Population correlation and population kinship

The processes of gene identity by descent and of allelic identities (or likenesses) between genes have been previously studied under a wide variety of migration and subdivision models of population evolution. Since the two processes follow probabilistically parallel paths, there has been a tendency to consider the two processes as equivalent, and to equate estimates of correlation of allele frequency with those of gene identity by descent. The adequacy of this procedure must depend upon the evolutionary history. Here, by distinguishing the processes and considering them jointly as a population evolves in time, we demonstrate the relationship between them in a simple situation, thus providing a basis for study of the extent to which observed allelic similarity between populations is a reflection of underlying gene identity.     

Inbreeding and relatedness coefficients: what do they measure?

This paper reviews and discusses what is known about the relationship between identity in state, allele frequency, inbreeding coefficients, and identity by descent in various uses of these terms. Generic definitions of inbreeding coefficients are given, as ratios of differences of probabilities of identity in state. Then some of their properties are derived from an assumption in terms of differences between distributions of coalescence times of different genes. These inbreeding coefficients give an approximate measurement of how much higher the probability of recent coalescence is for some pair of genes relative to another pair. Such a measure is in general not equivalent to identity by descent; rather, it approximates a ratio of differences of probabilities of identity by descent. These results are contrasted with some other formulas relating identity, allele frequency, and inbreeding coefficients. Additional assumptions are necessary to obtain most of them, and some of these assumptions are not always correct, for example when there is localized dispersal. Therefore, definitions based on such formulas are not always well-formulated. By contrast, the generic definitions are both well-formulated and more broadly applicable.     

The problem of using correlation methods in brain function]

In a series of publications, the author used the correlation hypothesis to explain the main mechanisms of functioning of bat and dolphin echo locators. A good fit of calculated parameters to experimental data was shown. In this work, by the example of generalization of the recognition problem, the use by the brain of correlation methods for solving more general problems independently on the modality of sensor signals was analyzed. In favor of the hypothesis that correlation methods are widely used in brain functioning are the data presented in the paper, which prove that an associative neuron is a suitable analog computer. It is suited for rapid "computation" of the intercorrelation function of discrete input and reference signals. The set of weighting coefficients of neuron synaptic inputs serve as such signals. The pool of associative neurons determines the values on the correlation function in the required range by changing the "numbers" of inputs from neuron to neuron at which discrete signals arrive.     

DLL4 和VEGFR 表达与肝细胞癌临床特征的相关性研究

目的:探讨DLL4和血管内皮生长因子受体(Vascular Endothelial Growth Factor Receptor,VEGFR)基因表达与临床特征的相关性,为肝细胞癌的防治提供新的靶点。方法:采用荧光定量PCR检测DLL4和VEGFR基因的表达,DLL4与VEGFR基因表达的关系采用Spearman相关系数分析。DLL4与肝癌临床病理特征的相关性分析采用Knlskal-Wallis H方法。结果:DLL4和VEGRR在肝细胞癌组织中呈高表达,且VEGFR随着DLL4基因表达的升高而升高,呈正相关关系。DLL4基因的高表达与有无包膜、肿瘤结节数目、肿瘤直径、Edmondson-Steiner分级及有无静脉浸润均有显著的相关性(P0.05)。结论:DLL4和VEGFR在肝细胞癌组织中的高表达与临床病理特征均有显著相关性。     

Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes

We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/. We have compiled the largest database of disordered patterns (141) from the clustered PDB where identity between chains inside of a cluster is larger or equal to 75% (version of 28 June 2010) by using simple rules of selection. The results of these analyses would help to further our understanding of the physicochemical and structural determinants of intrinsically disordered regions that serve as molecular recognition elements. We have analyzed the occurrence of the selected patterns in 97 eukaryotic and in 26 bacterial proteomes. The disordered patterns appear more often in eukaryotic than in bacterial proteomes. The matrix of correlation coefficients between numbers of proteins where a disordered pattern from the library of 141 disordered patterns appears at least once in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside of the considered kingdom than between them. The patterns with the frequent occurrence in proteomes have low complexity (PPPPP, GGGGG, EEEED, HHHH, KKKKK, SSTSS, QQQQQP), and the type of patterns vary across different proteomes, http://bioinfo.protres.ru/fp/search_new_pattern.html.     

Local correlation of expression profiles with gene annotations--proof of concept for a general conciliatory method

MOTIVATION: Integrated analysis of expression data and gene ontology annotations is a prime example of biological data that need co-explanatory interpretation. This particular application is used to validate a new method for integrated analysis of varied biological information. RESULTS: The proposed method consists of determining local correlation coefficients and the corresponding P-values calculated per biological entity. This measure considers the combined intensity and significance of the agreement or disagreement, between two data sources about the same biological entity. The method is applied to the integrated analysis of gene expression and annotation of two gene sets, one from yeast and other from mouse. The potential of the method to generate accurate mechanistic hypothesis is also demonstrated. Specially, negative correlation results pose a new kind of biological hypothesis. Method performance was compared with annotation enrichment methods, and optimal conditions for the superiority of local correlation results are discussed.     

