Correlations of amino acids in proteins

A correlation analysis among 20 amino acids is performed for four protein structural classes (, β, /β, and +β) in a total of 204 proteins. The correlation relationships among amino acids can be classified into the following four types: (1) strong positive correlation, (2) strong negative correlation, (3) weak correlation, and (4) no correlation. The correlation relationships are different for different proteins and are correlated with the features of their structural classes. The amino acids with the weak correlation relationship can be treated as the independent basis functions for the space where proteins are defined. The amino acids with large correlation coefficients are linear correlative with each other and they are not independent. The strong correlation among amino acids reflects their mutual constrained relationship, as exhibited by their relevant structural features. The information obtained through the correlation analysis is used for predicting protein structural classes and a better prediction quality is obtained than that by the simple geometry distance methods without taking into account the correlation effects.     

脑电图数据的相关性分析

目的:本文对客观记录的脑电图数据进行相关性分析,为正确理解人脑的不同局部以及局部与整体之间的相关性提供基础实验依据和理论根据,为脑电图研究的其它分析做基础分析.方法:分别对10导联电极和21导联电极的两组脑电图数据做互相关和自相关的相关性分析,得出在不同条件、事件下脑的各导联电极的自相关分析结果和左右对称导联电极的互相关分析结果,最后得出相关性值随实验条件和事件的具体变化.数据处理和统计分析采用独立设计的脑电图分析工具箱和相关性分析程序.结果:脑电图数据经过相关性分析后得到的相关图具有和脑电波相似的波形,具有周期性,时间滞后对应的标准化的相关图显示出相关性值的第一个主峰是最大的,主峰频率一般在8到13Hz的脑电波频段内;最后得到的相关性值随事件的变化而改变的结果说明实验事件对相关性的影响.结论:自相关和互相关都是随着时间滞后的增大而逐渐减小;波具有较强的相关性;相关图在从零延迟开始时间滞后所出现的第一个波峰是主峰,反应出相对较强的相关性;从大量数据的分析最后得到的相关性与事件的关系表明相关性是受事件影响的.     

Neural coding properties based on spike timing and pattern correlation of retinal ganglion cells

Correlation between spike trains or neurons sometimes indicates certain neural coding rules in the visual system. In this paper, the relationship between spike timing correlation and pattern correlation is discussed, and their ability to represent stimulus features is compared to examine their coding strategies not only in individual neurons but also in population. Two kinds of stimuli, natural movies and checkerboard, are used to arouse firing activities in chicken retinal ganglion cells. The spike timing correlation and pattern correlation are calculated by cross-correlation function and Lempel–Ziv distance respectively. According to the correlation values, it is demonstrated that spike trains with similar spike patterns are not necessarily concerted in firing time. Moreover, spike pattern correlation values between individual neurons’ responses reflect the difference of natural movies and checkerboard; neurons cooperate with each other with higher pattern correlation values which represent spatiotemporal correlations during response to natural movies. Spike timing does not reflect stimulus features as obvious as spike patterns, caused by their particular coding properties or physiological foundation. As a result, separating the pattern correlation out of traditional timing correlation concept uncover additional insight in neural coding.     

HETEROZYGOSITY AND GROWTH IN MARINE BIVALVES: FURTHER DATA AND POSSIBLE EXPLANATIONS

In a natural population of two-year-old mussels, shell length was correlated with degree of heterozygosity. There was no correlation between an individual's glycogen level and its degree of heterozygosity, but when individuals were grouped in heterozygosity classes a near-significant correlation was observed between degree of heterozygosity and mean glycogen level corrected for the effects of sex and stage of gonad development. There was no correlation between degree of heterozygosity and index of gonad development. Such a correlation would have provided support for the hypothesis (Zouros and Foltz, 1984) that dependence of time of spawning on heterozygosity may explain the observed heterozygote-deficiency. The causes of heterozygote-deficiency, a common phenomenon in populations of marine bivalves, remain obscure. The observed heterozygosity-growth correlation is examined in the light of the controversy of whether allozymes act as markers in linkage association with genetic conditions that are responsible for the differences in growth among individuals or are themselves the agents of the correlation. The observations that 1) the contributions of individual loci to the correlation vary among populations, 2) the correlation is observed in samples from natural populations but not among progeny from pair matings, and 3) the correlation is nearly always accompanied with heterozygote-deficiency in the population are more compatible with the first explanation and suggest that the growth-heterozygosity correlation results mostly from associative overdominance and to a lesser extent from the direct contributions of scored loci to growth.     

