The Point Evaluation Method for Approximating Function Means,Variances and Covariances

A perennial problem in statistics is the determination of biases, variances and covariances for functions of random variables X₁, X₂, …, X_n which themselves have a known distribution. A common approach is through equations based upon Taylor series approximations but a “point evaluation” method may sometimes be a useful alternative. This involves approximating the multivariate distribution of the X variables by the 2ⁿ points given by X₁=μ₁±₁, X₂ = μ₂ ±₂, …, X_n = = μ_n μ_n, where μ_i is the mean and σ_i the standard deviation of Xi, with appropriate point weights. An advantage over the Taylor series approach is that function derivatives do not have to be explicitely calculated. The point evaluation method is particularly useful in cases where the X variables are uncorrelated. Then the evaluation of the 2ⁿ points can be replaced by the evaluation of 2n points. The point evaluation method is illustrated with powers of a normally distributed variable, and with estimation of gene frequencies from ABO blood group frequencies.     

An illustration of variable precision rough set theory: the gender classification of the European barn swallow (Hirundo rustica)

This paper introduces a new technique in the investigation of object classification and illustrates the potential use of this technique for the analysis of a range of biological data, using avian morphometric data as an example. The nascent variable precision rough sets (VPRS) model is introduced and compared with the decision tree method ID3 (through a ‘leave n out’ approach), using the same dataset of morphometric measures of European barn swallows (Hirundo rustica) and assessing the accuracy of gender classification based on these measures. The results demonstrate that the VPRS model, allied with the use of a modern method of discretization of data, is comparable with the more traditional non-parametric ID3 decision tree method. We show that, particularly in small samples, the VPRS model can improve classification and to a lesser extent prediction aspects over ID3. Furthermore, through the ‘leave n out’ approach, some indication can be produced of the relative importance of the different morphometric measures used in this problem. In this case we suggest that VPRS has advantages over ID3, as it intelligently uses more of the morphometric data available for the data classification, whilst placing less emphasis on variables with low reliability. In biological terms, the results suggest that the gender of swallows can be determined with reasonable accuracy from morphometric data and highlight the most important variables in this process. We suggest that both analysis techniques are potentially useful for the analysis of a range of different types of biological datasets, and that VPRS in particular has potential for application to a range of biological circumstances.     

Species traits and abundance influence the organization of liana–tree antagonistic interaction

The interaction among species can be influenced by neutral processes, in which more abundant species have high effect on the structure of interaction, or can be influenced by trait matching. Despite both variables (abundance and species traits) influencing the interaction of species in mutualistic networks, few studies showed their importance in antagonistic networks. Here, we posed the question: what are the main predictors of the liana–tree interactions: species abundance, biological traits or both? In a savanna woodland fragment in south‐eastern Brazil, we sampled lianas and trees in 1 ha, where we recorded the abundance, maximum height and bark roughness of tree species, as well as abundance, maximum diameter and climbing system of liana species. For each species, we calculated their contribution to nestedness (n_i), which is a measure of network structure, and performed simple linear regressions between n_i and abundance and species traits. Abundant species contribute more to n_i than rare species, indicating that neutral processes affect interactions between lianas and trees, probably because lianas are opportunistic and climb trees in their neighbourhood. The only trait related to n_i was tree height, which can indicate that light availability can have a considerable role on network structure between both growth forms. Therefore, the importance of species abundance and tree height can be related to opportunism of lianas on climbing the most suitable tree in their neighbourhood.     

Distance-based tests for homogeneity of multivariate dispersions

Summary The traditional likelihood‐based test for differences in multivariate dispersions is known to be sensitive to nonnormality. It is also impossible to use when the number of variables exceeds the number of observations. Many biological and ecological data sets have many variables, are highly skewed, and are zero‐inflated. The traditional test and even some more robust alternatives are also unreasonable in many contexts where measures of dispersion based on a non‐Euclidean dissimilarity would be more appropriate. Distance‐based tests of homogeneity of multivariate dispersions, which can be based on any dissimilarity measure of choice, are proposed here. They rely on the rotational invariance of either the multivariate centroid or the spatial median to obtain measures of spread using principal coordinate axes. The tests are straightforward multivariate extensions of Levene's test, with P‐values obtained either using the traditional F‐distribution or using permutation of either least‐squares or LAD residuals. Examples illustrate the utility of the approach, including the analysis of stabilizing selection in sparrows, biodiversity of New Zealand fish assemblages, and the response of Indonesian reef corals to an El Niño. Monte Carlo simulations from the real data sets show that the distance‐based tests are robust and powerful for relevant alternative hypotheses of real differences in spread.     

