Evaluating conformational changes in protein structures binding RNA

Many protein-RNA recognition events are known to exhibit conformational changes from qualitative observations of individual complexes. However, a quantitative estimation of conformational changes is required if protein-RNA docking and template-based methods for RNA binding site prediction are to be developed. This study presents the first quantitative evaluation of conformational changes that occur when proteins bind RNA. The analysis of twelve RNA-binding proteins in the bound and unbound states using error-scaled difference distance matrices is presented. The binding site residues are mapped to each structure, and the conformational changes that affect these residues are evaluated. Of the twelve proteins four exhibit greater movements in nonbinding site residues, and a further four show the greatest movements in binding site residues. The remaining four proteins display no significant conformational change. When interface residues are found to be in conformationally variable regions of the protein they are typically seen to move less than 2 A between the bound and unbound conformations. The current data indicate that conformational changes in the binding site residues of RNA binding proteins may not be as significant as previously suggested, but a larger data set is required before wider conclusions may be drawn. The implications of the observed conformational changes for protein function prediction are discussed.     

USLE/RUSLE模型中植被覆盖管理因子的遥感定量估算研究进展

通用土壤流失方程（USLE）及其后续修正方程（RUSLE）是区域土壤侵蚀风险评估和水土保持规划的有效工具.植被覆盖管理因子作为USLE和RUSLE的重要参数之一,其合理估算对土壤侵蚀的准确预测尤为重要.基于野外实地调查和测量的传统估算法费时、费力且费用高,无法满足宏观尺度上植被覆盖管理因子的快速提取.近年来,遥感技术的发展为大尺度植被覆盖管理因子获取提供了丰富的数据和方法.本文基于国内外相关研究成果,综述了植被覆盖管理因子遥感定量估算方法的研究进展,评述了各类方法的优劣,以期为进一步开展大尺度植被覆盖管理因子的定量估算及拓展现有研究思路提供借鉴.     

Quantitative genetic tools for insecticide resistance risk assessment: estimating the heritability of resistance

Quantitative genetic studies of resistance can provide estimates of genetic parameters not available with other types of genetic analyses. Three methods are discussed for estimating the amount of additive genetic variation in resistance to individual insecticides and subsequent estimation of the heritability (h2) of resistance. Sibling analysis and offspring-parent regression permit direct estimates of h2 by comparing the resistance phenotypes of individuals of known relatedness. Threshold trait analyses, performed on data from selection experiments, provide estimates of realized heritability. Procedures are outlined for predicting changes in resistance to insecticides based on h2 estimates. Quantitative genetic theory is examined as it relates to resistance and resistance as a quantitative trait; quantitative genetic methods also are unique in providing estimates of genetic correlations between traits. Comments are included on estimates of genetic correlation between resistance and phenotypic traits (e.g., development time) and how they may be used to predict changes in the genetic aspects of phenology that result from insecticide applications (i.e., to predict how the reproductive capacity of future generations will differ from that of the treated generation).     

The quantitative assessment of the biological activity of angiogenin]

Methods have been developed for the in vivo quantitative estimation of biological activity of angiogenin, a protein growth factor of blood vessels. The quantitative analysis of angiogenin with the methods of angiogenetic disks in isotopic modification requires nanogram amounts of the angiogenetic. The cutireaction test is less sensitive though technically simple. The methods are developed on animal (mouse and rat) tissues.     

Prolonged hypokinesia and its influence on the tissues and vessels of the extremities in experiments]

The work describes the results of complex investigation of the state of the supporting-motor apparatus of extremities of dogs subjected to six-month-long restriction of motor activity and the following reparation during a month. Intravital rentgenological, anatomical, histochemical and electron microscopic methods were used. It was shown that continuous hypokinesia resulted in substantial alterations of the vascular bed in the macro-micro-ultrastructural level, disturbance of metabolism, focal reconstruction of tissues of the extremities by the type of natural death of ultrastructural elements without a following reparation. A one-month term appeared to be insufficient for reparation of structural disorders. Special attention was given to reactions of the vascular system. Signs of blood transport via extracapillary pathways from the arterial bed into the venous bed were noted.     

