定量地层对比常用方法的比较和适用性分析

定量地层学以生物地层学原理为核心,将地层学信息定量化,运用数学模型进行地层对比,作为传统地层学对比的重要补充。传统的生物地层学根据经验选取标准化石来建立生物地层序列,但同时也丢失了大量的化石信息。定量地层学则能够利用所有的化石信息,在传统生物地层学的基础上得到更高分辨率的地层对比结果。现阶段定量地层对比常用的方法主要有图形对比法、约束最优化法和单元组合法三种,但对于这三种方法各自适应的数据情况方面,目前成果较少。本文对这三种方法的原理进行了简要的介绍和分析,并建立数据模型,从标准化石的可对比性、数据集的物种总数、剖面间共有物种和单延限分子的比例四个方面对三种方法的适用条件进行了讨论。其中图形对比法更适用于单延限分子较少、标准化石可对比性强的数据集。单元组合法对数据集中物种间相互关系的复杂程度较为敏感,共有物种较多的数据集有更好的对比结果,但数据集中物种总数的增加会对其产生一定的负面影响,需要依靠进一步的人工调整。约束最优化法则对数据集各方面的优化均有响应,对物种总数较大的数据集有较好的对比结果,且剖面间共有物种占比越大,对比结果越理想。     

Comparison of stochastic and deterministic methods for modeling spur kinetics

Stochastic and deterministic kinetic methods have been used to model the temporal evolution of spatially nonhomogeneous clusters of reactants resulting from the dissociation of one to six water molecules into either H3O+, OH, and e-aq, or H atoms and OH radicals. When the ionic fragmentation initially producing H3O+, OH, and e-aq is considered, the stochastic and deterministic methods predict similar time dependences for the decay of the reactive species; however, the two methods suggest very different product yields. For a two-dissociation spur, the deterministic treatment overestimates both the H2 and the H2O2 yields by about 70%. The error decreases to less than 15% for a spur with six water dissociations. For a distribution of spurs representing a high-energy electron track, the differences in the predicted yields of reactants are less than 6% at 0.1 microseconds, but the stochastic and deterministic predictions for the yields of H2 and H2O2 differ by about 50%. The kinetics of spurs produced by the fragmentation of water to H atom and OH radical shows discrepancies in both the reactant and the product yields. The size of the discrepancy decreases as the number of H/OH pairs increases, and the predictions of the two techniques are almost the same for clusters of six water dissociations.     

三种不同方法检查尿液有形成分结果的比较研究

目的:探讨利用三种不同方法检查尿液有形成分的符合率及其影响因素.方法:采用AX-4280全自动干化学分析仪、IQ200全自动尿液分析仪和人工镜检法联合检测尿液,并对结果进行比较和分析.结果:尿液各种有形成分的检测结果均存在不同程度的假阳性,人工镜检法与AX-4280的符合率为:红细胞71.1%;白细胞76.4%.人工镜检法与IQ200全自动尿液分析仪人工修饰前和人工修饰后结果的符合率分别为:红细胞81.3%、91.5%;白细胞85.9%、93.8%;透明管型81.4%、89.7%,未分类管型52.6%、77.4%:结晶84.1%、92.4%;细菌65.1%、88.2%;精子72.0%、91.5%.以人工镜检为标准,IQ200全自动尿液分析仪人工修饰前和人工修饰后各检测项目的假阳性率分别为:红细胞23.0%、9.3%,白细胞16.4%、6.6%,透明管型22.9%、11.4%,未分类管型90.2%、29.2%.结晶19.004、8.2%,细菌53.7%、11.0%,精子38.9%、9.3%.结论:三种检查方法的联合应用更能提高尿液有形成分检查结果的准确性,为临床诊治提供依据.     

三种检验方法在诊断女性生殖道沙眼衣原体感染的比较研究

目的:比较不同方法对宫颈拭子样本沙眼衣原体的检测效果.方法:采集300例20-50岁无感染症状女性宫颈分泌物,分别采用细胞培养、聚合酶链式反应及胶体金法进行沙眼衣原体检测,培养阳性或两个非细胞培养方法检测为阳性,定为真阳性,称为"扩大金标准".结果:300例受检查者.按"扩大金标准"CT感染者共36例,发病率为12%(36/300),细胞培养、聚合酶链式反应、胶体金法敏感性分别为72.22%、91.67%、52.78%.特异性分别为100%、98.11%、98.86%.阳性预测值分别为100%、86.84%、86.36%.阴性预测值分别为96.35%、98.85%、93.88%.结论:三种检测方法均可用于CT感染的诊断.     

Comparative study of gene set enrichment methods

Background  

The analysis of high-throughput gene expression data with respect to sets of genes rather than individual genes has many advantages. A variety of methods have been developed for assessing the enrichment of sets of genes with respect to differential expression. In this paper we provide a comparative study of four of these methods: Fisher's exact test, Gene Set Enrichment Analysis (GSEA), Random-Sets (RS), and Gene List Analysis with Prediction Accuracy (GLAPA). The first three methods use associative statistics, while the fourth uses predictive statistics. We first compare all four methods on simulated data sets to verify that Fisher's exact test is markedly worse than the other three approaches. We then validate the other three methods on seven real data sets with known genetic perturbations and then compare the methods on two cancer data sets where our a priori knowledge is limited.     

