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Now showing items 1 - 16 of 67451

  • Bayesian Estimation of Sequence Damage in Ancient DNA

    Ho, S. Y. W.   Heupink, T. H.   Rambaut, A.   Shapiro, B.  

    DNA extracted from archaeological and paleontological remains is usually damaged by biochemical processes postmortem. Some of these processes lead to changes in the structure of the DNA molecule, which can result in the incorporation of incorrect nucleotides during polymerase chain reaction. These base misincorporations, or miscoding lesions, can lead to the inclusion of spurious additional mutations in ancient DNA (aDNA) data sets. This has the potential to affect the outcome of phylogenetic and population genetic analyses, including estimates of mutation rates and genetic diversity. We present a novel model, termed the delta model, which estimates the amount of damage in DNA data and accounts for its effects in a Bayesian phylogenetic framework. The ability of the delta model to estimate damage is first investigated using a simulation study. The model is then applied to 13 aDNA data sets. The amount of damage in these data sets is shown to be significant but low (about I damaged base per 750 nt), suggesting that precautions for limiting the influence of damaged sites, such as cloning and enzymatic treatment, are worthwhile. The results also suggest that relatively high rates of mutation previously estimated from aDNA data are not entirely an artifact of sequence damage and are likely to be due to other factors such as the persistence of transient polymorphisms. The delta model appears to be particularly useful for placing upper credibility limits on the amount of sequence damage in an alignment, and this capacity might be beneficial for future aDNA studies or for the estimation of sequencing errors in modem DNA.
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  • Bayesian Estimation of Sequence Damage in Ancient DNA

    Ho, S. Y. W.   Heupink, T. H.   Rambaut, A.   Shapiro, B.  

    DNA extracted from archaeological and paleontological remains is usually damaged by biochemical processes postmortem. Some of these processes lead to changes in the structure of the DNA molecule, which can result in the incorporation of incorrect nucleotides during polymerase chain reaction. These base misincorporations, or miscoding lesions, can lead to the inclusion of spurious additional mutations in ancient DNA (aDNA) data sets. This has the potential to affect the outcome of phylogenetic and population genetic analyses, including estimates of mutation rates and genetic diversity. We present a novel model, termed the delta model, which estimates the amount of damage in DNA data and accounts for its effects in a Bayesian phylogenetic framework. The ability of the delta model to estimate damage is first investigated using a simulation study. The model is then applied to 13 aDNA data sets. The amount of damage in these data sets is shown to be significant but low (about I damaged base per 750 nt), suggesting that precautions for limiting the influence of damaged sites, such as cloning and enzymatic treatment, are worthwhile. The results also suggest that relatively high rates of mutation previously estimated from aDNA data are not entirely an artifact of sequence damage and are likely to be due to other factors such as the persistence of transient polymorphisms. The delta model appears to be particularly useful for placing upper credibility limits on the amount of sequence damage in an alignment, and this capacity might be beneficial for future aDNA studies or for the estimation of sequencing errors in modem DNA.
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  • Elevated substitution rates estimated from ancient DNA sequences

    Ho, S. Y. W.   Kolokotronis, S. O.   Allaby, R. G.  

    Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have been made using a Bayesian phylogenetic method that explicitly accommodates heterochronous data. Stimulated by recent criticism of this method, we present a comprehensive simulation study that validates its performance. For datasets of moderate size, it produces accurate estimates of rates, while appearing robust to assumptions about demographic history. We then analyse a large collection of 749 ancient and 727 modern DNA sequences from 19 species of animals, plants and bacteria. Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels.
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  • Bayesian Estimation of Substitution Rates from Ancient DNA Sequences with Low Information Content

    Ho, S. Y. W.   Lanfear, R.   Phillips, M. J.   Barnes, I.   Thomas, J. A.   Kolokotronis, S.-O.   Shapiro, B.  

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  • The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus (vol 9, e85641, 2014)

    Yasaka, R.   Nguyen, H. D.   Ho, S. Y. W.   Duchene, S.   Korkmaz, S.  

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  • Hey ho, let\"s go

    Boyce   Niall  

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  • 146.4 W end-pumped Ho : YAG slab laser with two crystals

    Duan X M   Shen Y J   Yao B Q   Wang Y Z  

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  • Response of Dr. Ho\"s comments

    Weiss, Markus   Engelhardt, Thomas   Bissonnette, Bruno   Soriano, Sulpicio  

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  • (W, Y, X)-Gorenstein complexes

    Zhao, Renyu   Ding, Nanqing  

    Let W, Y, X be three classes of left R-modules. In this paper, we introduce and study (W, Y, X)-Gorenstein complexes as a common generalization of completely W-resolved complexes [26], Gorenstein projective (resp., injective) complexes [8], Ding projective (resp., injective) complexes [32] and Gorenstein AC-projective (resp., AC-injective) complexes [4]. It is shown that under certain hypotheses, a complex C is (W, Y, X)-Gorenstein if and only if each C-n is a (W, Y, X)-Gorenstein module and Hom(R)(Y, C), Hom(R)(C, X) are exact for any Y is an element of (Y) over tilde, X is an element of (X) over tilde X. This result unifies the corresponding results of the aforementioned complexes. As applications, the stability of (W, Y, X)Gorenstein complexes and modules are explored.
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  • Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands RID A-8417-2008

    Barik, S. S.   Sahani, R.   Prasad, B. V. R.   Endicott, P.   Metspalu, M.   Sarkar, B. N.   Bhattacharya, S.   Annapoorna, P. C. H.   Sreenath, J.   Sun, D.   Sanchez, J. J.   Ho, S. Y. W.   Chandrasekar, A.   Rao, V. R.  