Evaluation of the Spiral Plate Maker for the Enumeration of Micro-organisms in Foods

A statistically based comparison of five methods of enumerating bacteria in foods has been undertaken to assess the potential application of the Spiral Plate Maker (Gilchrist et al. 1973) which is claimed to reduce very significantly the costs involved in the quantitative estimation of viable micro-organisms in foods. The performance of the Spiral Plate Maker was compared with that of three conventional methods (pour plate, surface spread plate and drop count) for the examination of four types of food by four different operators. Analysis of variance showed that there were no differences between the methods at the 5% level although some isolated interactions occurred. Regression and correlation coefficients between the various methods were all highly significant and the results obtained by the spiral plate method were within the limits of error for traditional quantitative methods. The spiral plate method, in many cases, can replace advantageously any of the other methods for the quantitative estimation of viable microorganisms in foods. Labour requirements for the enumeration of micro-organisms by the spiral plate method were only 31% of that required for one conventional method. In addition considerable savings in materials were achieved.     

Current data on the exploration and the evaluation of clinical pain]

Pain is a complex, multidimensional and multifactorial neuropsychological phenomenon with sensory-discriminative, affective, cognitive and behavioral components. Issues on pain assessment are related to the objective evaluation of a subjective phenomenon. Different levels of evaluation are to be considered. Some methods like visual analogue scale, numerical scale and verbal permit a global pain estimation. The aim of other methods like the McGill Pain Questionnaire is a quantitative and qualitative evaluation of the sensory and affective pain components. The measure of objective behavioral changes is an interesting approach, but at the present time there is no valid, simple and commonly used method. There is also a need for methods permitting a better exploration of a pain, and in particular a selective evaluation of organic and functional factors. The limits of psychological factors evaluation are reported.     

Post-mortem changes in the metabolomic compositions of rabbit blood,aqueous and vitreous humors

Introduction

The analysis of post-mortem metabolomic changes in biological fluids opens the way to develop new methods for the estimation of post-mortem interval (PMI). It may also help in the analysis of disease-induced metabolomic changes in human tissues when the postoperational samples are compared to the post-mortem samples from healthy donors.

Objectives

The goals of this study are to observe and classify the post-mortem changes occurring in the rabbit blood, aqueous and vitreous humors (AH and VH), to identify the potential PMI markers among a wide range of metabolites, and also to determine which biological fluid—blood, AH or VH—is more suitable for the PMI estimation.

Methods

The quantitative metabolomic profiling of samples of the rabbit serum, AH and VH taken at different PMIs has been performed with the combined use of high-frequency NMR and high-resolution LC–MS methods.

Results

The quantitative levels of 61 metabolites in the rabbit serum, AH and VH at different PMIs have been measured. It has been found that the post-mortem metabolomic changes in AH and VH proceed slower than in blood, and the data scattering is lower. Among the metabolites whose concentrations increase with time, the most significant and linear growth is found for hypoxanthine, choline and glycerol.

Conclusion

The obtained results suggest that the ocular fluids AH and VH may have some advantages over blood serum for the search of potential biochemical markers for the PMI estimation. Among the compounds studied in the present work, hypoxanthine, choline and glycerol give the biggest promise as the potential PMI biomarkers.

     

A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses

The number of methods for pre-processing and analysis of gene expression data continues to increase, often making it difficult to select the most appropriate approach. We present a simple procedure for comparative estimation of a variety of methods for microarray data pre-processing and analysis. Our approach is based on the use of real microarray data in which controlled fold changes are introduced into 20% of the data to provide a metric for comparison with the unmodified data. The data modifications can be easily applied to raw data measured with any technological platform and retains all the complex structures and statistical characteristics of the real-world data. The power of the method is illustrated by its application to the quantitative comparison of different methods of normalization and analysis of microarray data. Our results demonstrate that the method of controlled modifications of real experimental data provides a simple tool for assessing the performance of data preprocessing and analysis methods.     