若尔盖高原退化沼泽群落植物多样性及种间相关性沿排水梯度的变化

植物多样性与种间相关性是植物群落生态学和生物多样性研究的核心问题, 然而有关二者之间关系的综合研究尚不多见。该文以若尔盖高原排水干扰下不同退化阶段的沼泽湿地植被为研究对象, 应用Spearman秩相关、回归分析等方法, 分析了沼泽植物群落物种多样性和种间相关性的变化及二者相互关系。结果表明: 沿排水梯度, 从相对原生沼泽至极度退化沼泽, 不同植物种群均有其特定的生态分布范围; 群落总种数、样方物种丰富度、Shannon-Wiener指数和Whittaker指数均单调增加; 植物种间相关强度增加; 正相关种对比例呈逐渐增加的趋势, 以极重度和极度退化阶段的较高, 相对原生沼泽和轻度退化阶段的较低, 负相关种对比例的变化趋势与之相反; Shannon-Wiener指数与正负相关种对比例均具有显著线性关系(p < 0.05), Whittaker指数均无显著关系(p > 0.05)。人为排水作用通过提高群落生境异质性, 促进正相关种对的共存, 增加沼泽群落植物多样性。     

Fluorescence correlation spectroscopy of finite-sized particles

A theory is presented to study fluorescence correlation spectroscopy for particles with size comparable to the beam waist of the observation volume. Analytical correlation curves are derived for some experimentally interesting particle geometries. It is found that the finiteness of the particle generally decreases the value of the correlation amplitude and increases the correlation time compared to a point particle model. Furthermore, not only the size but also the distribution of fluorophores affects the shape of the correlation function. This is experimentally demonstrated with surface and internally labeled fluorescent spheres. In addition, experiments are performed on fluorescent spheres of different radii to validate the model by comparing the results to theoretical predictions.     

长江三角洲地区城市化与植被活动之间的时空相关性

利用时间序列NDVI数据和统计资料,以长江三角洲地区为例,研究城市化与植被生长活力之间的时空相关性。在总体上,NDVI与人口和GDP之间均呈显著的负相关性;空间相关场进一步表明,在人口和GDP分布较高的地区,植被的生长活力越低,相关系数均在-1.0～0.5之间。选择地市行政单元为研究粒度,使用面板数据分析方法,研究单位面积NDVI与城市化率之间相关性的演变,结果表明,在时间序列上负相关性越来越强,两者之间有明显线性关系,这在一定程度上反映了区域社会发展与生态环境之间未达到双赢。     

Measuring Morphological Integration Using Eigenvalue Variance

The concept of morphological integration describes the pattern and the amount of correlation between morphological traits. Integration is relevant in evolutionary biology as it imposes constraint on the variation that is exposed to selection, and is at the same time often based on heritable genetic correlations. Several measures have been proposed to assess the amount of integration, many using the distribution of eigenvalues of the correlation matrix. In this paper, we analyze the properties of eigenvalue variance as a much applied measure. We show that eigenvalue variance scales linearly with the square of the mean correlation and propose the standard deviation of the eigenvalues as a suitable alternative that scales linearly with the correlation. We furthermore develop a relative measure that is independent of the number of traits and can thus be readily compared across datasets. We apply this measure to examples of phenotypic correlation matrices and compare our measure to several other methods. The relative standard deviation of the eigenvalues gives similar results as the mean absolute correlation (W.P. Cane, Evol Int J Org Evol 47:844–854, 1993) but is only identical to this measure if the correlation matrix is homogenous. For heterogeneous correlation matrices the mean absolute correlation is consistently smaller than the relative standard deviation of eigenvalues and may thus underestimate integration. Unequal allocation of variance due to variation among correlation coefficients is captured by the relative standard deviation of eigenvalues. We thus suggest that this measure is a better reflection of the overall morphological integration than the average correlation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Folding rate prediction using n-order contact distance for proteins with two- and three-state folding kinetics

It is a challenging task to understand the relationship between sequences and folding rates of proteins. Previous studies are found that one of contact order (CO), long-range order (LRO), total contact distance (TCD), chain topology parameter (CTP), and effective length (Leff) has a significant correlation with folding rate of proteins. In this paper, we introduce a new parameter called n-order contact distance (nOCD) and use it to predict folding rate of proteins with two- and three-state folding kinetics. A good linear correlation between the folding rate logarithm lnkf and nOCD with n=1.2, alpha=0.6 is found for two-state folders (correlation coefficient is -0.809, P-value<0.0001) and n=2.8, alpha=1.5 for three-state folders (correlation coefficient is -0.816, P-value<0.0001). However, this correlation is completely absent for three-state folders with n=1.2, alpha=0.6 (correlation coefficient is 0.0943, P-value=0.661) and for two-state folders with n=2.8, alpha=1.5 (correlation coefficient is -0.235, P-value=0.2116). We also find that the average number of contacts per residue Pm in the interval of m for two-state folders is smaller than that for three-state folders. The probability distribution P(gamma) of residue having gamma pairs of contacts fits a Gaussian distribution for both two- and three-state folders. We observe that the correlations between square radius of gyration S2 and number of residues for two- and three-state folders are both good, and the correlation coefficient is 0.908 and 0.901, and the slope of the fitting line is 1.202 and 0.795, respectively. Maybe three-state folders are more compact than two-state folders. Comparisons with nTCD and nCTP are also made, and it is found that nOCD is the best one in folding rate prediction.     

