Statistical methods for multipoint radiation hybrid mapping.

On the basis of the earlier work of Goss and Harris, Cox et al. introduced radiation hybrid (RH) mapping, a somatic cell genetic technique for constructing fine-structure maps of human chromosomes. Radiation hybrid mapping uses X-ray breakage of chromosomes to order a set of genetic loci and to estimate distances between them. To analyze RH mapping data Cox et al. derived statistical methods that employ information on sets of two and four loci, to build an overall locus order. Here we describe alternative nonparametric and maximum-likelihood methods for the analysis of RHs that use information on many loci simultaneously, including information on partially typed hybrids. Combination of these multipoint methods provides a statistically more efficient solution to the locus-ordering problem. We illustrate our approach by applying it to RH mapping data on 14 markers in 99 radiation hybrids for the proximal long arm of human chromosome 21.     

Comparative study of different methods for detection and enumeration of Salmonella spp. in natural waters

Seven enrichment media (two proposed by the authors) for detecting salmonellas from polluted freshwater were compared. The Most Probable Number technique for enumeration of salmonellas in water samples was used, directly adding filtered water to buffered peptone water as the pre-enrichment medium. The results indicate that Rappaport-Vassiliadis/43 and Rappaport-Vassiliadis/43 supplemented with 10 micrograms of sodium novobiocin per ml are the best media for the recovery and enumeration of salmonellas from water samples.     

Comparative study of different methods for detection and enumeration of Salmonella spp. in natural waters

Seven enrichment media (two proposed by the authors) for detecting salmonellas from polluted freshwater were compared. The Most Probable Number technique for enumeration of salmonellas in water samples was used, directly adding filtered water to buffered peptone water as the pre-enrichment medium. The results indicate that Rappaport-Vassiliadis/43 and Rappaport-Vassiliadis/43 supplemented with 10 μg of sodium novobiocin per ml are the best media for the recovery and enumeration of salmonellas from water samples.     

Comparative efficacy of laboratory methods for cytomegalovirus detection in autopsy material

Eighty eight autopsy specimens obtained from 30 fetuses, still-borns and infants died during the first year of life, all suspected for congenital virus infection at postmortem examination, were studied. The specimens were analyzed by 3 techniques: rapid culture method (RCM) for detection of cytomegalovirus (CMV) infectious activity, the immunocytochemical method for detection of CMV antigen in prints of organs and polymerase chain reaction (PCR) for detection CMV DNA. CMV was detected in 16 out of 26 specimens (61.5%) by PCR, in 43 out of 88 specimens (49%) by RCM and in 15 out of 64 specimens (23%) in prints. The comparison of immune reagents revealed that monoclonal antibodies (McAb) were more specific than polyclonal serum antibodies, as the latter yielded the positive reaction in 10 out of 26 cases (38%), found to be negative in PCR. The data thus obtained indicate that complex techniques, including PCR and RCM in combination with McAb, should be used for evaluation of CMV infection role in child mortality.     

Comparative study of different methods for detection of toxic and other enzymatic factors in Vibrio cholerae strains

The purpose of this work was to characterize the toxin profile and the presence of other virulence factors involved in the pathogenesis and biology of 13 V. cholerae O1 (11 clinical cases and 2 waters) and 6 V. cholerae non O1 strains (4 clinical cases and 2 waters) using genetic (PCR), immunological (RPLA), biochemical (NAD degradation, haemolysis, Kanagawa phenomenon, caseinase, lecithinase, mucinase, amylase, esculine hydrolysis) and cell culture (Vero E6, HEp-2) assays. The results indicated a concordance between PCR-RPLA (84%), PCR-NAD (73%) and RPLA-NAD (84%) methods. The sensitivity of RPLA and NAD degradation methods were comparable to PCR in detecting CT in Vibrio cholerae O1 strains. Although NAD degradation method was not exclusively specific for the CT detection, it proved its usefulness in screening certain virulent, CT-negative clones of V. cholerae. The cytotoxic effect on Vero E6 cells, enzyme production (Kanagawa haemolysins, lecithinase, caseinase, esculine hydrolysis) as well as adherence ability on inert substrate proved to be much more constant in V. cholerae non O1 (CT- negative) than in V. cholerae O1 (CT-positive). All V. cholerae non O1 strains isolated in diarrheal cases were Kanagawa positive. This complex of virulence factors detected in V. cholerae non O1 strains could probably contribute during interepidemic periods to human-to-human transmission and to greater resistance as compared to O1 strains in the environment.     