Detection and localization of a single binary trait locus in experimental populations

The advancements made in molecular technology coupled with statistical methodology have led to the successful detection and location of genomic regions (quantitative trait loci; QTL) associated with quantitative traits. Binary traits (e.g. susceptibility/resistance), while not quantitative in nature, are equally important for the purpose of detecting and locating significant associations with genomic regions. Existing interval regression methods used in binary trait analysis are adapted from quantitative trait analysis and the tests for regression coefficients are tests of effect, not detection. Additionally, estimates of recombination that fail to take into account varying penetrance perform poorly when penetrance is incomplete. In this work a complete probability model for binary trait data is developed allowing for unbiased estimation of both penetrance and recombination between a genetic marker locus and a binary trait locus for backcross and F2 experimental designs. The regression model is reparameterized allowing for tests of detection. Extensive simulations were conducted to assess the performance of estimation and testing in the proposed parameterization. The proposed parameterization was compared with interval regression via simulation. The results indicate that our parameterization shows equivalent estimation capabilities, requires less computational effort and works well with only a single marker.     

On the Agreement between Manual and Automated Methods for Single-Trial Detection and Estimation of Features from Event-Related Potentials

The agreement between humans and algorithms on whether an event-related potential (ERP) is present or not and the level of variation in the estimated values of its relevant features are largely unknown. Thus, the aim of this study was to determine the categorical and quantitative agreement between manual and automated methods for single-trial detection and estimation of ERP features. To this end, ERPs were elicited in sixteen healthy volunteers using electrical stimulation at graded intensities below and above the nociceptive withdrawal reflex threshold. Presence/absence of an ERP peak (categorical outcome) and its amplitude and latency (quantitative outcome) in each single-trial were evaluated independently by two human observers and two automated algorithms taken from existing literature. Categorical agreement was assessed using percentage positive and negative agreement and Cohen’s κ, whereas quantitative agreement was evaluated using Bland-Altman analysis and the coefficient of variation. Typical values for the categorical agreement between manual and automated methods were derived, as well as reference values for the average and maximum differences that can be expected if one method is used instead of the others. Results showed that the human observers presented the highest categorical and quantitative agreement, and there were significantly large differences between detection and estimation of quantitative features among methods. In conclusion, substantial care should be taken in the selection of the detection/estimation approach, since factors like stimulation intensity and expected number of trials with/without response can play a significant role in the outcome of a study.     

Histochemical Detection of Collagen Fibers by Sirius Red/Fast Green Is More Sensitive than van Gieson or Sirius Red Alone in Normal and Inflamed Rat Colon

Collagen detection in histological sections and its quantitative estimation by computer-aided image analysis represent important procedures to assess tissue localization and distribution of connective fibers. Different histochemical approaches have been proposed to detect and quantify collagen deposition in paraffin slices with different degrees of satisfaction. The present study was performed to compare the qualitative and quantitative efficiency of three histochemical methods available for collagen staining in paraffin sections of colon. van Gieson, Sirius Red and Sirius Red/Fast Green stainings were carried out for collagen detection and quantitative estimation by morphometric image analysis in colonic specimens from normal rats or animals with 2,4-dinitrobenzenesulfonic acid (DNBS) induced colitis. Haematoxylin/eosin staining was carried out to assess tissue morphology and histopathological lesions. Among the three investigated methods, Sirius Red/Fast Green staining allowed to best highlight well-defined red-stained collagen fibers and to obtain the highest quantitative results by morphometric image analysis in both normal and inflamed colon. Collagen fibers, which stood out against the green-stained non-collagen components, could be clearly appreciated, even in their thinner networks, within all layers of normal or inflamed colonic wall. The present study provides evidence that, as compared with Sirius Red alone or van Gieson staining, the Sirius Red/Fast Green method is the most sensitive, in terms of both qualitative and quantitative evaluation of collagen fibers, in paraffin sections of both normal and inflamed colon.     

