Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies

Sequence analysis of the mitochondrial genome has become a routine method in the study of mitochondrial diseases. Quite often, the sequencing efforts in the search of pathogenic or disease-associated mutations are affected by technical and interpretive pr

Fast and effective analysis methods for fiber Raman amplifiers

A series of new single-step methods and their corresponding algorithms with automatic step size adjustment for model equations of fiber Raman amplifiers are proposed and compared in this paper. On the basis of the Newton-Raphson method, multiple shooting algorithms for the two-point boundary value problems involved in solving Raman amplifier propagation equations are constructed. A verified example shows that, compared with the traditional Runge-Kutta methods, the proposed methods can increase the accuracy by more than two orders of magnitude under the same conditions. The simulations for Raman amplifier propagation equations demonstrate that our methods can increase the computing speed by more than 5 times, extend the step size significantly, and improve the stability in comparison with the Dormand-Prince method. The numerical results show that the combination of the multiple shooting algorithms and the proposed methods has the capacity to rapidly and effectively solve the model equations of multipump Raman amplifiers under various conditions such as co-, counter- and bi-directionally pumped schemes, as well as dual-order pumped schemes.

DEVELOPMENT OF CURRENT-BASED MICROSCOPIC DEFECT ANALYSIS-METHODS AND ASSOCIATED OPTICAL FILLING TECHNIQUES FOR THE INVESTIGATION ON HIGHLY IRRADIATED HIGH-RESISTIVITY SILICON DETECTORS

Current based microscopic defect analysis methods such as current deep level transient spectroscopy (I-DLTS) and thermally stimulated current (TSC) have been further developed in accordance with the need for the defect analysis of highly irradiated (Phi(n) > 10(13) n/cm(2)) high resistivity silicon detectors. The new I-DLTS/TSC system has a temperature range of 8 K less than or equal to T less than or equal to 450 K and a high sensitivity that can detect a defect concentration of less than 10(10)/cm(3) (background noise as low as 10 fA). A new filling method using different wavelength laser illumination has been applied, which is more efficient and suitable than the traditional voltage pulse filling. It has been found that the filling of a defect level depends on such factors as the total concentration of free carriers generated or injected, the penetration length of the laser (laser wavelength), the temperature at which the filling is taking place, as well as the decay time after the filling (but before the measurement). The mechanism of the defect filling can be explained by the competition between trapping and detrapping of defect levels, possible capture cross section temperature dependence, and interaction among various defect levels in terms of charge transferring. Optimum defect filling conditions have been suggested for highly irradiated high resistivity silicon detectors.

Earthquake Stability Analysis about Fine Grinded Tailings Dams

Based on the broken characteristics about earthquake to tailings dams, the earthquake stability analysis methods for tailings dams are introduced. Taking fine tailings dam in Longdu Tailings Pool as an example, the stability of the dam with various situations while earthquake with seven magnitude takes place there. The results can be used by Longdu Mine for tailings pool safety management.

Microscopic analysis of defects in a high resistivity silicon detector irradiated to 1.7x10(15)n/cm(2)

Current-based microscopic defect analysis methods with optical filling techniques, namely current deep level transient spectroscopy (I-DLTS) and thermally stimulated current (TSC), have been used to study defect levels in a high resistivity silicon detector (p(+)-n-n(+)) induced by very high fluence neutron (VHFN) irradiation (1.7x10(15) n/cm(2)). As many as fourteen deep levels have been detected by I-DLTS. Arrhenius plots of the I-DLTS data have shown defects with energy levels ranging from 0.03 eV to 0.5 eV in the energy band gap. Defect concentrations of relatively shallow levels (E(t) < 0.33 eV) are in the order of 10(13)cm(-3), while those for relatively deep levels (E(t) > 0.33 eV) are in the order of 10(14) cm(-3). TSC data have shown similar defect spectra. A full depletion voltage of about 27,000 volts has been estimated by C-V measurements for the as-irradiated detector, which corresponds to an effective space charge density (N-eff) in the order of 2x10(14) cm(-3). Both detector leakage current and full depletion voltage have been observed to increase with elevated temperature annealing (ETA). The increase of the full depletion voltage corresponds to the increase of some deep levels, especially the 0.39 eV level. Results of positron annihilation spectroscopy have shown a decrease of total concentration of vacancy related defects including vacancy clusters with ETA, suggesting the breaking up of vacancy clusters as possible source of vacancies for the formation of single defects during the reverse anneal.

