A between-class overlapping filter-based method for transcriptome data analysis

Feature selection algorithms play a crucial role in identifying and discovering important genes for cancer classification. Feature selection algorithms can be broadly categorized into two main groups: filter-based methods and wrapper-based methods. Filter-based methods have been quite popular in the literature due to their many advantages, including computational efficiency, simplistic architecture, and an intuitively simple means of discovering biological and clinical aspects. However, these methods have limitations, and the classification accuracy of the selected genes is less accurate. In this paper, we propose a set of univariate filter-based methods using a between-class overlapping criterion. The proposed techniques have been compared with many other univariate filter-based methods using an acute leukemia dataset. The following properties have been examined: classification accuracy of the selected individual genes and the gene subsets; redundancy check among selected genes using ridge regression and LASSO methods; similarity and sensitivity analyses; functional analysis; and, stability analysis. A comprehensive experiment shows promising results for our proposed techniques. The univariate filter based methods using between-class overlapping criterion are accurate and robust, have biological significance, and are computationally efficient and easy to implement. Therefore, they are well suited for biological and clinical discoveries.     

Fine-scale mapping in case-control samples using locus scoring and haplotype-sharing methods

Both haplotype-based and locus-based methods have been proposed as the most powerful methods to employ when fine mapping by association. Although haplotype-based methods utilize more information, they may lose power as a result of overparameterization, given the large number of haplotypes possible over even a few loci. Recently methods have been developed that cluster haplotypes with similar structure in the hope that this reflects shared genealogical ancestry. The aim is to reduce the number of parameters while retaining the genotype information relating to disease susceptibility. We have compared several haplotype-based methods with locus-based methods. We utilized 2 regions (D2 and D4) simulated to be in linkage disequilibrium and to be associated with disease susceptibility, combining 5 replicates at a time to produce 4 datasets that were analyzed. We found little difference in the performance of the haplotype-based methods and the locus-based methods in this dataset.     

蛋白质组学的研究方法

近年来,蛋白质组学的研究在生物医学领域正逐步深入,研究方法也正逐步完善。本文综述了蛋白质组学的几种研究方法,指出了各种方法的优点及局限性,并且对蛋白质组学的研究方法和前景进行了展望。     

Designing fast converging phylogenetic methods

Absolute fast converging phylogenetic reconstruction methods are provably guaranteed to recover the true tree with high probability from sequences that grow only polynomially in the number of leaves, once the edge lengths are bounded arbitrarily from above and below. Only a few methods have been determined to be absolute fast converging; these have all been developed in just the last few years, and most are polynomial time. In this paper, we compare pre-existing fast converging methods as well as some new polynomial time methods that we have developed. Our study, based upon simulating evolution under a wide range of model conditions, establishes that our new methods outperform both neighbor joining and the previous fast converging methods, returning very accurate large trees, when these other methods do poorly.     

Secondary structure prediction and determination of proteins--a review

The rapid increase in sequence data in combination with a greater understanding of the forces regulating protein structure has been the impetus for an upsurge in the development of theoretical prediction methods. These methods have afforded protein chemists the ability to identify and quantify the various secondary structures along the protein chain. Concurrently, various physico-chemical techniques have been developed such as nuclear Overhauser enhancement n.m.r. and laser Raman spectroscopy. In addition, traditional methods such as infrared and circular dichroism spectroscopy have been refined. Although both predictive and physico-chemical techniques are limited in the types of secondary structure they are capable of determining, they have provided valuable information with regards to protein folding and topology in the absence of X-ray data, and have formed the basis for the development of improved methods for secondary structure determination. This paper reviews some of the predictive and physico-chemical methods presently used to determine protein secondary structure.     

Haplotype frequency estimation in the presence of genotyping errors

Several statistical methods have been proposed to estimate haplotype frequencies, either based on unrelated individuals or based on families. These estimates may yield insights on population genetics as well as associations between candidate regions and disease of interest. One limitation of the existing methods is that all these methods make the implicit assumption that there are no genotyping errors. However, genotyping errors are unavoidable in practice. Numerous methods have been developed to incorporate genotyping errors in genetic studies, but none to date have addressed the issues of haplotype inference in the presence of genotyping errors. In this article, we develop statistical methods for haplotype inference incorporating genotyping errors. We describe how our methods can be applied to analyze unrelated individuals as well as nuclear families. Our simulation results show that the proposed methods perform well in the presence of genotyping errors.     

结构模型中预报方法的研究及其应用

本文对结构模型中未知真值在两种不同条件下的最佳预报方法进行了研究.其次,对因子模型预报方法进行了探讨.最后,分别举例说明了这些方法的应用.     

