Ploidy pattern analysis. Statistical considerations

Availability of large data sets of ploidy measurements makes it possible to study ploidy patterns for the diagnostic and prognostic clues they can provide. Appropriate statistical analyses can improve the accuracy and precision of these studies. Such statistical analyses include considerations of sample size requirements for the detection of different types of deviations from normal, analyses of sources of variability in ploidy patterns and assessment of the probabilities of both types of possible errors in patient classification. The advantages of statistical assessment in the classification of ploidy patterns associated with diagnostic categories are discussed in the context of these considerations.     

Proliferative index estimated by chromatin pattern analysis.

Chromatin pattern analysis at different density thresholds in Feulgen-stained meristems stimulated to proliferate by water inbibition, allows to estimate a proliferative potential index (PPI) which is a much earlier indicator of changes in proliferation than conventional labelling and mitotic indices. The PPI is but the ratio G1 cells to total 2C cells (or G2 to 4C cells, when cells also digress from the post-replicative stage of the cycle). The method is based in the fact that G1 and G2 cells have larger projected nuclear area and smaller dense chromatin area than their conterpart non-proliferating G0 and G0,2 cells.     

基于边界特征的景观格局分析

通过边界数量的长度谱分布分析。探讨了边界数量-长度特征与景观和组分碎裂化程度之间的相互关系;基于边界的数量和累积长度计算了景观多样性,均匀度、异质性和空间复杂性,并与基于斑快面积比重的传统格局指数计算结果进行了对比分析。研究表明,研究区内的快速城市化过程导致组分界面特征复杂化,空间分布的圈层结构简化;边界总体的数量谱分布方程系数α对于景观整体碎裂化程度有良好的指示意义,基于边界特征的景观格局指数对于传统的格局分析方法可以形成有益的补充。     

Entropy and community pattern analysis

A conceptual framework for the analysis of community types pattern (mosaic) is proposed and discussed in this paper. Within this framework, the pattern is viewed as a system whose freedom to take any particular state from among a set of possible microstates is restrained by ecological factors. This allows for the operationalization of an analytical procedure (PEGASE) based on information theory whereby the entropy of the pattern is reduced by a negentropy provided by various environmental factors.The introduction of these factors in a stepwise manner gives this method two of its essential characters: (i) its multivariate nature and (ii) the classification of sites in a divisive manner. Given a set of environmental factors, the level of organization of the pattern can be measured by the global environmental negentropy.Several properties of this model are discussed. Similarly to some early attempts at biophysical classification, the “Pegase” procedure emphasizes the ecological relationships. Indeed, it classifies sites into a set of site type which allows for the best prediction of community types. On the other hand, its basic structure is similar to that of a multiple regression model, without requiring any of the assumptions on data structure and distribution that multiple regression requires.     

Dietary pattern analysis: a new direction in nutritional epidemiology.

Recently, dietary pattern analysis has emerged as an alternative and complementary approach to examining the relationship between diet and the risk of chronic diseases. Instead of looking at individual nutrients or foods, pattern analysis examines the effects of overall diet. Conceptually, dietary patterns represent a broader picture of food and nutrient consumption, and may thus be more predictive of disease risk than individual foods or nutrients. Several studies have suggested that dietary patterns derived from factor or cluster analysis predict disease risk or mortality. In addition, there is growing interest in using dietary quality indices to evaluate whether adherence to a certain dietary pattern (e.g. Mediterranean pattern) or current dietary guidelines lowers the risk of disease. In this review, we describe the rationale for studying dietary patterns, and discuss quantitative methods for analysing dietary patterns and their reproducibility and validity, and the available evidence regarding the relationship between major dietary patterns and the risk of cardiovascular disease.     

A cluster pattern algorithm for the analysis of multiparametric cell assays.