香港地区湍蛙遗传多样性研究

依据线粒体上ND2和CO1两个变异较大的基因序列分析了香港地区香港湍蛙7种群、华南湍蛙1种群，以及大陆其他地区华南湍蛙7种群，戴云湍蛙1种群，武夷湍蛙1种群的系统发育关系，进而探讨香港湍蛙的遗传多样性、香港湍蛙特有性、如何确定香港湍蛙最佳保护单元以及这四种湍蛙的物种分类地位。 1． 香港湍蛙保护遗传学研究 香港湍蛙核苷酸传多样性较低，从其遗传多样性信息、单倍型网络分析、中性检验值以及岐点分布结果一致显示香港湍蛙很可能经历了瓶颈后的扩张，种群正在由一个较小的有效种群大小迅速增长, 有足够的时间通过变异用于积累单倍型的多态性, 而对于提高核苷酸多样化而言, 时间尚短（Nei M et al，1975，Avise J C，2000；李明等，2003）。 分子变异分析结果显示香港湍蛙种群间存在较多的基因交流，且系统发育树上各种群间交叉在一起，没有形成与地理单元相关的分支，而从其单倍型网络看，他们源于共同的祖先，是一个单系群，与地理单元间没有形成显著的遗传分化。因此应作为一个进化显著单元（ESU）。结合其与其他湍蛙发育关系及遗传距离以及野外采集信息认为香港湍蛙只在香港地区有分布，属于香港特有种。该物种内遗传多样性较低，又属于世界自然保护联盟红皮书中的近危种，同时也是《野生动物保护条例》中的受保护野生动物，且由于香港城市建设等使得其栖息环境受到威胁，因此在香港特别行政区应该受到重点保护。 从单倍型分布和核苷酸多样性可以看出大榄涌种群和城门种群具有较高的单倍型多样性和核苷酸多样性，应该作为保护的重点区域。 2. 华南湍蛙东、南沿海种群间系统关系 华南湍蛙分布广，各种群存在着丰富的遗传多样性信息且中部种群广西龙胜和湖南张家界种群核苷酸多样性明显高于其他边缘种群华南湍蛙。种群间几乎没有基因交流，且各种群间无共享单倍型，可见已形成了显著的遗传分化。各种群间遗传距离都较远，其中广东南昆山种群以及福建三港种群与其他种群距离最远，因此可以推测其他种群（广东深圳、香港大屿山、广西龙胜和防城以及湖南张家界种群）可能为独立进化的种群。但是否是一新种或一隐存种，还需要结合形态学进行更深入的研究。 本研究中无论从系统关系看还是从遗传距离看，大屿山种群与深圳种群最近，支持陈坚峰等将其定为华南湍蛙，即华南湍蛙新增一个分布点：香港大屿山。 系统树上广西防城种群（支B）与龙胜和湖南种群（支A）形成姐妹群。香港大屿山种群与深圳种群先形成姐妹群（支C），但却没有与其距离很近的广东南岭及南昆山种群（支D）形成姐妹群，可能粤北和粤中的环境及气候较复杂因此与粤南其他种群形成了明显的隔离。同时可以看出华南湍蛙种群遗传分化与地理距离没有显著的相关性。 3. 四种湍蛙间的系统关系 根据线粒体CO1基因建立四种湍蛙间的系统关系及其遗传距离，很清楚地看到，香港湍蛙与戴云湍蛙关系很近，而华南湍蛙则与武夷湍蛙较近。然而，戴云湍蛙同一个种群内部共有两个单倍型DY1和DY2，且两个单倍型间遗传距离大于DY1与香港湍蛙间遗传距离，更远远大于香港湍蛙种群内部的距离，即戴云湍蛙内部两个单倍型间遗传距离达到了种级水平，同样在系统发育树上这两个单倍型与香港湍蛙形成并系。但是，戴云湍蛙种内在形态上差异不显著。因此，其是否属于萌芽物种分化形成（budding speciation）或已经完全分化为两个不同的种值得进一步研究？ 与戴云湍蛙香港湍蛙关系类似，从系统树上看华南湍蛙不形成单系，而是分成两个大支，与武夷湍蛙形成并系，且福建和南昆山的华南湍蛙与武夷湍蛙遗传距离远大于武夷湍蛙种内福建种群与浙江种群的遗传距离，达到了种级分化水平。由此，可以推断武夷湍蛙是有效种。系统树上广东深圳、香港大屿山、广西防城和龙胜以及湖南张家界种群与华南湍蛙福建及南昆山各种群间遗传距离已超出了种内各种群间的遗传距离，但是至于这一支是否应为另外一个种，有必要扩大采样，并结合核基因及形态信息进行进一步研究。 MtDNA of ND2 and CO1 gene were used to investigate genetic diversity of Amolops in Hongkong .We collected seven populations of A. hongkongensis,，one population of A.ricketti from Hong Kong and other seven populations of A.ricketti from East and South of Chinese mainland. As well as one population of A. daiyunensis and one population of A.wuyiensis Phylogenetic relationship were analyzed of four species. Discussed whether A.hongkongensis is an endemic species and how can we make the conservation and management decisions. 1. Conservation Genetics of A. hongkongensis A. hongkongensis has a low nucleotide diversity, the results of genetic diversity, haplotype network, neutrality test and the mismatch distributions indicate that A. hongkongensis experienced a recent expansion after a bottle neck. They had enough time to accumulated haplotype diversity, but it’s too short to have a high nucleotide diversity（Nei M et al，1975，Avise J C，2000；Li et al，2003）. The result of AMOVA reveals that it has much gene exchange among the populations of A. hongkongensis. The clades of the phylogenetic tree were mixed together, no significant genetic differentiation among 8 populations and they share the same ancestor from the network analysis, these indicate that they are monophyly and should be protected as one ESU. Combined with the information of relationships of interspecies, genetic distance and distribution investigate, We