New xanthine oxidase inhibitors from the fruiting bodies of Tyromyces fissilis

Excessive uric acid production, which causes gout and hyperuricemia, can be blocked by inhibiting xanthine oxidase (XO). However, some agents to block on XO often cause side effects, thereby necessitating the identification of new inhibitors. During the screening of XO inhibitors from various mushroom extracts, we found that a methanolic extract of the fruiting bodies of Tyromyces fissilis, an inedible and non-toxic fungus, showed inhibitory activity. Both n-hexane and ethyl acetate layers, obtained by partitioning this extract exhibited XO inhibitory activity. Subsequently, using an activity-guided separation method, eight active compounds (1–8) were isolated. The structures of five of the new compounds, 2–4, 6, and 7, were elucidated by spectral analysis and chemical derivatization. All compounds had a salicylic acid moiety with an aliphatic group at the C-6 position. Notably, 2-hydroxy-6-pentadecylbenzoic acid (1) showed the highest level of XO noncompetitive inhibition (58.9 ± 2.2% at 25 µM).     

Chemical modification studies onCocos nucifera pollen allergens

Two highly active allergens C_n II (M _r 158,000) and C_nVII (M _r 2900) isolated fromCocos nucifera pollen extract were treated with various protein modifying reagents in order to ascertain the amino acid residues responsible for their allergenicity, In C_n II modification of carboxy group and tryptophan residue led to 30 and ≽ 75% loss in allergenicity and those of lysine and tyrosine reduced 62 and 38% activity, Lysine, tyrosine, tryptophan and carboxy group of C_nVII were also modified causing 81, 17, ≽ 70 and 26% loss of allergenicity respectively, Allergenicity of both was highly affected by pronase and moderately affected by heat, Periodate destroyed about 50% of their allergenicity and other chemical reagents except urea had no remarkable effect     

Disciplinary reporting affects the interpretation of climate change impacts in global oceans

Climate change is affecting marine ecosystems, but different investigative approaches in physical, chemical, and biological disciplines may influence interpretations of climate‐driven changes in the ocean. Here, we review the ocean change literature from 2007 to 2012 based on 461 of the most highly cited studies in physical and chemical oceanography and three biological subdisciplines. Using highly cited studies, we focus on research that has shaped recent discourse on climate‐driven ocean change. Our review identified significant differences in spatial and temporal scales of investigation among disciplines. Physical/chemical studies had a median duration of 29 years (n = 150) and covered the greatest study areas (median 1.41 × 10⁷ km², n = 148). Few biological studies were conducted over similar spatial and temporal scales (median 8 years, n = 215; median 302 km², n = 196), suggesting a more limited ability to separate climate‐related responses from natural variability. We linked physical/chemical and biological disciplines by tracking studies examining biological responses to changing ocean conditions. Of the 545 biological responses recorded, a single physical or chemical stressor was usually implicated as the cause (59%), with temperature as the most common primary stressor (44%). The most frequently studied biological responses were changes in physiology (31%) and population abundance (30%). Differences in disciplinary studies, as identified in this review, can ultimately influence how researchers interpret climate‐related impacts in marine systems. We identified research gaps and the need for more discourse in (1) the Indian and other Southern Hemisphere ocean basins; (2) research themes such as archaea, bacteria, viruses, mangroves, turtles, and ocean acidification; (3) physical and chemical stressors such as dissolved oxygen, salinity, and upwelling; and (4) adaptive responses of marine organisms to climate‐driven ocean change. Our findings reveal that highly cited biological studies are rarely conducted on scales that match those of physical and chemical studies. Rather, we suggest a need for measuring responses at biologically relevant scales.     

Partitioning the variation in a plot‐by‐species data matrix that is related to n sets of explanatory variables

Abstract. Variation partitioning by (partial) constrained ordination is a popular method for exploratory data analysis, but applications are mostly restricted to simple ecological questions only involving two or three sets of explanatory variables, such as climate and soil, this because of the rapid increase in complexity of calculations and results with an increasing number of explanatory variable sets. The existence is demonstrated of a unique algorithm for partitioning the variation in a set of response variables on n sets of explanatory variables; it is shown how the 2n– 1 non‐overlapping components of variation can be calculated. Methods for evaluation and presentation of variation partitioning results are reviewed, and a recursive algorithm is proposed for distributing the many small components of variation over simpler components. Several issues related to the use and usefulness of variation partitioning with n sets of explanatory variables are discussed with reference to a worked example.     

Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes of C. elegans

Abstract

By measuring prevailing distances between YY, YR, RR, and RY dinucleotides in the large database of the nucleosome DNA fragments from C. elegans, the consensus sequence structure of the nucleosome DNA repeat of C. elegans was reconstructed: (YYYYYRRRRR)_n. An actual period was estimated to be 10.4 bases. The pattern is fully consistent with the nucleosome DNA patterns of other eukaryotes, as established earlier, and, thus, the YYYYYRRRRR repeat can be considered as consensus nucleosome DNA sequence repeat across eukaryotic species. Similar distance analysis for [A, T] dinucleotides suggested the related pattern (TTTYTARAAA)_n where the TT and AA dinucleotides display rather out of phase behavior, contrary to the “AA or TT” in-phase periodicity, considered in some publications. A weak 5-base periodicity in the distribution of TA dinucleotides was detected.     

