Genomic outlier profile analysis: mixture models, null hypotheses, and nonparametric estimation

In most analyses of large-scale genomic data sets, differentialexpression analysis is typically assessed by testing for differencesin the mean of the distributions between 2 groups. A recentfinding by Tomlins and others (2005) is of a different typeof pattern of differential expression in which a fraction ofsamples in one group have overexpression relative to samplesin the other group. In this work, we describe a general mixturemodel framework for the assessment of this type of expression,called outlier profile analysis. We start by considering thesingle-gene situation and establishing results on identifiability.We propose 2 nonparametric estimation procedures that have naturallinks to familiar multiple testing procedures. We then developmultivariate extensions of this methodology to handle genome-widemeasurements. The proposed methodologies are compared usingsimulation studies as well as data from a prostate cancer geneexpression study.     

松阔混交林林分空间结构分析

利用混交度、大小比数和角尺度3种结构参数结合树种组成,分析了松阔混交林林分空间结构。结果表明,优势树种马尾松多呈单种聚集,其余树种中、强度混交占了相当大的比例;马尾松在空间大小对比上占有一定的优势,其余树种则分化严重,既有占优势的树种,也有受压的树种;从林木水平分布格局上看,该地林分是以团状分布为主。     

Design of polymeric microparticles for pH-responsive and time-sustained drug release

We described the design of uniform microencapsulates with almost 100% encapsulation efficiency, synthesized without organic solvents, via microfluidic spray drying of water-based dispersions of pH-responsive methacrylic acid polymers (Eudragit^® L 30D-55). The effects of incorporating water-based network-forming materials in the formulations on pH-responsiveness and controlled release patterns of enteric microparticles were observed. Acid hydrolysed tetraethoxysilane (TEOS) was used to form an interpenetrating, rigid framework of silica, whereas Eudragit^® NE (a copolymer based on ethyl acrylate and methyl methacrylate) was added to produce a more flexible polymeric network. The spray-dried microparticles generally displayed crumbled or buckled morphologies dependent on drying temperatures, due to large hydrodynamic sizes of solutes in feed dispersions. The drug release kinetics of microparticles were sensitive to the type and the added amount of network-forming materials, due to different colloidal interactions between Eudragit^® L and either silica or the copolymer. This study demonstrated a strategy to design enteric microparticles with different microstructural properties and drug release behaviours through understanding of colloidal interactions between constituents of matrix materials.     

Wavelet threshold based ECG compression using USZZQ and Huffman coding of DSM

In this paper, a new Wavelet threshold based ECG signal compression technique using uniform scalar zero zone quantizer (USZZQ) and Huffman coding on differencing significance map (DSM) is proposed. Wavelet coefficients are selected based on the energy packing efficiency of each sub-band. Significant Wavelet coefficients are quantized with uniform scalar zero zone quantizer. Significance map is created to store the indices of the significant coefficients. This map is encoded efficiently with less number of bits by applying Huffman coding on the differences between indices in the significance map. ECG records from the MIT-BIH arrhythmia database are selected as test data. For the record 117, the proposed technique achieves a compression ratio of 18.7:1 with lower percentage root mean square difference (PRD) compared to other threshold based methods. The proposed technique is tested for MIT-BIH arrhythmia record 119 and a compression ratio of 21.81:1 is achieved with a PRD value of 3.716% which is much lower compared to the reported PRD value of 5.0 and 5.5% of set partitioning in hierarchical tress (SPIHT) and analysis by synthesis ECG compressor (ASEC), respectively. The noise eliminating capability of the proposed technique is also demonstrated in this work. The proposed technique achieves the required compression ratio with less reconstruction error for GSM-based cellular telemedicine system.     

Nonparametric tests for continuous covariate effects with multistate survival data

SUMMARY: In clinical trials and observational studies, it is often of scientific interest to evaluate the effects of covariates on complex multistate event probabilities. With discrete covariates, nonparametric tests may be constructed using estimates of the relevant quantities. With continuous covariates, a common approach is to arbitrarily discretize the covariates, which may lead to substantial information loss. Another strategy is to formulate the covariate effects in a regression model. Model-based tests may have either low power or be biased under misspecification. We propose nonparametric tests not requiring arbitrary discretization. The tests involve integrals of estimates continuously indexed by dichotomizations of the covariates. General asymptotic results are derived under null and alternative hypotheses, and verified using empirical process theory in several special cases. The tests are consistent under stochastic ordering, which arises naturally with multistate data. A novel nonparametric measure of covariate effect is studied as a natural byproduct of the testing procedure. Simulation studies and two real data analyses demonstrate the gains of the new testing procedure over those based either on categorization or on regression models.     

一类带有扩散和时滞的非自台Lotka-Volterra系统

本文讨论有时滞的扩散系统,此系统有两个种群两个斑块,其中一种种群可以在两斑块中自由扩散,另一种群被限定在斑块中不能扩散,当系数数满足一定的条件时,得到系统有持续生存和全局稳定的解。     

絮凝酵母SPSC01连续培养最适生长条件的研究

采用均匀设计实验法对气升式内环流生物反应器中絮凝酵母SPSC01的高密度培养条件进行了研究,确定了各因素与目标函数之间的关系,并通过综合调优,获得该菌株的最佳培养条件：温度30℃;通气量0714vvm;培养基组成为：双酶法制备的玉米糖化液,糖浓度为220g/L,添加4 mL/L玉米浆和3g/L（NH4）2HPO4;稀释速率控制为0.02h－1。在上述条件下进行絮凝酵母的连续培养,培养液中的酵母细胞密度达到了20g(d.w)/L以上。     

A Quasistationary Analysis of a Stochastic Chemical Reaction: Keizer’s Paradox

For a system of biochemical reactions, it is known from the work of T.G. Kurtz [J. Appl. Prob. 8, 344 (1971)] that the chemical master equation model based on a stochastic formulation approaches the deterministic model based on the Law of Mass Action in the infinite system-size limit in finite time. The two models, however, often show distinctly different steady-state behavior. To further investigate this “paradox,” a comparative study of the deterministic and stochastic models of a simple autocatalytic biochemical reaction, taken from a text by the late J. Keizer, is carried out. We compute the expected time to extinction, the true stochastic steady state, and a quasistationary probability distribution in the stochastic model. We show that the stochastic model predicts the deterministic behavior on a reasonable time scale, which can be consistently obtained from both models. The transition time to the extinction, however, grows exponentially with the system size. Mathematically, we identify that exchanging the limits of infinite system size and infinite time is problematic. The appropriate system size that can be considered sufficiently large, an important parameter in numerical computation, is also discussed.     

生物工程专业“试验设计与数据处理”教学中常用软件的探讨

试验设计与数据处理在生物工程专业方向有着重要的应用,但是在本科教学中开设该课程的高校较少。本文结合生物工程中的常见案例,对该课程教学过程中常用的软件包括Excel、正交试验设计助手、Data processing system(DPS)和Design expert在单因素、多因素、正交、均匀、P-B(Plackett-Burman)和响应面等数据处理方法进行了探讨。通过比较分析各种软件和数据处理方法之间特点,增加该课程教学的实践性和应用性,从而提高教学质量。