A comparison of two popular statistical methods for estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences

We have compared two statistical methods of estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences, which have been proposed by Templeton (1993) and Bandeltet al. (1995). Monte-Carlo simulations were used for generating DNA sequence data. Different evolutionary scenarios were simulated and the estimation procedures were evaluated. We have found that for both methods (i) the estimates are insensitive to demographic parameters and (ii) the standard deviations of the estimates are too high for these methods to be reliably used in practice

Development of Estimation Procedure of Population Mean in Two-Phase Stratified Sampling

This article describes the problem of estimation of finite population mean in two-phase stratified random sampling. Using information on two auxiliary variables, a class of product to regression chain type estimators has been proposed and its characteristic is discussed. The unbiased version of the proposed class of estimators has been constructed and the optimality condition for the proposed class of estimators is derived. The efficacy of the proposed methodology has been justified through empirical investigations carried over the data set of natural population as well as the data set of artificially generated population. The survey statistician may be suggested to use it

Haplotype variation in the ACE gene in global populations, with special reference to India, and an alternative model of evolution of haplotypes

Angiotensin-I-converting enzyme (ACE) is known to be associated with human cardiovascular and psychiatric pathophysiology. We have undertaken a global survey of the haplotypes in ACE gene to study diversity and to draw inferences on the nature of selective forces that may be operating on this gene. We have investigated the haplotype profiles reconstructed using polymorphisms in the regulatory (rs4277405, rs4459609, rs1800764, rs4292, rs4291), exonic (rs4309, rs4331, rs4343), and intronic (rs4340; Alu [I/D]) regions covering 17.8 kb of the ACE gene. We genotyped these polymorphisms in a large number of individuals drawn from 15 Indian ethnic groups and estimated haplotype frequencies. We compared the Indian data with available data from other global populations. Globally, five major haplotypes were observed. High-frequency haplotypes comprising mismatching alleles at the loci considered were seen in all populations. The three most frequent haplotypes among Africans were distinct from the major haplotypes of other world populations. We have studied the evolution of the two major haplotypes (TATATTGIA and CCCTCCADG), one of which contains an Alu insertion (I) and the other a deletion (D), seen most frequently among Caucasians (68%), non-African HapMap populations (65–88%), and Indian populations (70–95%) in detail. The two major haplotypes among Caucasians are reported to represent two distinct clades A and B. Earlier studies have postulated that a third clade C (represented by the haplotypes TACATCADG and TACATCADA) arose from an ancestral recombination event between A and B. We find that a more parsimonious explanation is that clades A and B have arisen by recombination between haplotypes belonging to clade C and a high-frequency African haplotype CCCTTCGIA. The haplotypes, which according to our hypothesis are the putative non-recombinants (PuNR), are uncommon in all non-African populations (frequency range 0–12%). Conversely, the frequencies of the putative recombinant haplotypes (PuR) are very low in the Africans populations (2–8%), indicating that the recombination event is likely to be ancient and arose before, perhaps shortly prior to, the global dispersal of modern humans. The global frequency spectrum of the PuR and the PuNR is difficult to explain only by drift. It appears likely that the ACE gene has been undergoing a combination of different selective pressures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11568-011-9153-6) contains supplementary material, which is available to authorized users

A Model Checking based Converter Synthesis Approach for Embedded Systems

Protocol conversion problem involves identifying whether two or more protocols can be composed with or without an intermediary, referred to as a converter, to obtain a pre-specified desired behavior. We investigate this problem in formal setting and propose, for the first time, a temporal logic based automatic solution to the convertibility verification and synthesis. At its core, our technique is based on local model checking technique and determines the existence of the converter and if a converter exists, it is automatically synthesized. A number of key features of our technique distinguishes it from all existing formal and/or informal techniques. Firstly, we handle both data and control mismatches (for the first time), using a single unifying model checking based solution. Secondly, the proposed approach uses temporal logic for the specification of correct behaviors (unlike earlier automaton based specifications) which is both elegant and natural to express event ordering and data-matching requirements. Finally, we have have experimented extensively with the examples available in the existing literature to evaluate the applicability of our technique in wide range of applications

Isospin asymmetric nuclear matter and properties of axisymmetric neutron stars

Pure hadronic compact stars, above a limiting value ($\approx$1.6 M$_\odot$) of their gravitational masses, to which predictions of most of other equations of state (EoSs) are restricted, can be reached from the equation of state (EoS) obtained using DDM3Y effective interaction. This effective interaction is found to be quite successful in providing unified description of elastic and inelastic scattering, various radioactivities and nuclear matter properties. We present a systematic study of the properties of pure hadronic compact stars. The $\beta$-equilibrated neutron star matter using this EoS with a thin crust is able to describe highly-massive compact stars, such as PSR B1516+02B with a mass M=1.94$^{+0.17}_{-0.19}$ M$_\odot$ and PSR J0751+1807 with a mass M=2.1$\pm$0.2 M$_\odot$ to a 1$\sigma$ confidence level.Comment: 5 pages, 4 figure

Hindrance in heavy-ion fusion for lighter systems of astrophysical interest

The hindrance in fusion of heavy-ion reactions crops up in the region of extreme sub-barrier energies. This phenomenon can be effectively analyzed using a simple diffused barrier formula derived assuming a Gaussian distribution of fusion barrier heights. Folding the Gaussian barrier distribution with the classical expression for the fusion cross section for a fixed barrier, the fusion cross section is obtained. The energy dependence of the fusion cross section provides good description to the existing data on sub-barrier heavy-ion fusion for lighter systems of astrophysical interest. Using this simple formula, an analysis has been presented from $^{16}$O + $^{18}$O to $^{12}$C + $^{198}$Pt, all of which were measured down to $<$ 10 $\mu$b. The agreement of the present analysis with the measured values is better than those calculated even from the sophisticated coupled channels calculations. The relatively smooth variation of the three parameters of this formula implies that it may be exploited to estimate the excitation function or to extrapolate cross sections for pairs of interacting nuclei which are yet to be measured. Possible extensions of the present methodology and its limitations have also been discussed.Comment: 6 pages including 7 figures and 1 table. arXiv admin note: substantial text overlap with arXiv:1402.533

Comparative calculation of EPR spectral parameters in [Mo^VOX_4]^-, [Mo^VOX_5]^(2-), and [Mo^VOX_4(H_2O)]^- complexes

The EPR spectral parameters, i.e. g-tensors and molybdenum hyperfine couplings, for several d^1 systems of the general formula [Mo^VEX_4]^(n-), [Mo^VOX_5]^(2-), and [Mo^VOX_4(H_2O)]^- (E = O, N; X = F, Cl, Br; n = 1 or 2) were calculated using Density Functional Theory. The influence of basis sets, their contraction scheme, the type of exchange-correlation functional, the amount of Hartree-Fock exchange, molecular geometry, and relativistic effects on the calculated EPR spectra parameters have been discussed. The g-tensors and molybdenum hyperfine coupling parameters were calculated using a relativistic Hamiltonian coupled with several LDA, GGA, and 'hybrid' exchange-correlation functionals and uncontracted full-electron DGauss DZVP basis sets. The calculated EPR parameters are found to be sensitive to the Mo=E distance and E=Mo-Cl angle, and thus the choice of starting molecular geometry should be considered as an important factor in predicting the g-tensors and hyperfine coupling constants in oxo-molybdenum compounds. In the present case, the GGA exchange-correlation functionals provide a better agreement between the theory and the experiment