Comparison of statistical methods commonly used in predictive modelling

Logistic Multiple Regression, Principal Component Regression and Classification and Regression Tree Analysis (CART), commonly used in ecological modelling using GIS, are compared with a relatively new statistical technique, Multivariate Adaptive Regression Splines (MARS), to test their accuracy, reliability, implementation within GIS and ease of use. All were applied to the same two data sets, covering a wide range of conditions common in predictive modelling, namely geographical range, scale, nature of the predictors and sampling method. We ran two series of analyses to verify if model validation by an independent data set was required or cross‐validation on a learning data set sufficed. Results show that validation by independent data sets is needed. Model accuracy was evaluated using the area under Receiver Operating Characteristics curve (AUC). This measure was used because it summarizes performance across all possible thresholds, and is independent of balance between classes. MARS and Regression Tree Analysis achieved the best prediction success, although the CART model was difficult to use for cartographic purposes due to the high model complexity.     

Comparison of atomic force microscopy interaction forces between bacteria and silicon nitride substrata for three commonly used immobilization methods

Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanometer scale. For AFM, bacterial cells need to be firmly anchored to a substratum surface in order to withstand the friction forces from the silicon nitride tip. Different strategies for the immobilization of bacteria have been described in the literature. This paper compares AFM interaction forces obtained between Klebsiella terrigena and silicon nitride for three commonly used immobilization methods, i.e., mechanical trapping of bacteria in membrane filters, physical adsorption of negatively charged bacteria to a positively charged surface, and glutaraldehyde fixation of bacteria to the tip of the microscope. We have shown that different sample preparation techniques give rise to dissimilar interaction forces. Indeed, the physical adsorption of bacterial cells on modified substrata may promote structural rearrangements in bacterial cell surface structures, while glutaraldehyde treatment was shown to induce physicochemical and mechanical changes on bacterial cell surface properties. In general, mechanical trapping of single bacterial cells in filters appears to be the most reliable method for immobilization.     

A comparison of zooplankton production estimates obtained from three commonly used methods and a computer simulation program

SUMMARY 1. Zooplankton production in a eutrophic reservoir was estimated by three common methods.
2. Estimates of daily production from the growth increment method and the birth and death rate versions of the biomass turnover method were poorly correlated ( r =0.58–0.60). Estimates of daily production rates from the above two versions of the biomass turnover method were strongly correlated ( r =0.90).
3. The mortality rate version of the biomass turnover method is illogical and yields anomalous results.
4. The growth increment method assumes steady state conditions and zero deaths within each stage and hence calculates potential production for each stage.
5. Estimates from a new computer simulation (PROD) were strongly correlated with ( r =0.92) but lower than those from the growth increment method. Estimates from PROD were more poorly correlated ( r =0.78) with those from the biomass turnover method.
6. There is a strong need for improved methods for estimating secondary production; computer based methods would seem to be the most promising.     

Aligning amino acid sequences: comparison of commonly used methods

We examined two extensive families of protein sequences using four different alignment schemes that employ various degrees of "weighting" in order to determine which approach is most sensitive in establishing relationships. All alignments used a similarity approach based on a general algorithm devised by Needleman and Wunsch. The approaches included a simple program, UM (unitary matrix), whereby only identities are scored; a scheme in which the genetic code is used as a basis for weighting (GC); another that employs a matrix based on structural similarity of amino acids taken together with the genetic basis of mutation (SG); and a fourth that uses the empirical log-odds matrix (LOM) developed by Dayhoff on the basis of observed amino acid replacements. The two sequence families examined were (a) nine different globins and (b) nine different tyrosine kinase-like proteins. It was assumed a priori that all members of a family share common ancestry. In cases where two sequences were more than 30% identical, alignments by all four methods were almost always the same. In cases where the percentage identity was less than 20%, however, there were often significant differences in the alignments. On the average, the Dayhoff LOM approach was the most effective in verifying distant relationships, as judged by an empirical "jumbling test." This was not universally the case, however, and in some instances the simple UM was actually as good or better. Trees constructed on the basis of the various alignments differed with regard to their limb lengths, but had essentially the same branching orders. We suggest some reasons for the different effectivenesses of the four approaches in the two different sequence settings, and offer some rules of thumb for assessing the significance of sequence relationships.     

