模式识别在有机化合物碳—13核磁共振波谱中的应用

本文介绍了以碳—13 NMR 谱为基础,运用模式识别方法对于取代苯类有机化合物的分类情况。数据源为 CIAC-碳-13数据库。特征选择为简单的机率比率法。模式识别方法为Fisher 意义下的判别函数、KNN 及非线性映射。所得结果比较满意。

Phylogeography of the Northern Atlantic species Chondrus crispus (Gigartinales, Rhodophyta) inferred from nuclear rDNA internal transcribed spacer sequences

Eighteen isolates of the red algae Chondrus crispus were collected from Northern Atlantic sites, together with C. ocellatus, C. yendoi and C. pinnulatus from the North Pacific. The nuclear rDNA internal transcribed spacer (ITS) was sequenced and compared, spanning both the ITS regions and the 5.8S rRNA gene. Percentage of nucleotide variation for C. crispus ranged from 0.3% to 4.0%. Phylogenetic analyses were performed using maximum parsimony (MP), neighbor-joining (NJ) and minimum evolution methods. They showed that two main clades existed within the C. crispus samples examined and that suggested C. crispus had a single Atlantic origin. The clustering however did not follow the geographic origin. We hypothesized that the current distribution of C. crispus populations might be a result of three main factors: temperature boundaries, paleoclimate and paleoceanography. ITS data exhibited abundant molecular information not only for phylogeographical investigation but also for systematics studies.

Inter-simple sequence repeat (ISSR) analysis of genetic variation of Chondrus crispus populations from North Atlantic

ISSR analysis was used to investigate genetic variations of 184 haploid and diploid samples from nine North Atlantic Chondrus crispus Stackhouse populations and one outgroup Yellow Sea Chondrus ocellatus Holmes population. Twenty-two of 50 primers were selected and 163 loci were scored for genetic diversity analysis. Genetic diversity varied among populations, percentage of polymorphic bands (PPB) ranged from 27.0 to 55.8%, H(Nei's genetic diversity) ranged from 0.11 to 0.20 and I(Shannon's information index) ranged from 0.16 to 0.30. Estimators PPB, H and I had similar values in intra-population genetic diversity, regardless of calculation methods. Analysis of molecular variance (AMOVA) apportioned inter-population and intra-population variations for C crispus, showing more genetic variance (56.5%) occurred in intra-population, and 43.5% variation among nine populations. The Mantel test suggested that genetic differentiation between nine C. crispus populations was closely related with geographic distances (R = 0.78, P = 0.002). Results suggest that, on larger distance scale (ca. > 1000 km), ISSR analysis is useful for determining genetic differentiations of C crispus populations including morphologically inseparable haploid and diploid individuals. (c) 2007 Elsevier B.V. All rights reserved.

Isolation and mapping of telomeric pentanucleotide (TAACC)(n) repeats of the pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization

To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)(n) repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective I showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA),, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1 > P2 > P3 > P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

复杂背景下运动目标检测、分割与跟踪

本文研究的内容主要是序列图像中复杂背景下运动目标检测、分割与跟踪。分别提出了曲线演化策略及在运动目标检测与分割中的应用和基于特征点跟踪的运动目标检测与分割方法。关于目标跟踪，本文应用基于模型和基于特征的两种策略，提出了稳定、有效的四种跟踪方法。基于模型的算法包括基于粒子滤波和Hausdorff距离的运动目标跟踪及基于变形模板的目标跟踪。基于特征的方法分别是基于模糊测度的目标匹配与改进不变矩的目标匹配算法。 研究了曲线演化策略及在运动目标检测与分割中的应用，提出了基于最小半径准则和队列结构的聚类算法，消除孤立区域。提出基于试探策略并结合Fisher准则自适应地确定阈值的曲线演化算法分割运动目标。该算法具有良好的实时性和分割完整准确的优点。 在基于特征点跟踪的运动目标检测分割中，通过分析角点信息(灰度、梯度大小与方向)及其邻域信息，构造方向子邻域以提高匹配精度。提出了采用聚类方法消除运动目标上特征点对集合，同时也从剩余的特征点对集合中选取最优子集估计模型参数，检测运动目标。该算法可达到实时应用目的。 目标跟踪问题可看作状态空间中贝叶斯推理问题。在粒子滤波框架内，分别构造了跟踪过程的状态转移模型和测量模型，并提出了一种基于集合的模糊测度，实现了跟踪窗口随目标自适应变化、模板更新策略。对于刚体与非刚体的孤立目标，算法能够实现对目标的稳定跟踪。 在复杂场景下变形目标跟踪中，通过定义一种点到匹配点及其邻域的广义距离测度，增强了匹配的容错性。算法采用边缘相似点的距离均值和方差作为匹配的相似测度和置信准则。通过提出在8邻域内基于马尔可夫模型的启发式规则修正模板策略，阻止了模板窗口向背景的漂移。 在基于模糊测度的目标匹配中，提出了循环移位方法构造匹配特征向量，根据特征分布的模糊隶属度确定相似测度。该算法性能优于基于灰度相关匹配方法。 在基于不变矩的图像匹配中，引入误差带策略，计算图像边缘不变矩，取前N个匹配结果作为侯选目标，并根据契比雪夫不等式确定置信度。最后计算侯选目标的直方图的统计特性目标定位。该算法在性能上明显优于应用不变矩特征直接匹配方法和灰度相关的匹配方法。