Further Study on the Statistical Test to Detect Spatial Pattern

In the study of spatial patterns, the statistic I' = (n — 1)s²/x was commonly used. In this paper, we found that x — s² has an approximated normal distribution with zero mean if the x_i's (i = 1 to n) are independent identically distributed Poisson variables. Based on this conclusion, the hypothesis that a point pattern is completely random can be tested directly. And a method for the test of spatial patterns was proposed which can be sued as an alternative to the Chi-square based dispersion index test.     

Robust Gaussian Graphical Modeling Via l1 Penalization

Summary Gaussian graphical models have been widely used as an effective method for studying the conditional independency structure among genes and for constructing genetic networks. However, gene expression data typically have heavier tails or more outlying observations than the standard Gaussian distribution. Such outliers in gene expression data can lead to wrong inference on the dependency structure among the genes. We propose a l₁ penalized estimation procedure for the sparse Gaussian graphical models that is robustified against possible outliers. The likelihood function is weighted according to how the observation is deviated, where the deviation of the observation is measured based on its own likelihood. An efficient computational algorithm based on the coordinate gradient descent method is developed to obtain the minimizer of the negative penalized robustified‐likelihood, where nonzero elements of the concentration matrix represents the graphical links among the genes. After the graphical structure is obtained, we re‐estimate the positive definite concentration matrix using an iterative proportional fitting algorithm. Through simulations, we demonstrate that the proposed robust method performs much better than the graphical Lasso for the Gaussian graphical models in terms of both graph structure selection and estimation when outliers are present. We apply the robust estimation procedure to an analysis of yeast gene expression data and show that the resulting graph has better biological interpretation than that obtained from the graphical Lasso.     

Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes

An approach for conveniently implementing low-power CN _n ^ν and RN _n ^ν symmetry-based band-selective mixing sequences for generating homo- and heteronuclear chemical shift correlation NMR spectra of low γ nuclei in biological solids is demonstrated. Efficient magnetisation transfer characteristics are achieved by selecting appropriate symmetries requiring the application of basic RF elements of relatively long duration and numerically tailoring the RF field modulation profile of the basic element. The efficacy of the approach is experimentally shown by the acquisition of ¹⁵N–¹³C dipolar and ¹³C–¹³C scalar and dipolar coupling mediated chemical shift correlation spectra at representative MAS frequencies.     

Stable isotope dilution gas chromatography/mass spectrometry of prostaglandins and leukotrienes

The group of arachidonic acid metabolites comprising the prostaglandins, thromboxanes, and leukotrienes (eicosanoids) are extremely potent, biologically active compounds. Their properties include proaggregatory anti-aggregatory activity for platelets, chemotactic activity for neutrophils, vasoactive activity, and contractile activity to smooth muscle. In order to determine the role of these substances in pathophysiological conditions, it is essential to have highly sensitive methods available for their analysis. It is generally accepted that combined gas chromatography/mass spectrometry is the most specific technique available for the quantitative analysis of eicosanoids. However, methods based on electron impact ionization and positive ion chemical ionization are relatively insensitive, and many investigators have preferred the use of less specific but more sensitive methods based on radioimmunoassay. We have explored the use of negative ion chemical ionization mass spectrometry to improve sensitivity coupled with capillary column chromatography to maximize specificity. Conversion of the terminal carboxyl group (present in all eicosanoids) to the pentafluorobenzyl ester derivative confers excellent electron capturing properties to the molecule. The derivative undergoes highly efficient thermal electron capture in the gas phase, and any fragmentation that occurs subsequently is directed almost entirely away from the analyte molecule. The stabilized carboxylate anion that results carries at least 30% of the total ion current. Using selected ion monitoring techniques it is possible to detect eicosanoids in the range 1–8 pg on column. This methodology has been applied to the development of stable isotope dilution assays for plasma 6-oxo-prostaglandin (PG) F_1α (1) and for the simultaneous analysis of six biologically important PGs in biological fluids (2). In addition, stable isotope dilution techniques have been developed for the analysis of serum thromboxane B₂ and serum leukotriene B₄ (3). The application of this technology to understanding the role of arachidonic acid metabolism in humans will be discussed.     

