Next-generation sequencing technology enables the routine detection of bacterial pathogens for clinical diagnostics and genetic research. Whole-genome sequencing has been of importance in the epidemiologic analysis of bacterial pathogens. However, few whole-genome sequencing-based genotyping pipelines are available for practical applications. Here, we present the whole-genome sequencing-based single nucleotide polymorphism(SNP) genotyping method and apply to the evolutionary analysis of methicillin-resistant Staphylococcus aureus. The SNP genotyping method calls genome variants using next-generation sequencing reads of whole genomes and calculates the pair-wise Jaccard distances of the genome variants. The method may reveal the high-resolution whole-genome SNP profiles and the structural variants of different isolates of methicillin-resistant S. aureus(MRSA) and methicillin-susceptible S. aureus(MSSA) strains. The phylogenetic analysis of whole genomes and particular regions may monitor and track the evolution and the transmission dynamic of bacterial pathogens. The computer pro- grams of the whole genome sequencing-based SNP genotyping methods are available to the public at https://github. com/ cyinbox/NGS.

We study the random field Ising model on Z^2 where the external field is given by i.i.d. Gaussian variables with mean zero and positive variance. We show that the effect of boundary conditions on the magnetization in a finite box decays exponentially in the distance to the boundary.

We obtain two-sided sub-Gaussian estimates of heat kernels for strongly local Dirichlet forms on intervals, equipped with self-similar measures generated by iterated function systems (IFS's) that do not satisfy the open set condition (OSC) and have overlaps. We first give a framework for heat kernel estimates on intervals, and then consider examples of self-similar measures to illustrate this phenomenon. These examples include the infinite Bernoulli convolution associated with the golden ratio, and a family of convolutions of Cantor-type measures. We make use of Strichartz second-order identities defined by auxiliary IFS's to compute measures of cells on different levels. These auxiliary IFS's do satisfy the OSC and are used to define new metrics. The walk dimensions obtained under these new metrics are strictly greater than 2 and are closely related to the spectral dimension of fractal Laplacians.

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The embedded cobordism category under study in this paper generalizes the category of conformal surfaces, introduced by G. Segal in [S2] in order to formalize the concept of field theories. Our main result identifies the homotopy type of the classifying space of the embedded$d$-dimensional cobordism category for all$d$. For$d$= 2, our results lead to a new proof of the generalized Mumford conjecture, somewhat different in spirit from the original one, presented in [MW].