Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction

The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical and clinical studies （Wang and Li, 2013; Wang et al., 2014）. There are two kinds of extremely useful markers in Y chromosome, single nucle- otide polymorphism （SNP） and short tandem repeats （STRs）. With a very low mutation rate on the order of 3.0 x 10-8 mutations/nucleotide/generation （Xue et al., 2009）, SNP markers have been used in constructing a robust phylogeny tree linking all the Y chromosome lineages from world pop- ulations （Karafet et al., 2008）. Those lineages determined by the pattern of SNPs are called haplogroups. That is to say, we have to genotype an appropriate number of SNPs in order to assign a given Y chromosome to a haplogroup. Compared with SNPs, the mutation rates of STR markers are about four to five orders of magnitude higher （Gusmgo et al., 2005; Ballantyne et al., 2010）. Typing STR has advantages of saving time and cost compared with typing SNPs in phylogenetic assignment of a Y chromosome （Wang et al., 2010）. A set of STR values for an individual is called a haplotype. Because of the disparity in mutation rates between SNP and STR, one SNP haplogroup could actually comprise many STR haplotypes （Wang et al., 2010）. It is most interesting that STR variability is clustered more by haplogroups than by populations （Bosch et al., 1999; Behar et al., 2004）, which indicates that STR haplotypes could be used to infer the haplogroup information of a given Y chromosome. There has been increasing interest in this cost- effective strategy for predicting the haplogroup from a given STR haplotype when SNP data are unavailable. For instance, Vadim Urasin＇s YPredictor （http：//predictor.ydna.ru/）, Whit Atheys＇ haplogroup predictor （http：//www.hprg.com/hapest5/） （Athey, 2005, 2006）, and haplogroup classifier of Arizona University （Schlecht et al., 2008） have been widely employed in previous studies for haplogroup prediction （Larmuseau et al., 2010; Bembea et al., 2011; Larmuseau et al., 2012; Tarlykov et al., 2013）.

Cavitating/non-cavitating flows simulation by third-order finite volume scheme and power-law preconditioning method

Equations of steady inviscid and laminar flows are solved by means of a third-order finite volume （FV） scheme. For this purpose, a cell-centered discretization technique is employed. In this technique, the flow parameters at the cell faces are computed using a third-order weighted averages procedure. A fourth-order artificial dissipation is used for stability of the solution. In order to achieve the steady-state situation, four-step Runge-Kutta explicit time integration method is applied. An advanced progressive preconditioning method, named the power-law preconditioning method, is used for faster convergence. In this method, the preconditioning matrix is adjusted automatically from the velocity and/or pressure flow-field by a power-law relation. Attention is directed towards accuracy and convergence of the schemes. The results presented in the paper focus on steady inviscid and laminar flows around sheet-cavitating and fully-wetted bodies including hydrofoils and circular/elliptical cylinder. Excellent agreements are obtained when numerical predictions are compared with other available experimental and numerical results. In addition, it is found that using the power-law preconditioner significantly increases the numerical convergence speed.

An adaptive p-FEM for three-dimensional concrete aggregate models

Numerical simulation for concrete aggregate models(CAMs)with different shape aggregates usually requires high accuracy and convergence near the material interfaces.But high memory usage will be needed for those traditional finite element methods such as the method by using mesh refinement throughout the domain.Thus,an adaptive p-version finite element method(p-FEM)is proposed in this paper for the solution of 3D CAM problems,and meanwhile the resulting adaptive computational algorithm and post-processing program are presented.We firstly focused two typical 3D weak discontinuity problems on the influence of different convergence criterions for the computational results of each point on the interface in order to verify the efficiency and convergence of the resulting p-FEM,and then this method is successfully applied to the numerical simulation of CAMs with different shape aggregates.In addition,an efficient hybrid realization method which combines ANSYS and Hypermesh software is also presented in order to quickly establish the geometric models of 3D CAMs.The numerical results have been shown that the proposed p-FEM can efficiently solve the concrete-like particle-reinforced composite problems and more accurate numerical results can be obtained under the case of fewer elements used in simulation of CAMs,even there being some elements with poor quality.