Digital gene expression analysis of the zebra finch genome

Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates

Evidential-EM Algorithm Applied to Progressively Censored Observations

Evidential-EM (E2M) algorithm is an effective approach for computing maximum likelihood estimations under finite mixture models, especially when there is uncertain information about data. In this paper we present an extension of the E2M method in a particular case of incom-plete data, where the loss of information is due to both mixture models and censored observations. The prior uncertain information is expressed by belief functions, while the pseudo-likelihood function is derived based on imprecise observations and prior knowledge. Then E2M method is evoked to maximize the generalized likelihood function to obtain the optimal estimation of parameters. Numerical examples show that the proposed method could effectively integrate the uncertain prior infor-mation with the current imprecise knowledge conveyed by the observed data

Decision noise may mask criterion shifts: Reply to Balakrishnan and MacDonald (2008)

J. D. Balakrishnan and J. A. MacDonald (2008) argue that RTbased measures of signal detection processes provide evidence against signal detection theory’s notion of a flexible decision criterion. They argue that this evidence is immune to the alternative explanation proposed by S. T. Mueller and C. T. Weidemann (2008), that decision noise may mask criterion shifts. We show that noise in response times can produce the same effects as are produced by noise in confidence ratings. Given these results, the evidence is not sufficient to categorically reject the notion of a flexible response policy implemented through shifts in a decision criterion

Rate coefficients for rovibrational transitions in H_2 due to collisions with He

We present quantum mechanical and quasiclassical trajectory calculations of cross sections for rovibrational transitions in ortho- and para-H_2 induced by collisions with He atoms. Cross sections were obtained for kinetic energies between 10^-4 and 3 eV, and the corresponding rate coefficients were calculated for the temperature range 100<T<4000 K. Comparisons are made with previous calculations.Comment: 21 pages, 2 figures, AAS, eps

Precedence-type Test based on Progressively Censored Samples

In this paper, we introduce precedence-type tests for testing the hypothesis that two distribution functions are equal, which is an extension of the precedence life-test rst proposed by Nelson (1963), when the two samples are progressively Type-II censored. The null distributions of the test statistics are derived. Critical values for some combination of sample sizes and censoring schemes for the proposed tests are presented. Then, we present the exact power functions under the Lehmann alternative, and compare the exact power as well as simulated power (under location-shift) of the proposed precedence test based on nonparametric estimates of CDF with other precedence-type tests. We then examine the power properties of the proposed test procedures through Monte Carlo simulations. Two examples are presented to illustrate all the test procedures discussed here. Finally, we make some concluding remarks.Precedence test; Product-limit estimator; Type-II progressive censoring; Life-testing; level of significance; power; Lehmann alternative; Monte Carlo simulations

Studies of the superconducting properties of Sn1-xInxTe (x=0.38 to 0.45) using muon-spin spectroscopy

The superconducting properties of Sn1-xInxTe (x = 0.38 to 0.45) have been studied using magnetization and muon-spin rotation or relaxation (muSR) measurements. These measurements show that the superconducting critical temperature Tc of Sn1-xInxTe increases with increasing x, reaching a maximum at around 4.8 K for x = 0.45. Zero-field muSR results indicate that time-reversal symmetry is preserved in this material. Transverse-field muon-spin rotation has been used to study the temperature dependence of the magnetic penetration depth lambda(T) in the mixed state. For all the compositions studied, lambda(T) can be well described using a single-gap s-wave BCS model. The magnetic penetration depth at zero temperature lambda(0) ranges from 500 to 580 nm. Both the superconducting gap Delta(0) at 0 K and the gap ratio Delta(0)/kBTc indicate that Sn1-xInxTe (x = 0.38 to 0.45) should be considered as a superconductor with intermediate to strong coupling.Comment: 7 pages, 6 figures, 3 table

Distributed NEGF Algorithms for the Simulation of Nanoelectronic Devices with Scattering

Through the Non-Equilibrium Green's Function (NEGF) formalism, quantum-scale device simulation can be performed with the inclusion of electron-phonon scattering. However, the simulation of realistically sized devices under the NEGF formalism typically requires prohibitive amounts of memory and computation time. Two of the most demanding computational problems for NEGF simulation involve mathematical operations with structured matrices called semiseparable matrices. In this work, we present parallel approaches for these computational problems which allow for efficient distribution of both memory and computation based upon the underlying device structure. This is critical when simulating realistically sized devices due to the aforementioned computational burdens. First, we consider determining a distributed compact representation for the retarded Green's function matrix $G^{R}$. This compact representation is exact and allows for any entry in the matrix to be generated through the inherent semiseparable structure. The second parallel operation allows for the computation of electron density and current characteristics for the device. Specifically, matrix products between the distributed representation for the semiseparable matrix $G^{R}$ and the self-energy scattering terms in $\Sigma^{<}$ produce the less-than Green's function $G^{<}$. As an illustration of the computational efficiency of our approach, we stably generate the mobility for nanowires with cross-sectional sizes of up to 4.5nm, assuming an atomistic model with scattering