植被归一化指数(NDVI)及气候因子相关起伏型时间序列变化分析

利用中国大陆1km分辨率的月NDVI数据和相应的400个国家标准气象站点的月降水、月均温数据,依据中国气象局提出的气候分区,探讨了不同气候区NDVI与气候因子之间的时、空变化格局.结果表明,各月份降水与NDVI相关性均显著相关;起伏型时间序列模型能很好地拟合相关性的时间序列的动态变化,NDVI与降水的相关性拟合结果好于与温度相关性的拟合结果,全国范围内,与降水相关性拟合的R₂为0.91,与温度相关性拟合的R₂为0.86.     

Correlations between live and stillbirth outcomes in twin pairs

A relationship has been proposed to exist between individual outcomes (live or stillbirth) of twins in the same set. Here, we analyze this association between live births and stillbirths among individuals in different twin pairs. When national birth registers are analyzed, individuals in opposite-sex twin sets can be identified and the correlation between individual outcomes estimated. However, full information about the individuals in same-sex twin sets is not, as a rule, available, and consequently, correlation coefficients cannot be estimated, but upper and lower limits of the correlation coefficients can be obtained. The methods introduced here were applied to data from Sweden (1869-1967), the Aland Islands (Finland) (1750-1949), the Kingdom of Saxony (1881-1900), and England and Wales (1940-2003). Comparisons between the correlation coefficients among opposite-sex twins and the lower bound (minimum) of correlation coefficients among same-sex twins indicate that in all populations studied a stronger association exists between twins in same-sex rather than opposite-sex twin sets or pairs. For opposite-sex twin sets no general association between the correlation coefficient and the stillbirth rate was identified.     

云南金钱槭形态变异与遗传变异的相关性研究

对我国特有珍稀濒危保护植物云南金钱槭的形态变异水平、遗传变异模式以及两者之间的相关性进行了研究。形态学性状分析结果表明 :各居群形态性状变异系数的平均值从大到小排列为 :文山居群 (WSh)、屏边居群 (PB)、黑龙潭居群 (HL T)、蒙自居群 (MZ) ;文山居群与屏边、黑龙潭、蒙自居群间已产生显著或极显著水平的形态差异 ,而后三者间的差异未达显著水平。RAPD分析检测到 10 3个位点 ,其中多态位点 84个 ,云南金钱槭物种水平的多态位点比率为 81.5 5 % ,与其它珍稀濒危植物相比该种的遗传多样性水平不低。 AMOVA和 N ei基因多样性指数分析显示 ,尽管大部分遗传变异仍存在于居群内 (分别为5 7.86 %、5 7.33% ) ,但居群间的遗传变异已达较高水平 (分别为 4 2 .14 %、4 2 .6 7% )。相关分析结果显示 ,云南金钱槭的形态变异与海拔、土壤有机质等生态因子有着显著或极显著水平的相关性 ,但与遗传变异的相关性未达显著水平 ,说明云南金钱槭的形态变异虽然具有一定的遗传基础 ,但可塑性及环境压力对形态变异的产生作用更大一些。基于形态性状和 RAPD数据的聚类分析则进一步说明 ,云南金钱槭的形态变异受到环境因子的强烈影响而与遗传背景的关系不显著     

Hill coefficients of dietary polyphenolic enzyme inhibitiors: can beneficial health effects of dietary polyphenols be explained by allosteric enzyme denaturing?

Inspired by a recent article by Prinz, suggesting that Hill coefficients, obtained from four parameter logistic fits to dose–response curves, represent a parameter allowing distinction between a general allosteric denaturing process and real single site enzyme inhibition, Hill coefficients of a number of selected dietary polyphenol enzyme inhibitions were compiled from the available literature. From available literature data, it is apparent that the majority of polyphenol enzyme interactions reported lead to enzyme inhibition via allosteric denaturing rather than single site inhibition as judged by their reported Hill coefficients. The results of these searches are presented and their implications discussed leading to the suggestion of a novel hypothesis for polyphenol biological activity termed the insect swarm hypothesis.     