基于模糊集理论的二维线性鉴别分析新方法

二维线性鉴别分析（2DLDA）是一种直接基于矩阵的特征提取方法，跳过传统的基于Fisher鉴别准则的线性鉴别分析方法中必须先将二维矩阵转化成一维矢量的过程，有效地提高了特征提取速度且避免了小样本问题，其识别率优于传统的Fisherface方法。结合模糊集理论，提出了一种新的2DLDA算法——模糊2DLDA（FIDLDA）算法。首先采用FKNN算法得到相应的样本分布信息，并按其对最后得到的特征向量所作的贡献融入到特征抽取过程中，得到有效的样本特征向量集。实验表明，F2DLDA算法的性能优于传统的2DLDA算法和Fisherface方法。

广义统计不相关最优鉴别矢量集的一个理论结果

本文对统计不相关最优鉴别矢量集的理论问题进行研究 ,提出了广义统计不相关最优鉴别准则 ,并给出了广义统计不相关最佳鉴别矢量集的一个理论结果 ,研究表明 ,广义统计不相关最佳鉴别矢量集的计算公式与基于Fisher最优鉴别准则的统计不相关最佳鉴别矢量集的计算公式完全一样 ,但是以前这一点没有被认识到 .本文的研究丰富了统计不相关最优鉴别分析的特征抽取理论 .

一种新的图像特征抽取方法研究

对最佳鉴别矢量的求解方法进行了研究，根据矩阵的分块理论和优化理论，在一定的条件下，从理论上得到类间散布矩阵和总体散布矩阵的一种简洁表示方法，提出了求解最佳鉴别矢量的一种新算法，该算法的优点是计算量明显减少。ORL人脸数据库的数值实验，验证了上述论断的正确性。实验结果表明，虽然识别率与分块维数之间存在非线性关系，但可以通过选择适当的分块维数来获得较高的识别率。类间散布矩阵和总体散布矩阵的一种简洁表示方法适合于一切使用Fisher鉴别准则的模式识别问题。

A Unified Statistical and Information Theoretic Framework for Multi-modal Image Registration

We formulate and interpret several multi-modal registration methods in the context of a unified statistical and information theoretic framework. A unified interpretation clarifies the implicit assumptions of each method yielding a better understanding of their relative strengths and weaknesses. Additionally, we discuss a generative statistical model from which we derive a novel analysis tool, the "auto-information function", as a means of assessing and exploiting the common spatial dependencies inherent in multi-modal imagery. We analytically derive useful properties of the "auto-information" as well as verify them empirically on multi-modal imagery. Among the useful aspects of the "auto-information function" is that it can be computed from imaging modalities independently and it allows one to decompose the search space of registration problems.

An artificial immune system for continuous analysis of time-varying data

M. Neal, An Artificial Immune System for Continuous Analysis of Time-Varying Data, in Proceedings of the 1st International Conference on Artificial Immune Systems (ICARIS), 2002, eds J Timmis and P J Bentley, volume 1, pages 76-85,

A resource limited artificial immune system for data analysis.

Timmis J and Neal M J. A resource limited artificial immune system for data analysis. In Proceedings of ES2000 - Research and Development of Intelligent Systems, pages 19-32, Cambrige, U.K., 2000. Springer.

Investigating the evolution and stability of a resource limited artificial immune system.

Timmis J and Neal M J. Investigating the evolution and stability of a resource limited artificial immune system. In Proceedings of GECCO - special workshop on artificial immune systems, pages 40-41. AAAI press, 2000.

Rapid compensatory evolution promotes the survival of conjugative plasmids

Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome.

Human papillomavirus detection in women with and without human immunodeficiency virus infection in Colombia

Background: HIV infection leads to a decreasing immune response, thereby facilitating the appearance of other infections, one of the most important ones being HPV. However, studies are needed for determining associations between immunodeficiency caused by HIV and/or the presence of HPV during the course of cervical lesions and their degree of malignancy. This study describes the cytological findings revealed by the Papanicolaou test, laboratory characteristics and HPV molecular profile in women with and without HIV infection. Methods: A total of 216 HIV-positive and 1,159 HIV-negative women were invited to participate in the study; PCR was used for the molecular detection of HPV in cervical samples. Statistical analysis (such as percentages, Chi-square test and Fisher's exact test when applicable) determined human papillomavirus (HPV) infection frequency (single and multiple) and the distribution of six types of high-risk-HPV in women with and without HIV infection. Likewise, a logistic regression model was run to evaluate the relationship between HIV-HPV infection and different risk factors. Results: An association was found between the frequency of HPV infection and infection involving 2 or more HPV types (also known as multiple HPV infection) in HIV-positive women (69.0% and 54.2%, respectively); such frequency was greater than that found in HIV-negative women (44.3% and 22.7%, respectively). Statistically significant differences were observed between both groups (p = 0.001) regarding HPV presence (both in infection and multiple HPV infection). HPV-16 was the most prevalent type in the population being studied (p = 0.001); other viral types had variable distribution in both groups (HIV-positive and HIV-negative). HPV detection was associated with <500 cell/mm(3) CD4-count (p = 0.004) and higher HIV-viral-load (p = 0.001). HPV-DNA detection, <200 cell/mm(3) CD4-count (p = 0.001), and higher HIV-viral-load (p = 0.001) were associated with abnormal cytological findings. Conclusions: The HIV-1 positive population in this study had high multiple HPV infection prevalence. The results for this population group also suggested a greater association between HPV-DNA presence and cytological findings. HPV detection, together with low CD4 count, could represent useful tools for identifying HIV-positive women at risk of developing cervical lesions.