CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays

SUMMARY: To increase compatibility between different generations of Affymetrix GeneChip arrays, we propose a method of filtering probes based on their sequences. Our method is implemented as a web-based service for downloading necessary materials for converting the raw data files (*.CEL) for comparative analysis. The user can specify the appropriate level of filtering by setting the criteria for the minimum overlap length between probe sequences and the minimum number of usable probe pairs per probe set. Our website supports a within-species comparison for human and mouse GeneChip arrays. AVAILABILITY: http://www.crosschip.org     

Uniformly minimum variance unbiased estimation of gene diversity

Gene diversity is an important measure of genetic variability in inbred populations. The survival of species in changing environments depends on, among other factors, the genetic variability of the population. In this communication, I have derived the uniformly minimum variance unbiased estimator of gene diversity. The proposed estimator of gene diversity does not assume that the inbreeding coefficient is known. I have also provided the approximate variance of this estimator according to Fisher's method. In addition, I have developed a numerical resampling-based method for obtaining variances and confidence intervals based on the maximum likelihood estimator and the uniformly minimum variance unbiased estimator. Efficiency in estimation of the gene diversity based on these two estimators is discussed. In accordance with the simulation results, I found that the uniformly minimum variance estimator developed in this report is more accurate for estimation of gene diversity than the maximum likelihood estimator.     

基于生态水文学原理的湖泊最小生态需水量计算

近几十年来,由于人类活动的加剧以及全球气候的变化,湖泊普遍出现了萎缩、水位下降、水量锐减、湖水盐化、水质污染、富营养化、甚至干涸消亡等状况。确保湖泊生态系统必需的最小水量是解决可能出现的湖泊严重水资源和生态系统危机的区域问题之一。从生态水文学原理出发,对湖泊最小生态需水量的概念进行了探讨,并提出了计算最小生态需水量的3种方法:1曲线相关法;2功能法;3最低生态水位法。在最低生态水位法中,其方法有最低年平均水位法和年保证率设定法。一旦湖泊最小生态需水量得以确定,将为水资源管理部门的水资源合理配置和湖泊管理提供综合性、权威性及可操作性决策依据,为退化湖泊生态系统的恢复与重建提供科学基础。     

Pattern classification of phylogeny signals

In this paper we propose the minimum entropy clustering (MEC) method for clustering genes based on their phylogenetic signals. This entropy based method will cluster two genes together when their concatenation can decrease the entropy. An integral feature of MEC is that it chooses the number of clusters automatically, which is a major advantage over the other methods. Our simulation results show that this method is quite successful in clustering genes with a common phylogeny.     

Gene-based Genomewide Association Analysis: A Comparison Study

The study of gene-based genetic associations has gained conceptual popularity recently. Biologic insight into the etiology of a complex disease can be gained by focusing on genes as testing units. Several gene-based methods (e.g., minimum p-value (or maximum test statistic) or entropy-based method) have been developed and have more power than a single nucleotide polymorphism (SNP)-based analysis. The objective of this study is to compare the performance of the entropy-based method with the minimum p-value and single SNP–based analysis and to explore their strengths and weaknesses. Simulation studies show that: 1) all three methods can reasonably control the false-positive rate; 2) the minimum p-value method outperforms the entropy-based and the single SNP–based method when only one disease-related SNP occurs within the gene; 3) the entropy-based method outperforms the other methods when there are more than two disease-related SNPs in the gene; and 4) the entropy-based method is computationally more efficient than the minimum p-value method. Application to a real data set shows that more significant genes were identified by the entropy-based method than by the other two methods.     

A Reference Value for the Interior-to-Edge Ratio of Isolated Habitats

Isolated habitats, the consequence of the fragmentation process, are the object of external disturbance. This divides the patch area into two zones: interior and edge. The interior-to-edge ratio quantifies the potential disturbance impact. A method is presented to calculate a reference value for the interior-to-edge ratio, based upon the minimum edge for a given interior. The method is based on pixel geometry features and mathematical morphology. A corrected interior-to-edge ratio is defined using the reference value. The method is illustrated for woodlot fragments in the Belgian Kempen region.     