conclude that A. hongkongensis is an endemic species of Hong Kong. Considering on the status of low genetic diversity in A.hongkongensis, and this species was listed in the IUCN red list as near threatened, as well as listed in the . Furthermore, it’s habitat loss and degradation more rapidly as the human activity got higher and higher. So it’s urgent to protect them in Hong Kong. Our results suggest that Tai Lam Wu and TAI MO Shan -Shing Mun populations have the higher priority to be protected because their higher genetic diversity. 2．Phylogenetic relationships among populations of Amolops ricketti from the Southern and eastern China A. ricketti has the considerable genetic diversity of mitochondrial haplotypes within and among populations, and Mitochondrial DNA diversity was higher in populations at the central area of the present distribution range of the frog，i. e. the Longsheng population and Zhangjiajie population, than at the edges of their distribution range. They have no share haplotype among populations, and have a significant genetic differentiation. Genetic distance is high among the populations, especially the distance of Nankun and Sangang group with others, which suggested that they evolved independently. May be there is a cryptic species or a new species, a further study is needed. The results of gene tree and the genetic distance clearly demonstrate that the population from LanTau island is A. ricketti, so we agree with Chen et al(2005) . That means A.ricketti have a new distribution site: LanTau island, HongKong. Phylogenetic relationships were analyzed through NJ and Mrbayes methods and got a consistent topological structure, the structure indicated that the ingroup were comprised four groups. Populations Longsheng and Zhangjiajie were first clustered as clade A; Populations Fangcheng was clustered together (clade B) as a sister group to clade A；Populations Shenzhen and Lantau island were sister groups and clustered as clade C；Then the clade D included populations Nankunshan and Nanling in Guangdong province and Sangang in Fujian province. 3. Phylogenetic Relationships among these four specises Phylogenetic relationships based on 1503bp CO1 gene and the genetic distance show that A. hongkongensis close to A. daiyunensis whereas A.ricketti near to A.wuyiensis. Nevertheless, there are two haplotypes in A.daiyunensis and the genetic distance between them higher than the distance between DY1 with A. hongkongensis. A. hongkongensis is nested in the paraphyletic ancestral species A. daiyunensis. Without significant difference in the morphological characters, So, we considered both A.daiyunensis and A.hongkongensis are valid species, may be this represents a case of ‘budding speciation’ like Batrachuperus pinchonii(Fu and Zeng,2008) in the population of A. daiyunensis. Just like two species above A. wuyiensis and A. ricketti are not monophyly, instead, A.wuyiensis is nested in the paraphyletic ancestral species A.ricketti. We need do more research to make sure whether they are new species.