Separation of the rotational contribution in fluorescence correlation experiments

The theory of fluorescence correlation spectroscopy is reexamined with the aim of separating the contribution of rotational diffusion. Under constant excitation, fluorescence correlation experiments are characterized by three polarizations: one of the incident beam and two of the two photon detectors. A set of experiments of different polarizations is proposed for study. From the results of the experiments the isotropic factor of the fluorescence intensity correlation functions can be determined, which is independent of the rotational motion of the sample molecule. This function can be used to represent each fluorescence intensity correlation function as the product of the isotropic and the rotational factors. The theory is illustrated by an experiment in which rotational diffusion of porcine pancreatic lipase labeled with Texas Red was observed Texas Red is a label that allows precise fluorescence correlation experiments even in the nanosecond time range.     

Comparison between Determination of Free Thyroxine Index and Effective Thyroxine Ratio in Human Serum

Four thyroid function indices were determined in the sera of 181 patients: total thyroxine (T-4), the triiodothyronine resin uptake (T-3 B.C.-index), the free thyroxine (T-4) index, and the effective thyroxine ratio (E.T.R.).A statistically significant correlation between the free T-4 index and E.T.R. could be established though this correlation seemed to be worse than could be expected from the literature. Two sets of correlation coefficients were shown: one obtained with the ordinarily used Pearson or product-moment correlation and one with the Spearman rank correlation. Because the assumptions and requirements for the proper use of the product-moment correlation statistics, such as a normal distribution of both variables, are seldom met, expecially not if a selected number of controls and patients is used for the correlation, it is advisable to use some kind of rank correlation statistics instead.The advantages and disadvantages of the E.T.R. and free T-4 index determination are described.     

A novel correlation for protein diffusion coefficients based on molecular weight and radius of gyration

A new correlation is proposed for the prediction of protein diffusion coefficients in free solution. Molecular weight and radius of gyration of proteins are employed as correlation parameters in this method. Both parameters can be easily found in the literature. The correlation works well for diverse proteins with different shapes and extensive molecular weight. Furthermore, this method does not require a preassumption regarding the protein shape while it offers a rapid and convenient calculation with a high accuracy. Also, the proposed correlation can elucidate the estimation deviation of previous correlation methods in the literature.     

Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics

We demonstrate that chain length is the main determinant of the folding rate for proteins with the three-state folding kinetics. The logarithm of their folding rate in water (k(f)) strongly anticorrelates with their chain length L (the correlation coefficient being -0.80). At the same time, the chain length has no correlation with the folding rate for two-state folding proteins (the correlation coefficient is -0.07). Another significant difference of these two groups of proteins is a strong anticorrelation between the folding rate and Baker's "relative contact order" for the two-state folders and the complete absence of such correlation for the three-state folders.     

关联维数法在皮肤激光散斑测量中的应用

本文采用关联维数方法研究了皮肤厚度对皮肤激光散斑测量的影响。计算了６种模拟皮肤厚度情况下的生物散斑关联维数。结果表明,维数随皮肤厚度的增加而减小,而且重复性很好。这说明,关联维数方法可以应用在皮肤激光散斑的研究中     

1982-2003年东北林区森林植被NDVI与水热条件的相关分析

以气象站点为研究单元,将1982—2003年东北林区森林植被月平均、季平均和年平均NDVI数据与其对应的水热条件(温度和降水)进行相关、偏相关和复相关分析。结果表明:温度是影响东北林区森林植被NDVI的最主要气候因子。春季、秋季不同森林植被平均NDVI与温度和降水呈极显著相关(P<0.01),其与温度的相关性高于其与降水的相关性。寒温带针叶林NDVI在生长季与温度和降水呈极显著相关(P<0.01),其与降水的相关性略高于其与温度的相关性,而全年温度对寒温带针叶林生长的影响高于降水。寒温带针叶林NDVI在4月份与降水的时滞偏相关性高于其他月份,相关系数达-0.385。温带针阔叶混交林NDVI在4—7月与温度的时滞偏相关性较高,相关系数分别为0.581,0.490,-0.266和-0.297。暖温带落叶阔叶林NDVI在4月份与温度的时滞偏相关性高于其他月份,相关系数为0.571;在7月份与降水时滞偏相关性高于其他月份,相关系数为-0.367。森林植被生长增长阶段NDVI受综合水热条件(温度和降水)的滞后影响显著。     

Chloroplast coupling factor 1: dependence of rotational correlation time on polypeptide composition