Comparative study of various methods for determining Vibrio cholerae toxigenicity

Testing of 138 Vibrio cholerae strains for gene determinants responsible for the production of cholera enterotoxin by the polymerase chain reaction (PCR) and gene probing using molecular CT-probe showed good correlation of the results of different methods and correlation of these data with studies of V. cholerae strain virulence in vivo and in hemolytic activity test. The advantages of PCR in rapid assessment of the toxigenicity and epidemic significance of V. cholerae strains are demonstrated.     

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.     

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.     

新生隐球菌基因组DNA不同抽提方法的比较

目的 DNA是进行分子生物学研究的重要基础。在本研究中,我们建立了2种简单快速抽提基因组DNA的方法并可用作PCR扩增的模板。通过比较4种不同的DNA抽提方法以确定哪种更适合进行下一步的基因分析。方法这4种方法是:玻璃珠法,酶法,3%SDS法和氯化苄法。玻璃珠法是用玻璃珠在混漩器上剧烈振荡破碎细胞壁;3%SDS法是将细胞在含10mmol/LDTT的3%SDS溶液中加热,然后用5mmol/LKAc和异丙醇抽提,DNA的产量通过A260测定。结果 3%SDS溶解法、经典酶法、玻璃珠法和氯化苄法的DNA产量分别为0.4154±0.0367、0.8484±0.0756、1.2636±0.2040、0.4070±0.0339(g/L×108CFU/mL)。结论玻璃珠法是最敏感、重复性好、简单、费用合理的抽提方法 。     

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.     

Comparative methods with sampling error and within-species variation: contrasts revisited and revised

Comparative methods analyses have usually assumed that the species phenotypes are the true means for those species. In most analyses, the actual values used are means of samples of modest size. The covariances of contrasts then involve both the covariance of evolutionary changes and a fraction of the within-species phenotypic covariance, the fraction depending on the sample size for that species. Ives et al. have shown how to analyze data in this case when the within-species phenotypic covariances are known. The present model allows them to be unknown and to be estimated from the data. A multivariate normal statistical model is used for multiple characters in samples of finite size from species related by a known phylogeny, under the usual Brownian motion model of change and with equal within-species phenotypic covariances. Contrasts in each character can be obtained both between individuals within a species and between species. Each contrast can be taken for all of the characters. These sets of contrasts, each the same contrast taken for different characters, are independent. The within-set covariances are unequal and depend on the unknown true covariance matrices. An expectation-maximization algorithm is derived for making a reduced maximum likelihood estimate of the covariances of evolutionary change and the within-species phenotypic covariances. It is available in the Contrast program of the PHYLIP package. Computer simulations show that the covariances are biased when the finiteness of sample size is not taken into account and that using the present model corrects the bias. Sampling variation reduces the power of inference of covariation in evolution of different characters. An extension of this method to incorporate estimates of additive genetic covariances from a simple genetic experiment is also discussed.     

蚧虫基因组DNA不同提取方法的比较

实验以日本龟蜡蚧CeroplastesjaponicusGreen,白蜡绵粉蚧PhenacoccusfraxinusTang ,朝鲜球蚧DidesmococcuskoreanusBorchseniush和瘤大球坚蚧EulecaniumgiganteaShinji等 4种蚧虫为材料 ,分别用十二烷基硫酸钠 (SDS)法、十六烷基三乙基溴化铵 (CTAB)法、醋酸钾 (KAc)法和氯化钠 (NaCl)法等 4种方法 ,对单只蚧虫进行基因组DNA提取 ,用 0 8%琼脂糖凝胶电泳检测所提DNA。结果表明 ,4种方法都可以提取到基因组DNA ,但是比较而言 ,CTAB法和NaCl法所提取的DNA质量明显优于SDS法和KAc法 ,并适用于PCR。因此认为 ,CTAB法和NaCl法是实验室提取单只蚧虫基因组DNA更有效而实用的方法。