Parametric multiple sequence alignment and phylogeny construction

Bounds are given on the size of the parameter-space decomposition induced by multiple sequence alignment problems where phylogenetic information may be given or inferred. It is shown that many of the usual formulations of these problems fall within the same integer parametric framework, implying that the number of distinct optima obtained as the parameters are varied across their ranges is polynomially bounded in the length and number of sequences.     

A mathematical analysis of a fish school model

A model proposed in the literature for fish schools of relatively large size is studied for mathematical and qualitative properties. Existence, uniqueness and positivity of solutions are established and bifurcation properties relative to diffusion and alignment parameters are studied.     

压印光刻中的两步对正技术

压印光刻中套刻需要粗、精两级对正.实验采用一对斜纹结构光栅作为对正标记.利用物镜组观察光栅标记图像的边界特征进行粗对正,其准确度在精对正信号的捕捉范围内；利用光电接收器件阵列组合接收光栅莫尔信号，在莫尔信号的线区进行精对正.由于线性区的斜率大, 精对正过程中得到相应x,y方向的对正误差信号灵敏度高,利用高灵敏度对正误差信号作为控制系统的驱动信号,对承片台进行驱动定位,实现精对正.最终使X,Y方向上的重复对正准确度分别达到了± 21 nm(± 3σ)和±24 nm(± 3σ).     

Decomposition algorithms for the tree edit distance problem

We study the behavior of dynamic programming methods for the tree edit distance problem, such as [P. Klein, Computing the edit-distance between unrooted ordered trees, in: Proceedings of 6th European Symposium on Algorithms, 1998, p. 91–102; K. Zhang, D. Shasha, SIAM J. Comput. 18 (6) (1989) 1245–1262]. We show that those two algorithms may be described as decomposition strategies. We introduce the general framework of cover strategies, and we provide an exact characterization of the complexity of cover strategies. This analysis allows us to define a new tree edit distance algorithm, that is optimal for cover strategies.     

N(~4S)+NO(X~2II)→N_2(X~3Σ_g~-)+O(~3P)反应的立体动力学(英文)

采用准经典轨线方法研究了在不同碰撞能下,碰撞反应N(4S) NO(X2!)→N2(X3"g-) O(3P)在两个最低势能面3A″和3A′产物与反应物之间的矢量相关.结果表明,对于不同的碰撞能,在两个势能面上反应产物的转动取向展示了不同的特征和趋势.发生在3A″势能面上的反应主要由外平面机理支配,而发生在3A′势能面上的反应倾向于受内平面机理支配.这些差异来自于两个势能面的不同构型.     

软光刻技术制备液晶显示用定向层

以偶氮聚合物光致表面起伏光栅为模板,制备聚二甲基硅氧烷(PDMS)弹性印章,再以可溶性聚酰亚胺(PI)为“墨水”,在石英玻璃上压印出具有规则起伏结构的PI薄膜.由此制备的PI薄膜显示出很好的使液晶分子定向排列的效果.此方法成本低、效率高,是一种实用的液晶定向层薄膜制备方法.     

Carbon nanotube dielectrophoresis: Theory and applications

Carbon nanotubes (CNTs) are one of the most extensively studied nanomaterials in the 21st century. Since their discovery in 1991, many studies have been reported advancing our knowledge in terms of their structure, properties, synthesis, and applications. CNTs exhibit unique electrothermal and conductive properties which, combined with their mechanical strength, have led to tremendous attention of CNTs as a nanoscale material in the past two decades. To introduce the various types of CNTs, we first provide basic information on their structure followed by some intriguing properties and a brief overview of synthesis methods. Although impressive advances have been demonstrated with CNTs, critical applications require purification, positioning, and separation to yield desired properties and functional elements. Here, we review a versatile technique to manipulate CNTs based on their dielectric properties, namely dielectrophoresis (DEP). A detailed discussion on the DEP aspects of CNTs including the theory and various technical microfluidic realizations is provided. Various advancements in DEP-based manipulations of single-walled and multiwalled CNTs are also discussed with special emphasis on applications involving separation, purification, sensing, and nanofabrication.     

Non-rigid landmark-based large-scale image registration in 3-D reconstruction of mouse and rat kidney nephrons

BackgroundSerial histological sections are suffering from mechanical distortions that disturb the reconstruction of 3-D objects. We have corrected such artifacts with a non-rigid landmark-based method that respects the original geometry in the tissue block. The method is exemplified on a large scale in the registration of semi-thin serial sections of the mouse and rat kidneys, and has been tested on FFPE-sections.AimIn this study of mouse and rat kidneys, we have measured and characterized the deformations introduced in the preparation of 2.5-μm-thick Epon sections and then eliminated them by a landmark-based non-rigid transformation (NRT).MethodsWe obtained 2.5-μm-thick serial Epon sections from three mouse kidneys and three rat kidneys for 3-D reconstruction of the nephron tubules. First, the images from 3000 serial mouse and 13,000 serial rat sections underwent a classic rigid registration (CRR), and the distortions were measured and indexed. The section images underwent a further NRT in order to compensate for the deformations. The NRT used is a classic interactive landmark-based approach. The quality of the NRT was verified by comparing the geometry of the transformed images with corresponding block images.ResultsAfter CRR, the 2.5-μm-thick sections had a linear deformation of up to 2%, the tubular lengths were overestimated with up to 1.5×, and it was most difficult to trace the tubules from section to section. After the additional NRT, the geometry of the images reflected the original geometry in the block, the tubular lengths were no longer overestimated, and the NRT highly facilitated the tracing of the tubular system.ConclusionsNRT has facilitated the tracing of the tubular system in kidneys, a tracing, which would otherwise have been most difficult to perform. NRT has yielded substantial new knowledge to segmental and spatial nephron organization in the mouse and rat kidneys.     

DNA序列比对数目的算法研究

生物序列比对是生物信息学中非常重要的内容.文[1]中作者用差分方程理论给出了求两DNA序列间比对数目的一个计算公式,然而解法较为繁琐.本文将借助于组合数学中母函数这一计数工具给出另一简单、优美的算法,并在此基础上剔除非生物比对,得到进一步的计算公式,这一结果缩小了需要考查的比对范围.     

Comparison of two algorithmic data processing strategies for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry

The alignment algorithm Statistical Compare (SC) developed by LECO Corporation for the processing of comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOFMS) data was validated and compared to the in-house developed retention time correction and data alignment tool INCA (Integrative Normalization and Comparative Analysis) by a spike-in experiment and the comparative metabolic fingerprinting of a wild type versus a double mutant strain of Escherichia coli (E. coli). Starting with the same peak lists generated by LECO's ChromaTOF software, the accuracy of peak alignment and detection of 1.1- to 4-fold changes in metabolite concentration was assessed by spiking 20 standard compounds into an aqueous methanol extract of E. coli. To provide the same quality input signals for both alignment routines, the universal m/z 73 trace of the trimethylsilyl (TMS) group was used as a quantitative measure for all features. The performance of data processing and alignment was evaluated and illustrated by ROC curves. Statistical Compare performed marginally better at the lower fold changes, while INCA did so at the higher fold changes. Using SC, quantitative precision could be improved substantially by exploiting the signal intensities of metabolite-specific unique (U) m/z ion traces rather than the universal m/z 73 trace. A list of 56 features that distinguished the two E. coli strains was obtained by the SC alignment using m/z U with an estimated false discovery rate (FDR) of <0.05. Ultimately, 23 metabolites could be identified, one additional and five less than with INCA due to the failure of SC to extract unitized m/z U's across all fingerprints with suitable spectral intensities for the latter metabolites.