finite systems are asymptotically unbiased for essentially arbitrary target distributions. Numerical results based on more than $10^7$ independent population annealing runs of the two-dimensional Ising ferromagnet and the Edwards-Anderson Ising spin glass are presented in depth. In the latter case, we also discuss efficient ways of measuring spin overlaps in population annealing simulations.Comment: 21 pages, 13 figures, 3 tables, RevTeX4.

Responses of a bacterial pathogen to phosphorus limitation of its aquatic invertebrate host

Host nutrition is thought to affect the establishment, persistence, and severity of pathogenic infections. Nutrient-deficient foods possibly benefit pathogens by constraining host immune function or benefit hosts by limiting parasite growth and reproduction. However, the effects of poor elemental food quality on a host’s susceptibility to infection and disease have received little study. Here we show that the bacterial microparasite Pasteuria ramosa is affected by the elemental nutrition of its aquatic invertebrate host, Daphnia magna. We found that high food carbon : phosphorus (C:P) ratios significantly reduced infection rates of Pasteuria in Daphnia and led to lower within-host pathogen multiplication. In addition, greater virulent effects of bacterial infection on host reproduction were found in Daphniaconsuming P-deficient food. Poor Daphnia elemental nutrition thus reduced the growth and reproduction of its bacterial parasite, Pasteuria. The effects of poor host nutrition on the pathogen were further evidenced by Pasteuria’s greater inhibition of reproduction in P-limited Daphnia. Our results provide strong evidence that elemental food quality can significantly influence the incidence and intensity of infectious disease in invertebrate hosts.We thank H. Foy, C. Hibbert, M. Kingsbury, S. McCarthy, and D. Woolnough for their assistance with the experiments. This work was supported by grants from the Natural Sciences and Engineering Research Council of Canada and Trent University

Inheritance and Characterization of Strong Resistance to Phosphine in Sitophilus oryzae (L.)

Sitophilus oryzae (Linnaeus) is a major pest of stored grain across Southeast Asia and is of increasing concern in other regions due to the advent of strong resistance to phosphine, the fumigant used to protect stored grain from pest insects. We investigated the inheritance of genes controlling resistance to phosphine in a strongly resistant S. oryzae strain (NNSO7525) collected in Australia and find that the trait is autosomally inherited and incompletely recessive with a degree of dominance of -0.66. The strongly resistant strain has an LC50 52 times greater than a susceptible reference strain (LS2) and 9 times greater than a weakly resistant strain (QSO335). Analysis of F2 and backcross progeny indicates that two or more genes are responsible for strong resistance, and that one of these genes, designated So-rph1 , not only contributes to strong resistance, but is also responsible for the weak resistance phenotype of strain QSO335. These results demonstrate that the genetic mechanism of phosphine resistance in S. oryzae is similar to that of other stored product insect pests. A unique observation is that a subset of the progeny of an F1 backcross generation are more strongly resistant to phosphine than the parental strongly resistant strain, which may be caused by multiple alleles of one of the resistance genes

Sulfurous Gases As Biological Messengers and Toxins: Comparative Genetics of Their Metabolism in Model Organisms

Gasotransmitters are biologically produced gaseous signalling molecules. As gases with potent biological activities, they are toxic as air pollutants, and the sulfurous compounds are used as fumigants. Most investigations focus on medical aspects of gasotransmitter biology rather than toxicity toward invertebrate pests of agriculture. In fact, the pathways for the metabolism of sulfur containing gases in lower organisms have not yet been described. To address this deficit, we use protein sequences from Homo sapiens to query Genbank for homologous proteins in Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. In C. elegans, we find genes for all mammalian pathways for synthesis and catabolism of the three sulfur containing gasotransmitters, H2S, SO2 and COS. The genes for H2S synthesis have actually increased in number in C. elegans. Interestingly, D. melanogaster and Arthropoda in general, lack a gene for 3-mercaptopyruvate sulfurtransferase, an enzym for H2S synthesis under reducing conditions