A reliable phase unwrapping algorithm based on the local fitting plane and quality map

A fast and reliable phase unwrapping (PhU) algorithm, based on the local quality-guided fitting plane, is presented. Its framework depends on the basic plane-approximated assumption for phase values of local pixels and on the phase derivative variance (PDV) quality map. Compared with other existing popular unwrapping algorithms, the proposed algorithm demonstrated improved robustness and immunity to strong noise and high phase variations, given that the plane assumption for local phase is reasonably satisfied. Its effectiveness is demonstrated by computer-simulated and experimental results.

Novel method to construct a quality map for phase unwrapping based on modulation and the phase gradient

A novel method to construct a quality map, called modulation-phase-gradient variance (MPGV), is proposed, based on modulation and the phase gradient. The MPGV map is successfully applied to two phase-unwrapping algorithms - the improved weighted least square and the quality-guided unwrapping algorithm. Both simulated and experimental data testify to the validity of our proposed quality map. Moreover, the unwrapped-phase results show that the new quality map can have higher reliability than the conventional phase-derivative variance quality map in helping to unwrap noisy, low-modulation, and/or discontinuous phase maps. (c) 2006 Society of Photo-Optical Instrumentation Engineers.

Weighted least-squares phase unwrapping algorithm based on derivative variance correlation map

Among different phase unwrapping approaches, the weighted least-squares minimization methods are gaining attention. In these algorithms, weighting coefficient is generated from a quality map. The intrinsic drawbacks of existing quality maps constrain the application of these algorithms. They often fail to handle wrapped phase data contains error sources, such as phase discontinuities, noise and undersampling. In order to deal with those intractable wrapped phase data, a new weighted least-squares phase unwrapping algorithm based on derivative variance correlation map is proposed. In the algorithm, derivative variance correlation map, a novel quality map, can truly reflect wrapped phase quality, ensuring a more reliable unwrapped result. The definition of the derivative variance correlation map and the principle of the proposed algorithm are present in detail. The performance of the new algorithm has been tested by use of a simulated spherical surface wrapped data and an experimental interferometric synthetic aperture radar (IFSAR) wrapped data. Computer simulation and experimental results have verified that the proposed algorithm can work effectively even when a wrapped phase map contains intractable error sources. (c) 2006 Elsevier GmbH. All rights reserved.

色散管理孤子传输特性分析

色散管理孤子光波系统的色散图周期由具有正负色散值的两段光纤组成，并且在系统中周期性放置集中放大器及滤波器装置。采用变分法获得了描述此种系统性能的常微分方程组，并利用这组方程数值研究了各种参量对孤子传输性能的影响。研究结果表明，虽然从整体趋势上看，当要求色散管理孤子有较好的稳定性时，应适当降低系统的色散管理强度，但在一定条件下，调整光纤放大器的位置以及正负色散光纤的色散差值，可同时获得相对较大的色散管理强度和好的孤子稳定性；总体来讲，集总放大器的位置会对孤子传输的稳定性、色散管理孤子的能量增强因子、脉冲最佳

蔷薇类的分子系统学研究—兼论系统发育基因组学的原理和方法(以SET基因超家族为例)