Quantitation of glucose-6-phosphate dehydrogenase activity in cortical fractions of the nephron in sodium-depleted and sodium-loaded rabbits

Summary Glucose-6-phosphate dehydrogenase activity was measured quantitatively in isolated cortical fractions of the nephron in sodium-depeleted and sodium-loaded rabbits. The samples consisted of isolated fractions of macula densa, proximal convoluted tubule, distal convoluted tubule and glomerulus. In sodium-depleted rabbits enzyme activity was identical to that of normal rabbits. In sodium-loaded rabbits a significant decrease in enzyme activity was found in the macula densa and proximal convoluted tubule. However, using conventional histochemical incubation methods semiquantitative estimation of glucose-6-phosphate dehydrogenase showed a slight decrease in enzyme activity in the macula densa and distal convoluted tubule, and a slight increase in the proximal convoluted tubule during sodiumdepletion. During sodium-load a pronounced decrease in enzyme activity was seen in the macula densa and distal convoluted tubule. These results show that semiquantitative histochemical evaluation of changes in enzyme activity is less reliable than the more precise quantitative method especially when there are only slight changes in enzyme activity. Only where there were marked changes in histochemical enzyme activity might the results of quantitative and semiquantitative methods be in accord.     

Photographic assessment of coral chlorophyll contents: Implications for ecophysiological studies and coral monitoring

Assessing environmental impacts on coral reef communities has become a growing discipline. As most corals grow relatively slowly, the common method of monitoring changes in coral communities may limit our ability to identify stressors and stress responses. Since chlorophyll density (amount of chlorophyll a + c₂ per unit of coral surface area) in corals may correlate with coral color, the latter has been suggested as an indicator of the natural seasonal changes in undisturbed (“healthy”) corals, as well as an indicator of environmentally-induced stresses in corals, including those related to bleaching. However, the color of underwater objects as perceived through the naked eye or a camera is affected by attenuation of irradiance with depth, changes in spectral properties of underwater light, turbidity and dissolved materials in the water, among other factors. Thus, methodological issues have so far held back the use of color as a quantitative indicator for chlorophyll content. Presented here are two accurate and easy to use methods for quantitative measurements of chlorophyll density from digital photographs of corals. In these methods, the intensities of the red, green and blue channels in digital photographs were compared to measured chlorophyll densities in Stylophora pistillata. Variations in external light, known to bias the true color in underwater images, were eliminated either by photographing corals through a specially built funnel with an internal light source or by mathematically normalizing color channels to a gray reference scale. In both methods, chlorophyll density was highly correlated with the intensity of the red channel, despite large variations in lighting conditions during the photography.These photographic methods enabled the estimation of natural spatial and temporal changes of the chlorophyll density of corals. By predicting chlorophyll density in corals at very low costs, both methods presented here could facilitate the study of large-scale physiological changes in corals.     

A quantitative genetic method for estimating developmental instability

The concept of developmental instability (DI) is frequently used in evolutionary biology, and a range of definitions has been proposed. Moreover, numerous different statistical methods have been used for estimation of DI. The common basis for all methods is that measures need to be obtained from repeated structures within organisms. In the case of fluctuating asymmetry, mirror images could be interpreted as the repeats of each other. All repeats of a trait on one organism should, from a quantitative perspective, have the same genetic foundation. Most previous methods have not accounted for the genetics of the underlying trait. It is here shown how a statistical method from quantitative genetics (the repeated records animal model) can be used for assessment of DI, based on estimation of the variance due to the permanent environment. Moreover, Gibbs sampling is used for inference of the parameters, which provides a Bayesian framework where posterior distributions easily can be calculated from any functions of the variance components. The method is applied to a real dataset from two populations of the plant Scabiosa canescens, and results shows that it works well under realistic situations.     