The consequences of spatial structure for the design and analysis of ecological field surveys

In ecological field surveys, observations are gathered at different spatial locations. The purpose may be to relate biological response variables (e.g., species abundances) to explanatory environmental variables (e.g., soil characteristics). In the absence of prior knowledge, ecologists have been taught to rely on systematic or random sampling designs. If there is prior knowledge about the spatial patterning of the explanatory variables, obtained from either previous surveys or a pilot study, can we use this information to optimize the sampling design in order to maximize our ability to detect the relationships between the response and explanatory variables?
The specific questions addressed in this paper are: a) What is the effect (type I error) of spatial autocorrelation on the statistical tests commonly used by ecologists to analyse field survey data? b) Can we eliminate, or at least minimize, the effect of spatial autocorrelation by the design of the survey? Are there designs that provide greater power for surveys, at least under certain circumstances? c) Can we eliminate or control for the effect of spatial autocorrelation during the analysis? To answer the last question, we compared regular regression analysis to a modified t‐test developed by Dutilleul for correlation coefficients in the presence of spatial autocorrelation.
Replicated surfaces (typically, 1000 of them) were simulated using different spatial parameters, and these surfaces were subjected to different sampling designs and methods of statistical analysis. The simulated surfaces may represent, for example, vegetation response to underlying environmental variation. This allowed us 1) to measure the frequency of type I error (the failure to reject the null hypothesis when in fact there is no effect of the environment on the response variable) and 2) to estimate the power of the different combinations of sampling designs and methods of statistical analysis (power is measured by the rate of rejection of the null hypothesis when an effect of the environment on the response variable has been created).
Our results indicate that: 1) Spatial autocorrelation in both the response and environmental variables affects the classical tests of significance of correlation or regression coefficients. Spatial autocorrelation in only one of the two variables does not affect the test of significance. 2) A broad‐scale spatial structure present in data has the same effect on the tests as spatial autocorrelation. When such a structure is present in one of the variables and autocorrelation is found in the other, or in both, the tests of significance have inflated rates of type I error. 3) Dutilleul's modified t‐test for the correlation coefficient, corrected for spatial autocorrelation, effectively corrects for spatial autocorrelation in the data. It also effectively corrects for the presence of deterministic structures, with or without spatial autocorrelation.
The presence of a broad‐scale deterministic structure may, in some cases, reduce the power of the modified t‐test.     

SDS-PAGE analysis of surface proteins and antigens evidences high heterogenity in natural clones of Trypanosoma cruzi, correlated with isoenzyme variability

Surface protein and surface antigen patterns of 19 Trypanosoma cruzi laboratory clones, representing 17 different isozymic profiles (zymodemes), were compared by SDS-PAGE analysis. Surface protein patterns were found to be complex and heterogeneous. According to the number of common bands, we calculated similarity coefficients of surface protein patterns on the one hand, and of surface antigen patterns on the other hand, for 33 stock pairwise comparisons. In both cases, these coefficients were statistically correlated to the isozyme index of genetic identity. Such a correlation between independent genetic markers favours the clonal structure of T. cruzi natural populations previously evidenced. Moreover, we did not observe any notable differences in the surface antigen pattern among 4 T. cruzi cloned stocks precipitated by homologous as well as heterologous hyperimmune sera. The immunological significance of the molecular weight variability in surface antigen patterns among different zymodemes is discussed.     

A computational approach to measuring coherence of gene expression in pathways

This study uses a computational approach to analyze coherence of expression of genes in pathways. Microarray data were analyzed with respect to coherent gene expression in a group of genes defined as a pathway in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Our hypothesis is that genes in the same pathway are more likely to be coordinately regulated than a randomly selected gene set. A correlation coefficient for each pair of genes in a pathway was estimated based on gene expression in normal or tumor samples, and statistically significant correlation coefficients were identified. The coherence indicator was defined as the ratio of the number of gene pairs in the pathway whose correlation coefficients are significant, divided by the total number of gene pairs in the pathway. We defined all genes that appeared in the KEGG pathways as a reference gene set. Our analysis indicated that the mean coherence indicator of pathways is significantly larger than the mean coherence indicator of random gene sets drawn from the reference gene set. Thus, the result supports our hypothesis. The significance of each individual pathway of n genes was evaluated by comparing its coherence indicator with coherence indicators of 1000 random permutation sets of n genes chosen from the reference gene set. We analyzed three data sets: two Affymetrix microarrays and one cDNA microarray. For each of the three data sets, statistically significant pathways were identified among all KEGG pathways. Seven of 96 pathways had a significant coherence indicator in normal tissue and 14 of 96 pathways had a significant coherence indicator in tumor tissue in all three data sets. The increase in the number of pathways with significant coherence indicators may reflect the fact that tumor cells have a higher rate of metabolism than normal cells. Five pathways involved in oxidative phosphorylation, ATP synthesis, protein synthesis, or RNA synthesis were coherent in both normal and tumor tissue, demonstrating that these are essential genes, a high level of expression of which is required regardless of cell type.     