分子系统发育分析的主要任务包括：（1）帮助建立生命之树（tree of life）;（2）追踪基因和基因家族（gene family）的起源和进化, 以获知基因在进化过程中的功能分化和伴随发生的重要分子事件（key molecular events）和形态性状的关键创新（key innovation）。这两个方面在本研究中都有所涉及。对于前者，选用植物线粒体matR基因重建被子植物蔷薇类群的系统发育关系;对于后者，则以SET基因超家族为例，探讨其在真核生物中的进化分类以及与功能多样性的关系。 I 蔷薇类的分子系统学 蔷薇类（rosids）是基于分子数据建立的被子植物的主要分支之一，包含13个目，大约三分之一的被子植物物种。两个主要蔷薇类内部分支是豆类fabids（包含7个目）和锦葵类malvids（包含3个目）。然而，这两个分支内部，以及这两个分支与蔷薇类基部类群，包括牻牛儿苗目（Geraniales）、桃金娘目（Myrtales）和流苏子目（Crossosomatales）之间的关系大多是不清楚的。本研究中，我们选取174个物种来代表72个蔷薇类（rosids）的科，利用两个数据集，即线粒体matR单基因数据集和包括线粒体matR基因、两个质体基因(rbcL、 atpB)和一个核基因(18S rDNA) 的4基因数据集，重建蔷薇类在科以上分类阶元水平的系统发育关系。同时，还对线粒体matR基因的进化特征和用于大尺度系统发育分析的适合度和潜力进行了评价。 线粒体matR单基因数据支持malvids和大多数蔷薇类目的单系性质，然而，豆类（fabids）成员没有形成一个分支，其COM亚支，包括卫矛目（Celastrales）、酢浆草目（Oxalidales）、金虎尾目（Malpighiales）和蒜树科（Huaceae），分辨为锦葵类（malvids）的姐妹群。这个关系在最近根据花结构特征曾被提出过，但从未在之前的分子系统发育分析中得到分辨。4基因数据集支持首先是牻牛儿苗目（Geraniales），接着是桃金娘目（Myrtales）作为蔷薇类（rosids）的最基部的分支;流苏子目（Crossosomatales）是锦葵类（malvids）姐妹群，以及蔷薇类（rosids）的核心部分包括豆类（fabids），锦葵类（malvids）和流苏子目（Crossosomatales）。线粒体matR基因的进化特征分析显示，与两个叶绿体基因(rbcL 和atpB)比较，同义替代速率约是它们的1/4，而非同义替代速率接近于自身的同义替代速率，表明matR 基因具有松弛的选择压力。线粒体matR基因相对慢速的进化使非同源相似（homoplasious）突变减少，提高了系统发育信息的质量，同时，松弛的选择压力使非同义替代数量增加，弥补了慢速进化导致的系统发育信息数量不足的缺陷，这两个方面的结合使线粒体matR基因非常适用于被子植物在科以上水平的系统发育研究。 II SET基因超家族的系统发育基因组学分析 SET基因超家族基因编码含有SET结构域的蛋白，在真核生物中，SET-domain蛋白一般是多结构域（multi-domain）的。SET-domain蛋白具有对组蛋白H3和H4的N末端尾部进行赖氨酸残基甲基化修饰的酶活性;从异染色质形成到基因转录，甲基化的组蛋白广泛影响染色质水平的基因调控。依据SET结构域一级序列的相似性和结构域组织（domain architecture）特征，目前，SET-domain基因超家族被划分为4-7个家族。由于这些划分或者使用动物或者使用植物SET基因，只有少数其它类群的物种加入分析，因此这样的划分可能是不完整的。本研究采用系统发育基 因组学方法（phylogenomic approach），在真核生物范围内广泛取样，期望获得相对完整的SET-domain基因家族的 进化分类方案，在此基础上加深理解SET-domain基因的进化机制和功能多样性。 在提取了17个物种，代表5个真核超群的SET蛋白序列基础上，系统发育分析结合“结构域组织特征”鉴别了9个SET基因家族，其中一个是新的SET基因家族。以前的SET8和Class VI家族,及SMYD和SUV4-20家族分别合并为一个家族。大部分家族在进化过程中发生了2次以上的基因重复事件，通过获得不同的结构域产生具有不同功能的新基因。一个SET基因家族在进化过程中推测发生了从脊椎动物祖先向盘基网柄菌（Dictyostelium discoideum）的水平基因转移。

