Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

High-Resolution Finite Compact Difference Schemes for Hyperbolic Conservation Laws

A finite compact (FC) difference scheme requiring only bi-diagonal matrix inversion is proposed by using the known high-resolution flux. Introducing TVD or ENO limiters in the numerical flux, several high-resolution FC-schemes of hyperbolic conservation law are developed, including the FC-TVD, third-order FC-ENO and fifth-order FC-ENO schemes. Boundary conditions formulated need only one unknown variable for third-order FC-ENO scheme and two unknown variables for fifth-order FC-ENO scheme. Numerical test results of the proposed FC-scheme were compared with traditional TVD, ENO and WENO schemes to demonstrate its high-order accuracy and high-resolution.

Hybrid Finite Compact-WENO Schemes for Shock Calculation

Hybrid finite compact (FC)-WENO schemes are proposed for shock calculations. The two sub-schemes (finite compact difference scheme and WENO scheme) are hybridized by means of the similar treatment as in ENO schemes. The hybrid schemes have the advantages of FC and WENO schemes. One is that they possess the merit of the finite compact difference scheme, which requires only bi-diagonal matrix inversion and can apply the known high-resolution flux to obtain high-performance numerical flux function; another is that they have the high-resolution property of WENO scheme for shock capturing. The numerical results show that FC-WENO schemes have better resolution properties than both FC-ENO schemes and WENO schemes. In addition, some comparisons of FC-ENO and artificial compression method (ACM) filter scheme of Yee et al. are also given.

Latin hypercube sampling used in the calculation of the fracture probability

The paper proposes Latin hypercube sampling combined with the stratified sampling of variance reduction technique to calculate accurate fracture probability. In the compound sampling, the number of simulations is relatively small and the calculation error is satisfactory.

Difference schemes on non-uniform mesh and their application

High order accurate schemes are needed to simulate the multi-scale complex flow fields to get fine structures in simulation of the complex flows with large gradient of fluid parameters near the wall, and schemes on non-uniform mesh are desirable for many CFD (computational fluid dynamics) workers. The construction methods of difference approximations and several difference approximations on non-uniform mesh are presented. The accuracy of the methods and the influence of stretch ratio of the neighbor mesh increment on accuracy are discussed. Some comments on these methods are given, and comparison of the accuracy of the results obtained by schemes based on both non-uniform mesh and coordinate transformation is made, and some numerical examples with non-uniform mesh are presented.

On dispersion-controlled principles for non-oscillatory shock-capturing schemes

The role of dispersions in the numerical solutions of hydrodynamic equation systems has been realized for long time. It is only during the last two decades that extensive studies on the dispersion-controlled dissipative (DCD) schemes were reported. The studies have demonstrated that this kind of the schemes is distinct from conventional dissipation-based schemes in which the dispersion term of the modified equation is not considered in scheme construction to avoid nonphysical oscillation occurring in shock wave simulations. The principle of the dispersion controlled aims at removing nonphysical oscillations by making use of dispersion characteristics instead of adding artificial viscosity to dissipate the oscillation as the conventional schemes do. Research progresses on the dispersion controlled principles are reviewed in this paper, including the exploration of the role of dispersions in numerical simulations, the development of the dispersion-controlled principles, efforts devoted to high-order dispersion-controlled dissipative schemes, the extension to both the finite volume and the finite element methods, scheme verification and solution validation, and comments on several aspects of the schemes from author's viewpoint.

Improved sampling techniques for the direct simulation Monte Carlo method

The direct simulation Monte Carlo (DSMC) method is a widely used approach for flow simulations having rarefied or nonequilibrium effects. It involves heavily to sample instantaneous values from prescribed distributions using random numbers. In this note, we briefly review the sampling techniques typically employed in the DSMC method and present two techniques to speedup related sampling processes. One technique is very efficient for sampling geometric locations of new particles and the other is useful for the Larsen-Borgnakke energy distribution.

Wave-front analysis method of circular aperture sampling for collimation testing

A new type of wave-front analysis method for the collimation testing of laser beams is proposed. A concept of wave-front height is defined, and, on this basis, the wave-front analysis method of circular aperture sampling is introduced. The wave-front height of the tested noncollimated wave can be estimated from the distance between two identical fiducial diffraction planes of the sampled wave, and then the divergence is determined. The design is detailed, and the experiment is demonstrated. The principle and experiment results of the method are presented. Owing to the simplicity of the method and its low cost, it is a promising method for checking the collimation of a laser beam with a large divergence. © 2005 Optical Society of America.

Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation

It is extremely difficult to explore mRNA folding structure by biological experiments. In this report, we use stochastic sampling and folding simulation to test the existence of the stable secondary structural units of-mRNA, look for the folding units, and explore the probabilistic stabilization of the units. Using this method, We made simulations for all possible local optimum secondary structures of a single strand mRNA within a certain range, and searched for the common parts of the secondary structures. The consensus secondary structure units (CSSUs) extracted from the above method are mainly hairpins, with a few single strands. These CSSUs suggest that the mRNA folding units could be relatively stable and could perform specific biological function. The significance of these observations for the mRNA folding problem in general is also discussed. (c) 2004 Elsevier B.V. All rights reserved.

cryptanalysis of some signature schemes with message recovery

IEEE Computer Society

A 10-bit 50-MS/s sample-and-hold circuit with low distortion sampling switches

A fully-differential switched-capacitor sample-and-hold (S/H) circuit used in a 10-bit 50-MS/s pipeline analog-to-digital converter (ADC) was designed and fabricated using a 0.35-μm CMOS process. Capacitor fliparound architecture was used in the S/H circuit to lower the power consumption. In addition, a gain-boosted operational transconductance amplifier (OTA) was designed with a DC gain of 94 dB and a unit gain bandwidth of 460 MHz at a phase margin of 63 degree, which matches the S/H circuit. A novel double-side bootstrapped switch was used, improving the precision of the whole circuit. The measured results have shown that the S/H circuit reaches a spurious free dynamic range (SFDR) of 67 dB and a signal-to-noise ratio (SNR) of 62.1 dB for a 2.5 MHz input signal with 50 MS/s sampling rate. The 0.12 mm~2 S/H circuit operates from a 3.3 V supply and consumes 13.6 mW.

A New Method to Investigate InGaAsP Single-Photon Avalanche Diodes Using a Digital Sampling Oscilloscope

A near-infrared single-photon detection system is established by using pigtailed InGaAs/InP avalanche photodiodes. With a 50GHz digital sampling oscilloscope, the function and process of gated-mode (Geiger-mode) single-photon detection are intuitionally demonstrated for the first time. The performance of the detector as a gated-mode single-photon counter at wavelengths of 1310 and 1550nm is investigated. At the operation temperature of 203K,a quantum efficiency of 52% with a dark count probability per gate of 2. 4 * 10~(-3), and a gate pulse repetition rate of 50kHz are obtained at 1550nm. The corresponding parameters are 43% , 8. 5 * 10~(-3), and 200kHz at 238K.