Time-resolved fluorescence depolarization measurements were made on chloroplast coupling factor 1 (CF1) labeled with pyrenylmaleimide. Rotational correlation times were determined for native CF1, for CF1 lacking epsilon and/or delta polypeptides, and for activated enzyme. The rotational correlation time measured is characteristic of the rotation of the entire enzyme. Removal of the delta polypeptide resulted in a 25% smaller rotational correlation time, although the delta polypeptide contributes less than 5% of the mass of CF1. Removal of the epsilon polypeptide was without effect. Simultaneous removal of delta and epsilon polypeptides produced a 30% smaller rotational correlation time. Activation of CF1 ATPase by incubation with dithiothreitol reduced the rotational correlation time by 15% relative to that of the latent enzyme. The rotational correlation time of CF1 with delta and epsilon polypeptides removed is essentially that expected for a spherical molecule, whereas the other forms of the enzyme can be approximated as ellipsoids of revolution; the axial ratio of the latent enzyme is estimated from the rotational correlation time and the intrinsic viscosity. These data indicate that the delta polypeptide significantly alters the shape of the enzyme and that a conformational change accompanies dithiothreitol activation of the enzyme.     

Effect of inhibitory feedback on correlated firing of spiking neural network

Understanding the properties and mechanisms that generate different forms of correlation is critical for determining their role in cortical processing. Researches on retina, visual cortex, sensory cortex, and computational model have suggested that fast correlation with high temporal precision appears consistent with common input, and correlation on a slow time scale likely involves feedback. Based on feedback spiking neural network model, we investigate the role of inhibitory feedback in shaping correlations on a time scale of 100 ms. Notably, the relationship between the correlation coefficient and inhibitory feedback strength is non-monotonic. Further, computational simulations show how firing rate and oscillatory activity form the basis of the mechanisms underlying this relationship. When the mean firing rate holds unvaried, the correlation coefficient increases monotonically with inhibitory feedback, but the correlation coefficient keeps decreasing when the network has no oscillatory activity. Our findings reveal that two opposing effects of the inhibitory feedback on the firing activity of the network contribute to the non-monotonic relationship between the correlation coefficient and the strength of the inhibitory feedback. The inhibitory feedback affects the correlated firing activity by modulating the intensity and regularity of the spike trains. Finally, the non-monotonic relationship is replicated with varying transmission delay and different spatial network structure, demonstrating the universality of the results.     

典范相关分析技术在植被生态信息中的应用研究

典范相关分析是一种检验两组变量间最大相关的多元统计技术。本文运用此技术结合Pearson's相关系数、PCA分析,对植物群落中植物重要值与土壤组分的相关研究表明:典范相关分析能极好地定量解释生态学中两组变量的相关,并能指示出多个因子的复合作用。同时强调,由于典范相关分析技术对原始数据的线性要求,从而有必要对数据进行标准化和预先的PCA分析。     

不同菊花品种根系、地上部和叶片相关指标分析及抗逆性评价

采用盆栽法对6个菊花(Chrysanthemum morifolium Ramat.)品种幼苗的根系和地上部相关指标及叶片光合和气体交换参数进行了比较和相关性分析;并基于叶片相对含水量、相对电导率、丙二醛含量和可溶性糖含量4个生理生化指标,采用隶属函数法对不同菊花品种幼苗的抗旱性和耐热性进行了评价.结果表明:不同菊花品种间幼苗的根系和地上部相关指标及叶片光合和气体交换参数存在一定差异.相关性分析结果表明:根系的大多数相关指标与株高呈显著(P<0.05)或极显著(P<0.01)正相关,但与茎粗和单株叶数却没有显著相关性;并且,单株的根体积、根鲜质量和干质量与单株地上部鲜质量呈极显著正相关(相关系数分别为0.598、0.642和0.599),与单株地上部干质量呈极显著或显著正相关(相关系数分别为0.736、0.606和0.553).主根长与净光合速率和蒸腾速率,平均根长与水分利用效率及单株根鲜质量与蒸腾速率呈显著正相关(相关系数分别为0.475、0.517、0.570和0.477);单株根干质量与蒸腾速率及根系活力与净光合速率和水分利用效率呈极显著正相关(相关系数分别为0.641、0.877和0.814).抗逆性评价结果表明:品种'南农红霞'('Nannong Hongxia')、'大白托桂'('Qx073')和'天使'('Angelina')的平均隶属函数值分别为0.93、0.93和0.72,据此判断这3个菊花品种的抗旱性最强;品种'馒头菊'('Cayman')和'南农红霞'的平均隶属函数值分别为0.82和0.70,据此判断这2个菊花品种的耐热性最强.综上所述,不同菊花品种幼苗的根系相关指标差异明显,并且根系生长状况能够影响地上部的生长和发育,品种'南农红霞'的抗旱性和耐热性均很强,具有较高的抗性育种价值.