    The population genetics of the Indian subcontinent is central to understanding early human prehistory due to its strategic location on the proposed corridor of human movement from Africa to Australia during the late Pleistocene. Previous genetic research using mtDNA has emphasized the relative isolation of the late Pleistocene colonizers, and the physically isolated Andaman Island populations of Island South-East Asia remain the source of claims supporting an early split between the populations that formed the patchy settlement pattern along the coast of the Indian Ocean. Using whole-genome sequencing, combined with multiplexed SNP typing, this study investigates the deep structure of mtDNA haplogroups M31 and M32 in India and the Andaman Islands. The identification of a so far unnoticed rare polymorphism shared between these two lineages suggests that they are actually sister groups within a single haplogroup, M31'32. The enhanced resolution of M31 allows for the inference of a more recent colonization of the Andaman Islands than previously suggested, but cannot reject the very early peopling scenario. We further demonstrate a widespread overlap of mtDNA and cultural markers between the two major language groups of the Andaman archipelago. Given the "completeness" of the genealogy based on whole genome sequences, and the multiple scenarios for the peopling of the Andaman Islands sustained by this inferred genealogy, our study hints that further mtDNA based phylogeographic studies are unlikely to unequivocally support any one of these possibilities.
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  • The equation (w+x+y+z)(1/w+1/x+1/y+1/z)=3Dn

    Bremner, Andrew   Tho Nguyen Xuan  

    Bremner, Guy and Nowakowski [Which integers are representable as the product of the sum of three integers with the sum of their reciprocals? Math. Compos. 61(203) (1993) 117130] investigated the Diophantine problem of representing integers n in the form (x+y+z)(1/x+1/y+1/z) for rationals x, y, z. For fixed n, the equation represents an elliptic curve, and the existence of solutions depends upon the rank of the curve being positive. They observed that the corresponding equation in four variables, the title equation here (representing a surface), has infinitely many solutions for each n, and remarked that it seemed plausible that there were always solutions with positive w, x, y, z when n >=3D 16. This is false, and the situation is quite subtle. We show that there cannot exist such positive solutions when n is of the form 4m(2), 4m(2) + 4, where m not equivalent to 2 (mod 4). Computations within our range seem to indicate that solutions exist for all other values of n.
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  • CHANGING W > Y IN SYRIAC

    Aim, Emmanuel  

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  • Ternary arsenides RECo5As3 (RE?=?Y, Gd, Tb, Dy, Ho, Er)

    Zhak, O.   Senkiv, I.   Babyzhetskyy, V.   Dzevenko, M.   Bigun, I.   Havela, L.   Ma?ková, S.   Paukov, M.  

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  • The equation (w + x + y + z)(1/w + 1/x + 1/y + 1/z) = n

    Bremner, Andrew   Xuan, Tho Nguyen  

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  • Ternary arsenides RECo5As3 (RE =3D Y, Gd, Tb, Dy, Ho, Er)

    Zhak, O.   Senkiv, I.   Babyzhetskyy, V.   Dzevenko, M.   Bigun, I.   Havela, L.   Maskova, S.   Paukov, M.  

    A series of new ternary arsenides RECo5As3 (RE =3D Y, Gd, Tb, Dy, Ho, Er) was synthesized from pure constituents. The crystal structure of TbCo5As3 and ErCo5As3 was determined by X-ray single-crystal diffraction, the structure of the other arsenides was refined from X-ray powder diffraction data. These compounds are isotypic with the YCo5P3 structure (space group Pnma, Pearson code oP36): a =3D 12.249(8), b =3D 3.803(5), c =3D 10.749(5)angstrom for GdCo5As3; a =3D 12.2350(10), b =3D 3.7896(2), c =3D 10.7290(7) angstrom, (R1 =3D 0.030 (wR2 =3D 0.038) for 828 reflections with I-o > 2 sigma(I-o)) for TbCo5As3; a =3D 12.225(2), b =3D 3.781(7), c =3D 10.715(5) angstrom for DyCo5As3; a =3D 12.214(4), b =3D 3.775(4), c =3D 10.709(1) angstrom for HoCo5As3; a =3D 12.2033(7), b =3D 3.7685(2), c =3D 10.7009(4) angstrom, (R1 =3D 0.039 (wR2 =3D 0.062) for 921 reflections with I-o > 2 sigma(I-o)) for ErCo5As3. The structure contains distorted trigonal prisms [AsRE2Co4] condensed together by edges from RE atoms to infinite zig-zag chains. TbCo5As3 was identified as having an antiferromagnetic ground state with the Neel temperature T-N =3D 55-60 K, which is obscured by spurious metallic Co. (C) 2016 Elsevier B.V. All rights reserved.
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  • M OVIE REVIEWS: W HO ARE THE READERS?

    Jose Ignacio Azuela-Flores   Victor Fernandez-Blanco   Maria Jose Sanzo-Perez  

    The analysis of the relationship between movie reviews and consumer's decision process has focused mainly on the side of critics, who have been defined as "influencers" or as "predictors" (Eliashberg & Shugan, 1997). Also, new ways to measure the impact of the critic have been introduced (Gemser, van Oostrum & Leenders, 2007) and the consistency of their opinions over time has been proved (Ginsburgh & Weyers, 1999). However, there is scarce evidence about the readers of movie reviews: who are they and what is their profile. The objective of this paper is to fill this gap. Using information of Spanish consumers, we estimate a nested logit model that identifies movie review readers. The preliminary results suggest that movie review readers are mainly employed young women without family responsibilities
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