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。     

Assay development and screening of a serine/threonine kinase in an on-chip mode using caliper nanofluidics technology

Kinases are key targets for drug discovery. In the field of screening in general and especially in the kinase area, because of considerations of efficiency and cost, radioactivity-based assays tend to be replaced by alternative, mostly fluorescence-based, assays. Today, the limiting factor is rarely the number of data points that can be obtained but rather the quality of the data, enzyme availability, and cost. In this article, the authors describe the development of an assay for a kinase screen based on the electrophoretic separation of fluorescent product and substrate using a Caliper-based nanofluidics environment in on-chip incubation mode. The authors present the results of screening a focused set of 32,000 compounds together with confirmation data obtained in a filtration assay. In addition, they have made a small-scale comparison between the on-chip and off-chip nanofluidics screening modes. In their hands, the screen in on-chip mode is characterized by high precision most likely due to the absence of liquid pipetting; an excellent confirmation rate (62%) in an independent assay format, namely, filtration; and good sensitivity. This study led to the identification of 4 novel chemical series of inhibitors.     

Globalizing Languages: Ideologies and Realities of the Contemporary Global System

Globalization is best understood as a phase of decentralization of wealth and power in the world arena that is a hallmark of a decline in economic hegemony, a phase accompanied by enormous dislocations and migrations of people, by class polarization and cultural fragmentation, and by the rise of new powerful regions. The current period of globalization is also characterized by a decline in the capacity of states to nationalize, and, consequently, by the upsurge of a series of alternative identifications, such as those based on indigenousness, regional location, and immigrant status. These fluctuations in power, as well as the formation of new identities that accompanies them, have significant implications for understanding contemporary linguistic ideologies and practices: Reconfigurations of identification lead to the formation of hierarchical spaces reflected in ranked local usages of languages. Using the example of Hawaii, this article outlines fundamental relations between contemporary global processes and cultural identity with an eye to assessing their significance for understanding linguistic change. [Keywords: globalization, linguistic change, language identity, Hawaiian language]     

Just a hypothesis: a reply to Hanski

Hanski's critique of the habitat amount hypothesis (Hanski, 2015, Journal of Biogeography, 42 , 989–993) does not actually constitute a test of the hypothesis, but rather a series of arguments for why he suspects that it is not correct. But the habitat amount hypothesis is exactly that – a hypothesis. It will remain ‘just’ a hypothesis until it has been rigorously tested against empirical data. To facilitate such testing, in Fahrig (2013, Journal of Biogeography, 40 , 1649–1663) I presented specific, testable predictions of the hypothesis. Here, I reiterate the main tests needed, in the hope that some readers will be encouraged to carry them out. I appreciate this opportunity to emphasize that the habitat amount hypothesis needs to be tested against empirical data, and I look forward to seeing the results of such tests.     

A contribution to the theory of preferential interaction coefficients

A simple and complete derivation of the relation between concentration-based preferential interaction coefficients and integrals over the relevant pair correlation functions is presented for the first time. Certain omissions from the original treatment of pair correlation functions in multicomponent thermodynamics are also addressed. Connections between these concentration-based quantities and the more common molality-based preferential interaction coefficients are also derived. The pair correlation functions and preferential interaction coefficients of both solvent (water) and cosolvent (osmolyte) in the neighborhood of a macromolecule contain contributions from short-range repulsions and generic long-range attractions originating from the macromolecule, as well as from osmolyte-solvent exchange reactions beyond the macromolecular surface. These contributions are evaluated via a heuristic analysis that leads to simple insightful expressions for the preferential interaction coefficients in terms of the volumes excluded to the centers of the water and osmolyte molecules and a sum over the contributions of exchanging sites in the surrounding solution. The preferential interaction coefficients are predicted to exhibit the experimentally observed dependence on osmolyte concentration. Molality-based preferential interaction coefficients that were reported for seven different osmolytes interacting with bovine serum albumin are analyzed using the this formulation together with geometrical parameters reckoned from the crystal structure of human serum albumin. In all cases, the excluded volume contribution, which is the volume excluded to osmolyte centers minus that excluded to water centers in units of V1, exceeds in magnitude the contribution of the exchange reactions. Under the assumption that the exchange contribution is dominated by sites in the first surface-contiguous layer, the ratio of the average exchange constant to its neutral random value is determined for each osmolyte. These ratios all lie in the range 1.0 +/- 0.15, which indicates rather slight deviations from random occupation near the macromolecular surface. Finally, a mechanism is proposed whereby the chemical identity of an osmolyte might be concealed from partially ordered multilayers of water in clefts, grooves, and pits, and its consequences are noted.     

The core of affects: namer and named in Bahia (Brazil)

This article is a study of personal naming using drawings made by secondary school students from two small towns in coastal Bahia (Brazil) of the persons who gave them their names. The article explores the relation between namer and named as one of continued identity created by imaginative processes of surrogation akin to pretend‐play. In early ontogeny, the person is constituted through a series of mutualities of being that come to constitute a core of affects. The article aims to contribute towards a better understanding of the processes of constitution of personhood in the context of human relatedness.