The issue of multiparametric analysis of complex single cell assays of both static and flow cytometry (SC and FC, respectively) has become common in recent years. In such assays, the analysis of changes, applying common statistical parameters and tests, often fails to detect significant differences between the investigated samples. The cluster pattern similarity (CPS) measure between two sets of gated clusters is based on computing the difference between their density distribution functions' set points. The CPS was applied for the discrimination between two observations in a four-dimensional parameter space. The similarity coefficient (r) ranges between 0 (perfect similarity) to 1 (dissimilar). Three CPS validation tests were carried out: on the same stock samples of fluorescent beads, yielding very low r's (0, 0.066); and on two cell models: mitogenic stimulation of peripheral blood mononuclear cells (PBMC), and apoptosis induction in Jurkat T cell line by H2O2. In both latter cases, r indicated similarity (r < 0.23) within the same group, and dissimilarity (r > 0.48) otherwise. This classification and algorithm approach offers a measure of similarity between samples. It relies on the multidimensional pattern of the sample parameters. The algorithm compensates for environmental drifts in this apparatus and assay; it also may be applied to more than four dimensions.     

功能性脑成像的多维模式分析方法

利用非侵入式的功能性脑成像记录大脑活动极大地提升了我们对人类认知功能的理解.与此同时,分析成像数据的手段也逐渐从传统的一元方式向更加有效的多元分析转变.在本综述中,特别针对在认知神经科学领域占主导地位的功能性磁共振成像技术,介绍其多元数据分析方法的发展以及这种分析方法的生理学基础和未来发展方向.     

Mosaic pattern and lineage analysis in chimeras

Mammalian chimeras have been used in a number of developmental studies over the years. A major limitation in these studies has been the lack of in situ procedures for establishing mosaic pattern in the tissues of these animals. Recently, a number of procedures have become available for the histochemical demonstration of mosaicism in chimeras. These include the elucidation of various enzymes, receptors, or surface antigens, which have variant expression between strains. The observation of pattern in organs of mosaic animals can suggest possible modes of organogenesis and organ maintenance. Experimentation with such animals can be used to establish some mechanisms of pathogenesis as well.     

Short note Successive approximation in pattern analysis

The analysis of vegetation pattern in semi-arid eucalypt woodland by Harrington et al, (1981), and its recent critique by Dale (1982), place insufficient emphasis on the important role of successive approximation in pattern analysis. A single stage analysis can reveal first order patterns effectively, but is generally ineffective and inefficient in revealing vegetation patterns of higher order, no matter how sophisticated the numerical techniques employed. For a given total analytical effort, a more effective and efficient strategy to reveal such higher order patterns will generally be to partition the overall analytical effort into successive stages of sampling and interpretation, one stage for each order of pattern, with the sampling strategy at each stage based on the patterns determined during previous stages.     

Spectral analysis of breathing pattern in man

The periodic oscillations of breathing pattern parameters were studied in 34 healthy subjects. In a three minutes' resting spirometric recording we determined the duration of inspiration, expiration and tidal volume in successive breaths and computed autocorrelation functions and power spectral density. Ten of the subjects were re-examined 2 years later. Pulmonary functions were examined in all of them. Rhythmic changes lasting several respiratory cycles were found in the breathing pattern. Rhythmic changes in the duration of inspiration, expiration and tidal volume differed from one another in the same individual. The spectrograms of the individual breathing pattern parameters in the same individual changed during a 2-year period. Despite individual differences, the power spectral density correlations in the same subject and between different subjects two years later, and the mean curves for power spectral densities, show that in all the subjects the power fell at values of 0 to 0.05 Hz and was then maintained at a roughly constant level. Differences in the spectrograms of the various parameters in the same subject can hardly be attributed to a feedback between peripheral receptors and respiratory centres. Rhythmic changes are probably of central origin.     

Transgene insertion pattern analysis using genomic walking in a transgenic mouse line.

A transgene mapping technique (Noguchi et al., Exp. Anim. 53:103-111, 2004) is described that can be used to analyze transgene integration patterns in transgenic mice. The technique was used to reveal that a transgenic mouse line (GM1-sy#116) harbored inverted and direct tandem repeats of both intact and partial pCAGGS-based transgenes in the G2 region of chromosome 1. This complicated concatenation of transgenes may have been caused by simple end-joining of DNA constructs fragmented by exposure to UV transillumination during gel-purification, and by nuclease digestion inside zygote pronuclei. The results suggest that care should be taken to avoid unwanted fragmentation during the preparation of vector constructs.     