The use of hemoglobin for determination of phospholipase A2 activity

A spectrophotometric method is proposed for determining phospholipase A2 activity, which is based on the conversion of hemoglobin into hemichrome under the fatty acid action. The spectral difference between hemoglobin and hemichrome was registered by the difference spectrum with a minimum at 405 nm and a maximum at 423 nm. The absorption value determined as the difference between the spectrum maximum and minimum was proportional to the amount of the fatty acid derived from hydrolysis of phospholipids. The method enables the enzyme activity to be determined directly in the spectrophotometric cell.     

Ear tags--a prospective method for the long-term protection of livestock from ectoparasites

Ear tags are a most effective method for protecting animals from ectoparasites for a long time with minimum expenditures and without polluting the environment. The method is based on a long evaporation of highly toxic insecticides, mainly pyrethroids, homogeneously spread in the substance of the filler which by penetrating into the animal's hair provide its constant protection. Ear tags were successfully used for control of population of bloodsucking Diptera, mites and myiasis flies.     

Determination of standardized transpiration used as an indirect method for considering stomatal aperture under field conditions

An indirect method for determination of stomata apertures is described. It is based on comparison of two simultaneous curves: the one obtained under natural conditions and the second obtained under standard conditions with minimum air humidity which can be considered as a criterion of stomata apertures.     

Calculating the target exposure index using a deep convolutional neural network and a rule base

PurposeThe objective of this study is to determine the quality of chest X-ray images using a deep convolutional neural network (DCNN) and a rule base without performing any visual assessment. A method is proposed for determining the minimum diagnosable exposure index (EI) and the target exposure index (EIt).MethodsThe proposed method involves transfer learning to assess the lung fields, mediastinum, and spine using GoogLeNet, which is a type of DCNN that has been trained using conventional images. Three detectors were created, and the image quality of local regions was rated. Subsequently, the results were used to determine the overall quality of chest X-ray images using a rule-based technique that was in turn based on expert assessment. The minimum EI required for diagnosis was calculated based on the distribution of the EI values, which were classified as either suitable or non-suitable and then used to ascertain the EIt.ResultsThe accuracy rate using the DCNN and the rule base was 81%. The minimum EI required for diagnosis was 230, and the EIt was 288.ConclusionThe results indicated that the proposed method using the DCNN and the rule base could discriminate different image qualities without any visual assessment; moreover, it could determine both the minimum EI required for diagnosis and the EIt.     

Determination of standardized transpiration used as an indirect method for considering stomatal aperture under field conditions

An indirect method for determination of stomata apertures is described. It is based on comparison of two simultaneous curves : the one obtained under natural conditions and the second obtained under standard conditions with minimum air humidity which can be considered as a criterion of stomata apertures.     

Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis.

The accurate measurement of bacterial and protistan cell biomass is necessary for understanding their population and trophic dynamics in nature. Direct measurement of fluorescently stained cells is often the method of choice. The tedium of making such measurements visually on the large numbers of cells required has prompted the use of automatic image analysis for this purpose. Accurate measurements by image analysis require an accurate, reliable method of segmenting the image, that is, distinguishing the brightly fluorescing cells from a dark background. This is commonly done by visually choosing a threshold intensity value which most closely coincides with the outline of the cells as perceived by the operator. Ideally, an automated method based on the cell image characteristics should be used. Since the optical nature of edges in images of light-emitting, microscopic fluorescent objects is different from that of images generated by transmitted or reflected light, it seemed that automatic segmentation of such images may require special considerations. We tested nine automated threshold selection methods using standard fluorescent microspheres ranging in size and fluorescence intensity and fluorochrome-stained samples of cells from cultures of cyanobacteria, flagellates, and ciliates. The methods included several variations based on the maximum intensity gradient of the sphere profile (first derivative), the minimum in the second derivative of the sphere profile, the minimum of the image histogram, and the midpoint intensity. Our results indicated that thresholds determined visually and by first-derivative methods tended to overestimate the threshold, causing an underestimation of microsphere size. The method based on the minimum of the second derivative of the profile yielded the most accurate area estimates for spheres of different sizes and brightnesses and for four of the five cell types tested. A simple model of the optical properties of fluorescing objects and the video acquisition system is described which explains how the second derivative best approximates the position of the edge.     

Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis

The accurate measurement of bacterial and protistan cell biomass is necessary for understanding their population and trophic dynamics in nature. Direct measurement of fluorescently stained cells is often the method of choice. The tedium of making such measurements visually on the large numbers of cells required has prompted the use of automatic image analysis for this purpose. Accurate measurements by image analysis require an accurate, reliable method of segmenting the image, that is, distinguishing the brightly fluorescing cells from a dark background. This is commonly done by visually choosing a threshold intensity value which most closely coincides with the outline of the cells as perceived by the operator. Ideally, an automated method based on the cell image characteristics should be used. Since the optical nature of edges in images of light-emitting, microscopic fluorescent objects is different from that of images generated by transmitted or reflected light, it seemed that automatic segmentation of such images may require special considerations. We tested nine automated threshold selection methods using standard fluorescent microspheres ranging in size and fluorescence intensity and fluorochrome-stained samples of cells from cultures of cyanobacteria, flagellates, and ciliates. The methods included several variations based on the maximum intensity gradient of the sphere profile (first derivative), the minimum in the second derivative of the sphere profile, the minimum of the image histogram, and the midpoint intensity. Our results indicated that thresholds determined visually and by first-derivative methods tended to overestimate the threshold, causing an underestimation of microsphere size. The method based on the minimum of the second derivative of the profile yielded the most accurate area estimates for spheres of different sizes and brightnesses and for four of the five cell types tested. A simple model of the optical properties of fluorescing objects and the video acquisition system is described which explains how the second derivative best approximates the position of the edge.     

Conformational analysis of stiff chiral polymers with end-constraints

We present a Lie-group-theoretic method for the kinematic and dynamic analysis of stiff chiral polymers with end constraints. The first is to determine the minimum energy conformations of stiff polymers with end constraints and the second is to perform normal mode analysis based on the determined minimum energy conformations. In this paper, we use concepts from the theory of Lie groups and principles of variational calculus to model such polymers as inextensible or extensible chiral elastic rods with coupling between stiffnesses. This method is general enough to include any stiffness and chirality parameters in the context of elastic filament models with the quadratic elastic potential energy function. As an application of this formulation, the analysis of DNA conformations is discussed. We demonstrate our method with examples of DNA conformations in which topological properties such as writhe, twist and linking number are calculated from the results of the proposed method. Given these minimum energy conformations, we describe how to perform the normal mode analysis. The results presented here build both on recent experimental work in which DNA mechanical properties have been measured and theoretical work in which the mechanics of non-chiral elastic rods has been studied.     

Quantitative determination of anhydroleandomycin and glycol in oleandomycin phosphate]

A spectrophotometric method for determination of inactive admixtures in oleandomycin phosphate-anhydrooleandomycin was developed. The method was based on measuring optical density of methanol solutions of oleandomycin and its admixtures at a wave length of 235 nm of UV-spectrum. The minimun detectable amount was 0.5 per cent. A method of thin-layer chromatography in a buffered fixed layer was developed for determination of the 2nd inactive admixture, i.e. glycole. The chromatogrammes were developed with xanthydrol. The minimum detectable amount was 3 mug.     