应用SVM预测杜鹃属（Rhododendron L.）在中国的潜在分布中心

杜鹃属(Rhododendron L.)是中国种子植物中最大的属，其现代分布和分化中心是我国西南部的横断山区和东喜马拉雅地区。我国西部、西南部的云南、四川、西藏等地共有杜鹃达450种，仅特有种就有约300种。对杜鹃属分布的深入研究是横断山区生物多样性保护不可缺少的重要部分。 由于物种分布与环境因子之间存在着紧密的联系，利用环境因子作为预测物种分布模型的变量是当前最普遍的建模思路。但是绝大多数物种分布预测模型都遇到了难以解决的“高维小样本”问题――模型在标本数据不足时无法给出合理的预测，或者模型无法处理大量的环境变量。机器学习领域的理论和实践已经证明，基于结构风险最小化原理的支持向量机(Support Vector Machine, SVM)算法非常适合“高维小样本”的分类问题。为了探索其应用在物种分布预测问题上的可能性，本文创新性的实现了基于SVM算法的物种分布预测系统。然后，本文以30个杜鹃属(Rhododendron L.)物种为检验对象，利用其标本数据和11个1km的栅格环境变量图层作为模型变量，预测其在中国的潜在分布区。本文通过全面的模型评估——专家评估，ROC (Receiver Operator Characteristic)曲线和曲线下方面积AUC (Area Under the Curve)——来比较模型的性能。试验结果表明，我们所实现的以SVM为核心的物种分布预测系统无论在计算速度还是预测效果上都远远优于当前广泛使用的GARP (Genetic Algorithm for Rule-Set Prediction)预测系统。 之后，本文进一步探讨了SVM预测系统预测效果与环境变量维数和标本点个数的关系。试验结果表明，对于只有少量标本点的物种SVM的预测结果仍然具有相当的合理性。由此可见， SVM预测系统很好的解决了以前众多模型无法克服的稀有种和标本点稀少的物种的潜在分布区模拟问题。同时本文发现大的环境维数（高维）对于物种潜在分布区的预测有着决定性的作用，因此模型处理高维问题的能力显得至关重要。 最后，我们使用中国所有可获取的杜鹃属标本数据，以及83个1km的栅格环境变量图层，对400种杜鹃属物种的潜在分布区进行预测。根据预测出来的物种潜在分布区，我们得到了中国杜鹃属物种潜在多样性分布格局，特有物种潜在多样性分布格局，濒危杜物种潜在的分布格局，各亚属物种潜在分布格局，以及不同生活型物种潜在多样性分布格局。这些分布区图不仅可以对杜鹃属起源研究提供分析验证的条件，还能为其引种、保护和新种的搜寻提供有利的空间依据。

Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.

Comparative map between the domestic pig and dog

Cross-species chromosome painting with probes derived from flow-sorted dog and human chromosomes was used to construct a high-resolution comparative map for the pig. In total 98 conserved autosomal segments between pig and dog were detected by probes specific for the 38 autosomes and X Chromosome of the dog. Further integration of our results with the published human-dog and cat-dog comparative maps, and with data from comparative gene mapping, increases the resolution of the current pig-human comparative map. It allows for the conserved syntenies detected in the pig, human, and cat to be aligned against the putative ancestral karyotype of eutherian mammals and for the history of karyotype evolution of the pig lineage to be reconstructed. Fifteen fusions, 17 fissions, and 23 inversions are required to convert the ancestral mammalian karyotype into the extant karyotype of the pig.

Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints

Chromosomal homologies have been established between the Chinese muntjac (Muntiacus reevesi, MRE, 2n = 46) and five ovine species: wild goat (Capra aegagrus, CAE, 2n = 60), argall (Ovis ammon, OAM, 2n = 56), snow sheep (Ovis nivicola, ONI, 2n = 52), red goral (Naemorhedus cranbrooki, NCR, 2n = 56) and Sumatra serow (Capricornis sumatraensis, CSU, 2n = 48) by chromosome painting with a set of chromosome-specific probes of the Chinese muntjac. In total, twenty-two Chinese muntjac autosomal painting probes detected thirty-five homologous segments in the genome of each species. The chromosome X probe hybridized to the whole X chromosomes of all ovine species while the chromosome Y probe gave no signal. Our results demonstrate that almost all homologous segments defined by comparative painting show a high degree of conservation in G-banding patterns and that each speciation event is accompanied by specific chromosomal rearrangements. The combined analysis of our results and previous cytogenetic and molecular systematic results enables us to map the chromosomal rearrangements onto a phylogenetic tree, thus providing new insights into the karyotypic evolution of these species.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Heroin impairs map-picture-following and memory tasks dependent on gender and orientation of the tasks

Male and female heroin-dependent patients (HDPs) matched with "normal" people were tested on 4 topographical orientation tasks: schematic map-following, map-memory, schematic picture-following, and picture-memory tasks. The results showed that, in general