Cell lineage analysis of pattern formation in the Tubifex embryo. I. Segmentation in the mesoderm.

Annelids are strongly segmented animals that display a high degree of metamerism in their body plan. The embryonic origin of metameric segmentation was examined in an oligochaete annelid Tubifex using lineage tracers. Segmental organization arises sequentially in the anterior-to-posterior direction along the longitudinal axis of the mesodermal germ band, a coherent column of primary blast cells that are produced from the mesodermal teloblast. Shortly after its birth, each primary blast cell undergoes a spatiotemporally stereotyped sequence of cell divisions to generate three classes of cells (in terms of cell size), which together give rise to a distinct cell cluster. Each cluster is composed of descendants of a single primary blast cell; there is no intermingling of cells between adjacent clusters. Relatively small-sized cells in each cluster become localized at its periphery, and they form coelomic walls including an intersegmental septum to establish individuality of segments. A set of cell ablation experiments showed that these features of mesodermal segmentation are not affected by the absence of the overlying ectodermal germ band. These results suggest that each primary blast cell serves as a founder cell of each mesodermal segment and that the boundary between segments is determined autonomously. It is concluded that the metameric body plan of Tubifex arises from an initially simple organization (i.e., a linear series) of segmental founder cells.     

扩展点格局分析方法在灌木种群空间分布格局研究中的应用

当研究对象个体差异很大或者研究尺度与植物大小属于一个数量级时,传统的以种群空间分布的坐标点图为基础的点格局分析方法存在局限性.本文引入一种在传统点格局分析方法基础上发展起来的以栅格数据为分析对象的新方法——扩展点格局分析方法,用以分析具有一定面积和形状对象的空间格局和生态过程,该方法适用于灌木研究对象.以狭域特有种四合木(Tetraena mongolica)种群的空间分布格局分析为例,采用摄影定位法,用图像处理软件及地理信息系统软件将样地信息数字化后,利用扩展点格局分析方法分析了群落中四合木单种的空间分布格局及其与群落中霸王(Zygophyllum xanthoxylum)种群的关系,四合木种群在69～ 99 cm尺度上表现为均匀分布,四合木与霸王在350 ～570cm尺度上表现出显著的负关联关系.结果揭示了灌木种群的空间结构特征.     

Cytologic uniformity of breast cancer from different localizations: a pattern analysis study.

Using cytologic pattern analysis it is shown that regions of different histologic structure in one breast cancer are of cytologic homogeneity. The so-called PFORM -- the quotient of the total outline length of DNA-particles to the nuclear area -- gives an objective cytologic parameter which is independent of DNA content of cancer cells. This objective parameter together with the subjective cytologic parameters described earlier may be a better basis for describing the biologic behavior of breast cancer than histologic structure which is inhomogeneous very often in a lump.     

Establishment of HEp-2 cell preparation for automated analysis of ANA fluorescence pattern.

BACKGROUND: Identification of antinuclear antibodies (ANAs) has large clinical importance for the assessment of autoimmune diseases. HEp-2 cell preparations on microscopic slides are commonly used as antigenic substrate. Methods used for cell preparation are important for ANA pattern analysis; however, these methods differ widely and are mostly not specified. METHODS: HEp-2 cells were fixed using acetic acid-ethanol, methanol-acetone, acetone, formaldehyde, paraformaldehyde, or glutaraldehyde. Morphological analysis was done after haematoxylin-eosin staining and DAPI-staining of cell nuclei. RESULTS: The results demonstrate a high variability of cell and nuclear morphology depending on the used fixatives. Aldehyde fixatives conserved the cell structures best, acetone fixatives revealed remarkable changes. CONCLUSIONS: After selecting appropriate fixation procedures to preserve nuclear structures further experiments are necessary to find out which fixation procedure preserves the disease-linked antigens the best way and are, therefore, suitable to be used in ANA-testing of AABs.