Ulva and Enteromorpha (Ulvaceae, Chlorophyta) from two sides of the Yellow Sea: analysis of nuclear rDNA ITS and plastid rbcL sequence data

Ulvacean green seaweeds are common worldwide; they formed massive green tides in the Yellow Sea in recent years, which caused marine ecological problems as well as a social issue. We investigated two major genera of the Ulvaceae, Ulva and Enteromorpha, and collected the plastid rbcL and nuclear ITS sequences of specimens of the genera in two sides of the Yellow Sea and analyzed them. Phylogenetic trees of rbcL data show the occurrence of five species of Enteromorpha (E. compressa, E. flexuosa, E. intestinalis, E. linza and E. prolifera) and three species of Ulva (U. pertusa, U. rigida and U. ohnoi). However, we found U. ohnoi, which is known as a subtropical to tropical species, at two sites on Jeju Island, Korea. Four ribotypes in partial sequences of 5.8S rDNA and ITS2 from E. compressa were also found. Ribotype network analysis revealed that the common ribotype, occurring in China, Korea and Europe, is connected with ribotypes from Europe and China/Japan. Although samples of the same species were collected from both sides of the Yellow Sea, intraspecific genetic polymorphism of each species was low among samples collected worldwide.

Thermocapillary Convection in Floating Zones

This paper provides an overview of ongoing studies in the area of thermocapillary convection driven by a surface tension gradient parallel to the free surface in a floating zone. Here, research interests are focused around the onset of oscillatory thermocapillary convection, also known as the transition from quasisteady convection to oscillatory convection. The onset of oscillation depends on a set of critical parameters, and the margin relationship can be represented by a complex function of the critical parameters. The experimental results indicate that the velocity deviation of an oscillatory flow has the same order of magnitude as that of an average flow, and the deviations of other quantities, such as temperature and free surface radii fluctuations, are much smaller when compared with their normal counterparts. Therefore, the onset of oscillation should be a result of the dynamic process in a fluid, and the problem is a strongly nonlinear one. In the past few decades, several theoretical models have been introduced to tackle the problem using analytical methods, linear instability analysis methods, energy instability methods, and unsteady 3D numerical methods. The last of the above mentioned methods is known to be the most suitable for a thorough analysis of strong nonlinear processes, which generally leads to a better comparison with the experimental results. The transition from oscillatory thermocapillary convection to turbulence falls under the studies of chaotic behavior in a new system, which opens a fascinating new frontier in nonlinear science, a hot research area drawing many recent works. This paper reviews theoretical models and analysis, and also experimental research, on thermocapillary connection in floating zones. It cites 93 references.

波片相位延迟的精确测量及影响因素分析

提出一种精确测量波片相位延迟的方法。将待测波片置于起偏器和检偏器之间,转动待测波片和检偏器至不同的位置并探测输出的光强,得到波片的相位延迟。采用光源调制技术和解调技术,抑制了连续光所无法克服的背景光干扰和电子噪声的干扰;将光路分为测量光路和参考光路,采用软件除法技术,消除了光源波动的影响,从而实现波片相位延迟的精确测量。详细分析了影响测量精度的误差因素,主要有光源波长变化、温度变化、入射角倾斜、转台转角误差和光源波动,计算了1064 nm波长时厚度为0.52 mm的λ/4多级结晶石英波片产生的相位延迟误差

Persistent Photoconductivity in n-type GaN

The persistent photoconductivity（PPC） phenomena in n-type GaN Films grown by metalorganic chemical vapor deposition（MOCVD） have been studied. After using some testing and analysis methods, such as the double crystal X-ray diffraction（DCXRD）, the photolumineseence（PL） spectra, etc, it is found that the issue which influences PPC in n-type GaN is not relative to the dislocations and yellow band （YB）, and is caused by the doping level of Si most likely.

二进制程序安全缺陷静态分析方法的研究综述

对现有二进制程序安全缺陷静态分析方法进行了综述和分析,提出了整个程序分析过程中的关键问题以及二进制程序安全分析的主要研究方向.通过对二进制程序缺陷静态分析流程的总结,发现二进制程序信息恢复是整个分析过程的关键,构造内容丰富的、通用的中间表示是二进制程序缺陷分析的重要研究方向.

Optimization of magnetic field for CR dipole magnet

High homogeneity of the CR (collector ring) dipole magnet for FAIR (Facility for Antiproton and Ion Research) project at GSI is essential. The two optimized and analysis methods are introduced in detail. In order to obtain an ideal integral magnetic field distribution, the complicated end chamfer has been designed. By chamfering the removable pole, the distribution tolerance of high magnetic field is optimized to +/- 2 x 10(-4). The method of adding a mirror plane is suitable for the high magnetic field and it doesn't fit the low one. The OPERA is used to optimize the dipole magnetic field.

小麦抗旱生态分类中适合性聚类方法的研究

探索了适合于小麦品种抗旱生态分类的聚类方法 .选用 2 1个农艺性状和 15个冬小麦品种 (系 ) ,在聚类分析的各环节上 ,通过采用不同的策略 ,大规模进行了各种分类结果的比较 .结果表明 ,在与专家经验分类接近程度上 ,数据转换方法中 ,原始数据法依次大于普通相关阵基础上的方差极大正交旋转法、Promax斜交旋转法、主成份法 ;相似性度量上 ,欧氏距离大于马氏距离 ;聚类方式上 ,对应分析法和模糊聚类法大于最短距离法、最长距离法、类平均法 ;所有可组合的方法中 ,以对应分析法和直接用原始数据的模糊聚类法的分类结果最接近专家经验分类 .结合各方法理论上优缺点的分析与检验 ,认为这两种方法也是较理想的方法 .