Characteristics of users of traditional contraceptive methods in Bangladesh

Various national surveys suggest that the % of eligible couples in Bangladesh who are using traditional methods of contraception has been growing. This article presents detailed information on knowledge and use patterns of traditional methods and compares the use patterns of traditional and modern methods of contraception. The data are derived from the 1981 Contraceptive Prevalence Survey and information collected from a nationally representative sample of ever married women aged under 50, by way of field interviews using female interviewers. Quality of data was checked at different phases of the survey. Over 96% of the women reported that they knew at least 1 traditional method of contraception. The safe period was the most well known method (36.5%); about 30% reported knowledge of abstinence and 22% knew about withdrawal. Compared with modern methods, where knowledge declined with increased age, the knowledge of traditional methods shows no systematic pattern by age. Respondents with primary and higher education have higher knowledge of traditional methods than women who have never been to school. A similar pattern exists for employment status; non-Muslim women have consistently higher levels of knowledge than Muslim women. Data on patterns of use suggest that about 36% have used at least 1 contraceptive method, 15% having used traditional methods and 20.4% modern methods. The number of women who have used traditional methods increases from ages 20 to 44 and then declines. Use of traditional methods is relatively higher by the number of living children than by the number of children ever born. A similar pattern of association between background characteristics (education, employment and religion) and contraceptive knowledge is evident regarding level of use. Husband's level of education does not show any significant relationship with the use of traditional methods. The use rate of traditional methods was more than doubled among the women owning land compared to those having no land. The total current use rate of modern methods was higher among women aged 40-44 having relatively higher numbers of living children. As with current use, a positive relationship was observed between the socioeconomic variables and ever use. In general, it is concluded that socioeconomic variables played a dominant role in the decision of couples in choosing various methods of contraception. It is suggested that traditional methods still have an important role in family planning and that this should not be disregarded.     

Analysis of continuous covariables in epidemiological studies: Dose‐response modelling and confounder adjustment

The analysis of continuous covariables with regression models commonly used in epidemiology are reviewed and compared. While some methods have been in use for decades, other more recent methods are not yet common or have not yet been formally described. It is shown that recently developed methods such as fractional polynomials and others are very useful to obtain dose‐response curves or for confounder adjustment. Different methods have their specific merits making it difficult to give general recommendations. The application of some of the methods is demonstrated with real data examples from epidemiological studies. Some suggestions for practical strategies in analysing continuous covariables are given.     

Clinical applications of molecular biology for infectious diseases

Molecular biological methods for the detection and characterisation of microorganisms have revolutionised diagnostic microbiology and are now part of routine specimen processing. Polymerase chain reaction (PCR) techniques have led the way into this new era by allowing rapid detection of microorganisms that were previously difficult or impossible to detect by traditional microbiological methods. In addition to detection of fastidious microorganisms, more rapid detection by molecular methods is now possible for pathogens of public health importance. Molecular methods have now progressed beyond identification to detect antimicrobial resistance genes and provide public health information such as strain characterisation by genotyping. Treatment of certain microorganisms has been improved by viral resistance detection and viral load testing for the monitoring of responses to antiviral therapies. With the advent of multiplex PCR, real-time PCR and improvements in efficiency through automation, the costs of molecular methods are decreasing such that the role of molecular methods will further increase. This review will focus on the clinical utility of molecular methods performed in the clinical microbiology laboratory, illustrated with the many examples of how they have changed laboratory diagnosis and therefore the management of infectious diseases.     

Statistical methods for detecting molecular adaptation

The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.     

Searching for functional sites in protein structures

An ability to assign protein function from protein structure is important for structural genomics consortia. The complex relationship between protein fold and function highlights the necessity of looking beyond the global fold of a protein to specific functional sites. Many computational methods have been developed that address this issue. These include evolutionary trace methods, methods that involve the calculation and assessment of maximal superpositions, methods based on graph theory, and methods that apply machine learning techniques. Such function prediction techniques have been applied to the identification of enzyme catalytic triads and DNA-binding motifs.     

基因治疗载体及其基因转移技术的关键问题与研究现状

目前使用的基因治疗载体及其基因转移技术中还没有一种能用于临床并永久有效的基因转移技术 .该文分析了直接体内转移、间接体内转移及其非载体法、病毒载体法、非病毒性生物载体法等基因治疗转移技术存在的一些关键问题 ,并探讨了各问题的解决办法或研究策略以及基因治疗载体研究的发展方向     

Limited agreement among three global gene expression methods highlights the requirement for non-global validation

MOTIVATION: DNA microarrays have revolutionized biological research, but their reliability and accuracy have not been extensively evaluated. Thorough testing of microarrays through comparison to dissimilar gene expression methods is necessary in order to determine their accuracy. RESULTS: We have systematically compared three global gene expression methods on all available histologically normal samples from five human organ types. The data included 25 Affymetrix high-density oligonucleotide array experiments, 23 expressed sequence tag based expression (EBE) experiments and 5 SAGE experiments. The reported gene-by-gene expression patterns showed a wide range of correlations between pairs of methods. This level of agreement was sufficient for accurate clustering of datasets from the same tissue and dissimilar methods, but highlights the need for thorough validation of individual gene expression measurements by alternate, non-global methods. Furthermore, analyses of mRNA abundance distributions indicate limitations in the EBE and SAGE methods at both high- and low-expression levels.     