Aligning amino acid sequences: Comparison of commonly used methods

Summary We examined two extensive families of protein sequences using four different alignment schemes that employ various degrees of weighting in order to determine which approach is most sensitive in establishing relationships. All alignments used a similarity approach based on a general algorithm devised by Needleman and Wunsch. The approaches included a simple program, UM (unitary matrix), whereby only identities are scored; a scheme in which the genetic code is used as a basis for weighting (GC); another that employs a matrix based on structural similarity of amino acids taken together with the genetic basis of mutation (SG); and a fourth that uses the empirical log-odds matrix (LOM) developed by Dayhoff on the basis of observed amino acid replacements. The two sequence families examined were (a) nine different globins and (b) nine different tyrosine kinase-like proteins. It was assumed a priori that all members of a family share common ancestry. In cases where two sequences were more than 30% identical, alignments by all four methods were almost always the same. In cases where the percentage identity was less than 20%, however, there were often significant differences in the alignments. On the average, the Dayhoff LOM approach was the most effective in verifying distant relationships, as judged by an empirical jumbling test. This was not universally the case, however, and in some instances the simple UM was actually as good or better. Trees constructed on the basis of the various alignments differed with regard to their limb lengths, but had essentially the same branching orders. We suggest some reasons for the different effectivenesses of the four approaches in the two different sequence settings, and offer some rules of thumb for assessing the significance of sequence relationships.     

Reevaluation of colorimetric iron determination methods commonly used in geomicrobiology

The ferrozine and phenanthroline colorimetric assays are commonly applied for the determination of ferrous and total iron concentrations in geomicrobiological studies. However, accuracy of both methods depends on slight changes in their protocols, on the investigated iron species, and on geochemical variations in sample conditions. Therefore, we tested the performance of both methods using Fe(II)((aq)), Fe(III)((aq)), mixed valence solutions, synthetic goethite, ferrihydrite, and pyrite, as well as microbially-formed magnetite and a mixture of goethite and magnetite. The results were compared to concentrations determined with aqua regia dissolution and inductively coupled plasma atomic emission spectroscopy (ICP-AES). Iron dissolution prior to the photometric assays included dissolution in 1M or 6M HCl, at 21 or 60°C, and oxic or anoxic conditions. Results indicated a good reproducibility of quantitative total iron determinations by the ferrozine and phenanthroline assays for easily soluble iron forms such as Fe(II)((aq)), Fe(III)((aq)), mixed valence solutions, and ferrihydrite. The ferrozine test underestimated total iron contents of some of these samples after dissolution in 1M HCl by 10 to 13%, whereas phenanthroline matched the results determined by ICP-AES with a deviation of 5%. Total iron concentrations after dissolution in 1M HCl of highly crystalline oxides such as magnetite, a mixture of goethite and magnetite, and goethite were underestimated by up to 95% with both methods. When dissolving these minerals in 6M HCl at 60°C, the ferrozine method was more reliable for total iron content with an accuracy of ±5%, related to values determined with ICP-AES. Phenanthroline was more reliable for the determination of total pyritic iron as well as ferrous iron after incubation in 1M HCl at 21°C in the Fe(II)((aq)) sample with a recovery of 98%. Low ferrous iron concentrations of less than 0.5mM were overestimated in a Fe(III) background by up to 150% by both methods. Heating of mineral samples in 6M HCl increased their solubility and susceptibility for both photometric assays which is a need for total iron determination of highly crystalline minerals. However, heating also rendered a subsequent reliable determination of ferrous iron impossible due to fast abiotic oxidation. Due to the low solubility of highly crystalline samples, the determination of total iron is solely possible after dissolution in 6M HCl at 60°C which on the other hand makes determination of ferrous iron impossible. The recommended procedure for ferrous iron determination is therefore incubation at 21°C in 6M HCl, centrifugation, and subsequent measurement of ferrous iron in the supernatant. The different procedures were tested during growth of G. sulfurreducens on synthetic ferrihydrite. Here, the phenanthroline test was more accurate compared to the ferrozine test. However, the latter provided easy handling and seemed preferable for larger amounts of samples.     

Comparative bone anatomy of commonly used laboratory animals: implications for drug discovery

To accommodate functional demands, the composition and organization of the skeleton differ among species. Microcomputed tomography has improved our ability markedly to assess structural parameters of cortical and cancellous bone. The current study describes differences in cortical and cancellous bone structure, bone mineral density, and morphology (geometry) at the proximal femur, proximal femoral diaphysis, lumbar vertebrae, and mandible in mice, rats, rabbits, dogs, and nonhuman primates. This work enhances our understanding of bone gross and microanatomy across lab animal species and likely will enable scientists to select the most appropriate species and relevant bone sites for research involving skeleton. We evaluated the gross and microanatomy of the femora head and neck, lumbar spine, and mandible and parameters of cancellous bone, including trabecular number, thickness, plate separation, and connectivity among species. The skeletal characteristics of rabbits, including a very short femoral neck and small amounts of cancellous bone at the femoral neck, vertebral body, and mandible, seem to make this species the least desirable for preclinical research of human bone physiology; in comparison, nonhuman primates seem the most applicable for extrapolation of data to humans. However, rodent (particularly rat) models are extremely useful for conducting basic research involving the skeleton and represent reliable and affordable alternatives to dogs and nonhuman primates. Radiology and microcomputed tomography allow for reliable evaluation of bone morphology, microarchitecture, and bone mineral density in preclinical and clinical environments.     

Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks

Background  

Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discretization has been conducted, in the context of gene regulatory network inference from time series gene expression data.