Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44

Gene clusters are becoming promising tools for gene identification. The study reveals the purposive genomic distribution of genes toward higher inheritance rates of intact metabolic pathways/phenotypes and, thereby, higher fitness. The co-localization of co-expressed, co-interacting, and functionally related genes was found as genome-wide trends in humans, mouse, golden eagle, rice fish, Drosophila, peanut, and Arabidopsis. As anticipated, the analyses verified the co-segregation of co-localized events. A negative correlation was notable between the likelihood of co-localization events and the inter-loci distances. The evolution of genomic blocks was also found convergent and uniform along the chromosomal arms. Calling a genomic block responsible for adjacent metabolic reactions is therefore recommended for identification of candidate genes and interpretation of cellular functions. As a case story, a function in the metabolism of energy and secondary metabolites was proposed for Slc25A44, based on its genomic local information. Slc25A44 was further characterized as an essential housekeeping gene which has been under evolutionary purifying pressure and belongs to the phylogenetic ETC-clade of SLC25s. Pathway enrichment mapped the Slc25A44s to the energy metabolism. The expression of peanut and human Slc25A44s in oocytes and Saccharomyces cerevisiae strains confirmed the transport of common precursors for secondary metabolites and ubiquinone. These results suggest that SLC25A44 is a mitochondrion-ER-nucleus zone transporter with biotechnological applications. Finally, a conserved three-amino acid signature on the cytosolic face of transport cavity was found important for rational engineering of SLC25s.     

Simulation of polymer systems

The present paper describes an algorithm which can generate, even on a small computer, arbitrarily long polymer chains, making sure that the configurations generated do not suffer from boundary effects. This has been achieved by employing the concept of a window, which is an analogue of virtual memory scheme. The algorithm has been tested for the case of dilute polymer solution.     

加工时间线性递减的链约束单机排序问题

讨论了工件的加工时间是开工时间的线性递减函数、工件之间有平行链约束的单机排序问题.对于链可中断和不可中断两种情况,给出了极小化总完工时间的最优算法.     

Side‐chain effects on the morphology and properties of fluorene‐based alternating copolymers

Soluble fluorene‐based alternating copolymers containing benzene as the comonomer were synthesized and characterized, in which three different side chains (hydrogen atom, linear octyloxy and bulky benzyloxy groups) were attached to the phenylene ring. The effect of the side chains with different steric hindrances on the photophysical, thermal and electrochemical properties as well as the morphology were investigated. Moreover, the chain conformation and spectroscopic properties in dilute solution were studied to understand the solvent effect. Aliphatic and aromatic solvents were demonstrated to have different influences on the spectra of the polymers owing to various interaction mechanisms in the excited states. Also, a significant decrease of up to 80 °C in the thermal degradation temperature was observed as a result of the introduction of large benzyloxy units. The energy levels of the highest occupied molecular orbital and the lowest unoccupied molecular orbital of the polymers were estimated to be ? 5.76 to ? 5.82 eV and ? 2.19 to ? 2.27 eV, respectively, from cyclic voltammetry measurements. In addition, the electronic structures of the polymers were described via quantum chemical calculations. Copyright © 2007 Society of Chemical Industry     

Markoff chain modelling of NDI techniques

A procedure for non‐destructive inspection by taking into account the effects of stochastic fatigue crack growth is presented. For this purpose a Markoff chain model is used to update the crack statistics, allowing an efficient computational implementation and a clear account of the involved concepts. In this context, perfect and imperfect removal of cracks, respectively, are considered, which represent idealizations defining bounds for actual situations.     

Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t ≤ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-μs conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 μs timescale to a compact intermediate I_C containing some native-like secondary structure. Although the existence and nature of I_C as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of I_C as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that I_C may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.     

Certainty equivalence control with forcing: revisited

Certainty equivalence control with forcing has been shown to be optimal for several stochastic adaptive control problems with the average cost per unit time criterion. Recently researchers have started looking at stochastic adaptive control problems with a view to minimizing the rate of increase of the learning loss. This criterion is stronger than the average cost per unit time criterion. Certainty equivalence control with forcing does not usually suffice for the learning loss criterion and one has to develop fairly complicated schemes in order to achieve optimality. The objective of this paper is to see how well one might be able to do with a certainty-equivalence-control-with-forcing type of scheme. In particular we construct a class of such schemes whose learning loss is O((log n)^1+δ) for δ > 0, whereas optimal schemes typically have a O(log n)learning loss.     

Vine Copula Specifications for Stationary Multivariate Markov Chains

Vine copulae provide a graphical framework in which multiple bivariate copulae may be combined in a consistent fashion to yield a more complex multivariate copula. In this article, we discuss the use of vine copulae to build flexible semiparametric models for stationary multivariate higher‐order Markov chains. We propose a new vine structure, the M‐vine, that is particularly well suited to this purpose. Stationarity may be imposed by requiring the equality of certain copulae in the M‐vine, while the Markov property may be imposed by requiring certain copulae to be independence copulae.     

汕头市基于改进Markov链的空气质量预报模型的研究

为了更有效的对汕头市空气质量进行预测,我们将基于Markov链理论的空气质量的统计预报模型进行了改进,加入了气象因素对模型进行修正,并作实例验证其可行性及准确率检验。证明了该模型具有较好的短期预测正确率,有一定的实用价值。     

基于MCFM模型的集贸市场火灾致灾因素分析

为降低大型集贸市场的火灾风险,探究大型集贸市场火灾致灾因素,运用解释结构模型分析各因素间的内在联系。结合交叉影响分析法和马尔可夫链预测构建定量分析模型,获得火灾致灾因素的稳态概率矩阵。研究结果表明：马尔可夫修正概率更加准确,该模型可明确大型集贸市场火灾致灾因素排查和管控的重点。