Stability analyses for estimating relative durability of quantitative resistance

Summary Experiments in which a series of host cultivars are inoculated in all combinations with a series of pathogen isolates have been used to detect specificity in the host resistance. A theoretical model of polygenic resistance involving both general and specific interactions with pathogen virulence was developed to test the abilities of statistical analyses to discriminate between host genotypes with different levels of general and specific resistance. Estimates of levels of specific resistance could be obtained in regressions of disease severity scores for each host cultivar X pathogen isolate combination vs. the virulence index of each isolate. If the virulence index was based on the mean disease severity induced by the isolate over all host cultivars, the slopes of the regression lines were correlated with the levels of specific resistance in host cultivars. If the virulence index was based on the disease severity induced by the isolate on a host cultivar with a minimum of specific resistance, the mean squares for deviations from the regression were correlated with the levels of specific resistance in host cultivars. A method was developed to consistently choose host cultivars with minimum specific resistance. The two regression analyses gave estimates of specificity in randomly generated, model genotypes of approximately equal accuracy, although the second method appeared to be more accurate when the numbers of loci controlling resistance and virulence were small. The best estimates of numbers of genes for specific resistance were obtained by calculating a rating based on mean disease severity, the mean square for deviation from the regression on the virulence index based on disease severity on the cultivar with minimum specific resistance and the slope of the regression on the virulence index based on the mean disease severity. The best estimates of proportions of resistance genes that were specific were obtained by calculating a rating based on the above deviation mean square and slope alone.Cooperative investigation of the U.S. Department of Agriculture, Agricultural Research Service and the North Carolina Agricultural Research Service. Journal Series Paper No. 8326 of the North Carolina Agricultural Research Service     

Determination of octopine by pre-column fluorescence derivatization using benzoin

A sensitive fluorimetric method for the determination of octopine, a member of opine family, is presented. The method is based on the formation of a fluorescent derivative of octopine with benzoin and the separation by high performance liquid chromatography using a reversed-phase column (Kaseisorb LC ODS-300) within 20 min. The octopine derivative is completely separated from other guanidino compounds including arginine which is generally very high in marine invertebrates. This method gives higher sensitivity, 5 pmol minimum detection, and better reproducibility than the electrophoresis method and colorimetric method.     

Simultaneous assessment of average fragment size and amount in minute samples of degraded DNA

There is currently no method allowing routine characterization of minute amounts of degraded DNA samples such as those encountered in forensic science, archived tissues, ancient DNA, extracellular or stool DNA, and processed food. Here we describe and directly validate such a method based, on the one hand, on a generalized DNA random fragmentation model and, on the other, on two quantitative polymerase chain reaction (PCR) experiments using two different target sizes. The model also makes it possible to determine the minimum sample amount, the minimum mass average fragment size, and the maximum degradation time necessary to obtain a positive PCR.     

Estimation of transformation parameters for microarray data

MOTIVATION AND RESULTS: Durbin et al. (2002), Huber et al. (2002) and Munson (2001) independently introduced a family of transformations (the generalized-log family) which stabilizes the variance of microarray data up to the first order. We introduce a method for estimating the transformation parameter in tandem with a linear model based on the procedure outlined in Box and Cox (1964). We also discuss means of finding transformations within the generalized-log family which are optimal under other criteria, such as minimum residual skewness and minimum mean-variance dependency. AVAILABILITY: R and Matlab code and test data are available from the authors on request.     

Optimal Design of a Series of GSTR's Performing Reversible Reactions Catalyzed by Soluble Enzymes: A Theoretical Study

The condition for the minimum overall reactor volume of a given number of CSTR's in series is theoretically determined for a reversible, single reactant-single product (Uni-Uni) enzyme catalyzed reaction. The reactor network is assumed to operate in steady-state, isothermal conditions with a single phase and a constant activity of biocatalyst. The method is based on a mathematical analysis of the discrete substrate concentration profile along the CSTR's assuming complete micromixing. The algebraic equations describing the critical loci are obtained for the general case, the mathematical proof that these equations define a minimum is presented, and an exact solution arising from an asymptotic situation is found. An approximate analytical method of optimization based on the aforementioned critical behavior is reported and its validity and usefulness discussed. The formulae introduced can be used in more general situations as tools for getting the approximate range where the optimal overall volume of the series of CSTR's lies. Hence, the reasoning developed is important for the preliminary CSTR design and relevant in the initial steps of the more involved methods of numerical optimization. Finally, the enzymatic conversion of fumarate to L-malate is examined as a model system in order to assess the usefulness and applicability of the analysis developed.