Analysis of metabolism by mathematical programming techniques

A method is presented for analyzing metabolic interactions by procedures based on mathematical programming techniques. In the procedures described it is assumed that the organism has (through natural selection) maximized (within the constraints imposed on it by its genetic constitution) its fitness to the environment. A practical experimental procedure is described through which the constraints imposed on reaction rates can be observed and from which the metabolic objective function which, it is presumed, metabolism has optimized can be calculated. A method for testing the validity of the objective function is given. Discussion is carried out in terms of a two-dimensional example but the procedures are valid for any number of dimensions. The results of the procedures are expressed by statements of the sort: the metabolic interactions of the cell are such that Q is maximized where Q = a₁x₁ + a₂x₂ + ... + a_nx_n, where a₁, ..., a_n are constants and x₁, ..., x_n are reaction rates. Some possible uses of metabolic objective functions are given.     

Valence orbital response to conformers of n-butane

Individual outer valence orbital responses to rotations of the C–C central bond of butane (C₄H₁₀) are explored on the torsional potential energy surface. Orbital ionization energies, topologies and momentum distributions for the four most significant butane conformation are presented, as snapshots of the conformational variations. The analysis is based on quantum mechanically generated information from coordinate space and momentum space, a technique called dual space analysis (DSA). By comparison with experimental measurements of photo-electron spectra (PES) for energies and of electron momentum spectra (EMS) for energies and Dyson orbitals, we demonstrate that the individual outer valence orbitals of these conformers response differently to the rotations of the central C–C bond of n-butane. Orbital signatures of other higher energy conformations, such as orbitals la ₂ and 5a ₁ of conformation D (C_2v ), are identified. This finding indicates a co-existence of butane conformations, although the global minimum structure of anti-butane, A (C_2h ), is dominant. Orbital topology and electron charges redistribution during the transformation provide useful information on the chemical bonding and related chemical reactions.     

A spectrophotometric method for the quantification of 2-phenylethylamine in biological specimens

An efficient and specific extraction procedure is described for the isolation of 2-phenylethylamine (PEA) from biological material. The method employed, which involves n-hexane extraction from highly alkalinized samples, substantially eliminates most of catecholamines, indoleamines, their presumed metabolites and amino acid precursors as well as those of PEA itself.Characteristics of a chemical reaction used for the quantitation of this amine, which involves a pH and chloride ion dependent oxidation of this compound by Ce(SO₄)₂, are also described. This reaction could also be used for the quantitation of 2-hydroxy-2-phenylethylamine, phenylacetic acid, phenylacetaldehyde and phenylethanol. Using the described procedure, PEA levels were determined in different human, cat and rabbit organs, including brain, of nonpretreated animals as well as in human urine.     

Center-augmented ℓ2-type regularization for subgroup learning

The existing methods for subgroup analysis can be roughly divided into two categories: finite mixture models (FMM) and regularization methods with an ℓ₁-type penalty. In this paper, by introducing the group centers and ℓ₂-type penalty in the loss function, we propose a novel center-augmented regularization (CAR) method; this method can be regarded as a unification of the regularization method and FMM and hence exhibits higher efficiency and robustness and simpler computations than the existing methods. In particular, its computational complexity is reduced from the $O(n^2)$ of the conventional pairwise-penalty method to only $O(nK)$, where n is the sample size and K is the number of subgroups. The asymptotic normality of CAR is established, and the convergence of the algorithm is proven. CAR is applied to a dataset from a multicenter clinical trial, Buprenorphine in the Treatment of Opiate Dependence; a larger R² is produced and three additional significant variables are identified compared to those of the existing methods.     

富油微藻布朗葡萄藻分子生态学研究进展

分子生态学是研究生命系统与环境系统相互作用机理及其分子机制的科学,可以从宏观和微观结合的角度真实反映生态现象的本质。简述产烃布朗葡萄藻形态与化学种等生理生态特征的基础上,综述了近年来国内外布朗葡萄藻分子生态学研究的新进展,主要包括分子系统发育学及其与化学种、基因组、地理来源等之间的关系。经典分类学上,关于布朗葡萄藻属于绿藻门(Chlorophyta)还是黄藻门(Xanthophyta)存在争议,而基于18S核糖体核糖核酸(18S ribosomal ribonucleic acid,18S rRNA)序列的分子系统发育学研究结果将布朗葡萄藻界定为绿藻门、共球藻纲(Trebouxiophyceae)。依据藻株的产烃种类和化学结构特征,可将布朗葡萄藻划分为A、B和L 3个化学种,而布朗葡萄藻的分子系统学进化关系与化学种间高度统一。在基因组大小上,位于同一大亚聚群中的化学种B与L间却存在明显差异,而进化关系较远的化学种B与A间则更相近。不同地理来源布朗葡萄藻的18S rRNA序列和内部转录间隔区(internal transcribed spacer,ITS)多态性较高,提示不同地缘藻株间存有较高的遗传多样性。探讨了布朗葡萄藻分子生态学研究尚待解决的问题,并对今后相关研究做了展望。