Estimation of quantitative trait locus effects with epistasis by variational Bayes algorithms

Bayesian hierarchical shrinkage methods have been widely used for quantitative trait locus mapping. From the computational perspective, the application of the Markov chain Monte Carlo (MCMC) method is not optimal for high-dimensional problems such as the ones arising in epistatic analysis. Maximum a posteriori (MAP) estimation can be a faster alternative, but it usually produces only point estimates without providing any measures of uncertainty (i.e., interval estimates). The variational Bayes method, stemming from the mean field theory in theoretical physics, is regarded as a compromise between MAP and MCMC estimation, which can be efficiently computed and produces the uncertainty measures of the estimates. Furthermore, variational Bayes methods can be regarded as the extension of traditional expectation-maximization (EM) algorithms and can be applied to a broader class of Bayesian models. Thus, the use of variational Bayes algorithms based on three hierarchical shrinkage models including Bayesian adaptive shrinkage, Bayesian LASSO, and extended Bayesian LASSO is proposed here. These methods performed generally well and were found to be highly competitive with their MCMC counterparts in our example analyses. The use of posterior credible intervals and permutation tests are considered for decision making between quantitative trait loci (QTL) and non-QTL. The performance of the presented models is also compared with R/qtlbim and R/BhGLM packages, using a previously studied simulated public epistatic data set.     

The quantitative estimation of diphtheria and tetanus toxoids. 1. The flocculation test and the Lf-unit

Considerable confusion exist in the quantitative estimation of diphtheria and tetanus toxoids. The present paper is the first in a series of papers comparing various quantitative methods. It describes the flocculation test, gives a mathematical model for the three-dimensional reaction surface, and suggests different designs which facilitate the unbiased calculation of the end-point.     

Comparative efficiencies of different methods for removing blink artifacts in analyzing quantitative electroencephalogram and event-related potentials

Different methods for blink artifact correction in multichannel electoencephalogram (EEG) have been compared with respect to their efficiency and the relative systemic error of the estimation of the parameters of EEG spectra and event-related potentials (ERPs). Three methods of blink artifact correction have been used: distraction of the electrooculogram (EOG) signals from EEG signals, zeroing independent EEG components associated with vertical eye movement, and zeroing the principal EEG components related to blinking. The results have shown that these correction methods can substantially improve the accuracy of the estimation of quantitative EEG parameters while only slightly distorting signals from most EEG sites. It is concluded that wide use of these methods for EEG processing in fundamental and applied studies would be advisable.     

Permanent plot research in wet meadows and cutting experiment

Vegetation mowing is usually recommended for preserving wet meadows, in particular for the prevention of land warping and brushwood encroachment. The concept and the methods for the study of the influence of different cutting rhythms on the vegetation of two wet meadows, as well as some short term results are presented. Cutting experiments with permanent plots have been undertaken in vegetation communities such as Orchio-Schoenetum nigricantis and Caricetum elatae, abandoned for many years. The strategy of the study was to have diverse but complementary methodological approaches in order to assess changes in the vegetation and species abundance, especially concerning the botanical composition, the vegetation structure and the species vitality. The methods include counting of plants or part of plants, morphometry of Phragmites communis, biomass measurements, phenological records, structure relevés with the point-intercept technique as well as classical vegetation relevés with coverage estimation.On a short term base we can conclude, on the whole, that the yearly winter cut treatment induces a better vitality (number of individuals, flowering, biomass) of the studied species, while in the control plots the vitality is low, due notably to the important layer of accumulating litter and the lack of light on the ground, which hamper soil warming. The yearly summer cut treatment and the winter cut made every three years show in general intermediate characteristics. Furthermore, the vegetation structure is noticeably different according to whether the vegetation is cut (with hay removal) or not. Concerning the methodology, it is concluded that a diverse approach is a good way to assess changes in the vegetation with a minimum loss of information. If the rather subjective method of vegetation relevés with cover estimation may be suitable for long term survey on permanent plots, more quantitative and objective techniques have to be set if short term or precise changes in the botanical composition, the species vitality and the biomass, as well as structural changes, are sought.This paper was presented at the meeting of the working Group for Succession on Permanent Plots, held in Bern (Switzerland), 4th–7th September 1991.