Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event

Streptococcus pneumoniae ('pneumococcus') causes an estimated 14.5 million cases of serious disease and 826,000 deaths annually in children under 5 years of age(1). The highly effective introduction of the PCV7 pneumococcal vaccine in 2000 in the United States(2,3) provided an unprecedented opportunity to investigate the response of an important pathogen to widespread, vaccine-induced selective pressure. Here, we use array-based sequencing of 62 isolates from a US national monitoring program to study five independent instances of vaccine escape recombination(4), showing the simultaneous transfer of multiple and often large (up to at least 44 kb) DNA fragments. We show that one such new strain quickly became established, spreading from east to west across the United States. These observations clarify the roles of recombination and selection in the population genomics of pneumococcus and provide proof of principle of the considerable value of combining genomic and epidemiological information in the surveillance and enhanced understanding of infectious diseases.     

Correspondence on the selection of error measures for comparisons among forecasting methods

Clements and Hendry (1993) proposed the Generalized Forecast Error Second Moment (GFESM) as an improvement to the Mean Square Error in comparing forecasting performance across data series. They based their conclusion on the fact that rankings based on GFESM remain unaltered if the series are linearly transformed. In this paper, we argue that this evaluation ignores other important criteria. Also, their conclusions were illustrated by a simulation study whose relationship to real data was not obvious. Thirdly, prior empirical studies show that the mean square error is an inappropriate measure to serve as a basis for comparison. This undermines the claims made for the GFESM.     

Editorial

Systemic Practice and Action Research -     

Murine type C endogenous virus expression in murine 129 teratocarcinoma cell line]

Murine type C viral information is detectable in the cellular genome of both differentiated and undifferentiated cell lines derived from 129 Mouse teratocarcinoma. Cytoplasmic RNA expression which is negligible in differentiated cells, is significantly higher in multipotential undifferentiated cells. Furthermore it was observed that in vitro differentiation of multipotent cells leads to a decrease of this expression.     

General systems: A basis for knowledge engineering

General systems formalizations of expert knowledge play a foundational role in the process of knowledge engineering of intelligent systems. Canonical definitions of systems (knowledge structures) which have been arrived at by a crossdisciplinary inductive modeling process are shown to be the basis for the modeling of certain generic categories of expert reasoning processes which are of current interest in knowledge engineering. The methodology for transforming the representation of knowledge expressed in general systems formalizations to the representation of that knowledge in expert systems is also developed. In particular, transformations from general systems formalizations into frames are presented.