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This paper presents a maximum likelihood approach to estimating the variation of substitution rate among nucleotide sites. We assume that the rate varies among sites according to an invariant+gamma distribution, which has two parameters: the gamma parameter alpha and the proportion of invariable sites theta. Theoretical treatments on three, four, and five(More)
In this article, we explore the pattern of type I functional divergence (i.e., altered functional constraints or site-specific rate difference) in the caspase gene family that is important for apoptosis (programmed cell death) and cytokine maturation. By taking advantage of substantial experimental data from caspases, the functional/structural basis of our(More)
When the rate variation among sites is described by a gamma distribution, an important problem is how to estimate the shape parameter alpha, which is an index of the degree of among-site rate variation. The parsimony-based methods for estimating alpha are simple but biased, i.e., alpha tends to be overestimated. On the other hand, the likelihood-based(More)
The three-dimensional structure of native SHL-I, a lectin from the venom of the Chinese bird spider Selenocosmia huwena, has been determined from two-dimensional 1H NMR spectroscopy recorded at 500 and 600 MHz. The best 10 structures have NOE violation <0.3 A, dihedral violation <2 deg, and average root-mean-square differences of 0.85 + 0.06 A over backbone(More)
It is well known that the rate of amino acid substitution varies among different proteins and among different sites of a protein. It is, however, unclear whether the extent of rate variation among sites of a protein and the mean substitution rate of the protein are correlated. We used two approaches to analyze orthologous protein sequences of 51 nuclear(More)
Abstract: Evaluation of human leukocyte antigen (HLA) class I and class II genes was performed on patients from China with Schistosomiasis japonica. Patients were categorized as grade 0 (n=44), grade I (n=81), grade II (n=99), or grade III (n=6) based on increasing severity of hepatic fibrosis due to repeated Schistosoma japonicum infections. These results(More)
The discovery of copy number variation (CNV) in the genome has provided new insight into genomic polymorphism. Studies with chickens have identified a number of large CNV segments using a 385k comparative genomic hybridization (CGH) chip (mean length >140 kb). We present a detailed CNV map for local Chinese chicken breeds and commercial chicken lines using(More)
  • X Gu
  • 1997
In this paper, a simple distance measure was used to estimate the age (T) of the common ancestor of eukaryotes and prokaryotes which takes the rate variation among sites and the pattern of amino acid substitutions into account. Our new estimate of T based on Doolittle et al.'s data is about 2.5 billion years ago (Ga), with 95% confidence interval from 2.1(More)
BACKGROUND Prompt injection of epinephrine is the cornerstone of systemic anaphylaxis treatment. The rate of epinephrine absorption has not been reported previously in allergic children. OBJECTIVE Our objective was to study the clinical pharmacology of epinephrine in this population. METHODS We performed a prospective, randomized, blinded,(More)
Isothiocyanates (ITCs) are nonnutrient compounds in cruciferous vegetables with anticarcinogenic properties. One proposed mechanism for their protective action is through down-regulation of cytochrome P-450 biotransformation enzyme levels and induction of phase II detoxifying enzymes. Because ITCs also serve as a substrate for GSTs, we evaluated dietary(More)