An evaluation of beta-turn prediction methods

MOTIVATION: beta-turn is an important element of protein structure. In the past three decades, numerous beta-turn prediction methods have been developed based on various strategies. For a detailed discussion about the importance of beta-turns and a systematic introduction of the existing prediction algorithms for beta-turns and their types, please see a recent review (Chou, Analytical Biochemistry, 286, 1-16, 2000). However at present, it is still difficult to say which method is better than the other. This is because of the fact that these methods were developed on different sets of data. Thus, it is important to evaluate the performance of beta-turn prediction methods. RESULTS: We have evaluated the performance of six methods of beta-turn prediction. All the methods have been tested on a set of 426 non-homologous protein chains. It has been observed that the performance of the neural network based method, BTPRED, is significantly better than the statistical methods. One of the reasons for its better performance is that it utilizes the predicted secondary structure information. We have also trained, tested and evaluated the performance of all methods except BTPRED and GORBTURN, on new data set using a 7-fold cross-validation technique. There is a significant improvement in performance of all the methods when secondary structure information is incorporated. Moreover, after incorporating secondary structure information, the Sequence Coupled Model has yielded better results in predicting beta-turns as compared with other methods. In this study, both threshold dependent and independent (ROC) measures have been used for evaluation.     

Insights from linked single nucleotide polymorphisms: what we can learn from linkage disequilibrium

New methods for analyzing sequence polymorphism data have uncovered some striking patterns of linkage disequilibrium in both humans and fruitflies. These methods have revealed examples where the observed amount of linkage disequilibrium is either much more or much less than expected, and have led to advances in our understanding of the forces that affect naturally occurring genetic variation. With the recent explosion of sequence polymorphism data, the prospects for further progress from these methods are quite promising.     

嗅鞘细胞的不同纯化方法及结果

培养的嗅鞘细胞的最终纯度受到多种因素的影响,如嗅鞘细胞的取材来源、分离方法等等;对培养的嗅鞘细胞进行纯化可获得高纯度的嗅鞘细胞。纯化嗅鞘细胞的方法有许多种,主要有单纯差速贴壁法、免疫吸附法、化学药物抑制法、无血清饥饿法等,现在的实验研究更趋向于以上2-3种方法联合应用对嗅鞘细胞进行纯化,这些联合纯化方案主要是在采用单纯差速贴壁方法的基础上再次运用其他一种或几种方法进行嗅鞘细胞的纯化。就获取的嗅鞘细胞的最终纯度而言,许多方法取得了可观的效果。但不同的纯化方法各有利弊,除了价格不同外,不同的纯化方法对嗅鞘细胞的生物活性造成不同程度的影响。因此在选择纯化方法时,应综合考虑各方面因素,根据研究目的和实际需要选择合理的方案进行纯化。本文通过查阅各数据库中与嗅鞘细胞的分离培养及纯化有关的文献和其他相关书籍,来探讨纯化嗅鞘细胞的不同方法以及这些纯化方法对嗅鞘细胞最终纯度的影响。     

Cytochemical studies of the vascular endothelium

Cytochemical methods have been used to examine the vascular endothelium. With hemeproteins and immunocytochemistry, investigators have demonstrated the pathways that blood-borne molecules can take to gain access to the extravascular space (Ghitescu et al. 1986; Milici et al. 1987; Schneeberger and Karnovsky 1971; Simionescu et al. 1975). These same cytochemical methods have also provided evidence that morphologically similar endothelia may have different permeability properties (Hart and Pino 1985b, 1986; Pino 1985; Pino and Essner 1980, 1981). Differences in the location and chemical composition of cell surface moieties have been ascertained with enzyme digestion methods, lectins, and cationic ferritin (De Bruyn and Michelson 1978; Pino 1984c, 1986a, b; Simionescu et al. 1981a). The author hopes that he has provided the reader with representative examples of how investigators have used these cytochemical methods for their studies. As new methods are developed and applications are found for existing techniques such as ultracryomicrotomy (Milici et al. 1987) and colloidal gold markers (Pino 1987b), cytochemistry will remain a fundamental tool for the study of the structure and function of the vascular endothelium.     

The separation of enantiomeric sugars by chromatographic methods

This paper has reviewed the number of chromatographic methods by which one may determine the absolute configuration of sugars. Both indirect methods (converting the enantiomeric pair into diastereomers) and direct methods (using chiral stationary phases) have been discussed. Resolving reagents for the indirect methods include chiral hydroxy compounds, chiral amines, and chiral thiols; with subsequent separation of the diastereomers either by gas-liquid chromatography or by high pressure liquid chromatography. Direct methods discussed have exclusively utilized chiral substitution of organopolysiloxane phases for the separation of enantiomeric sugars as volatile derivatives by gas-liquid chromatography.     

Comparison of a culture‐based and a PCR‐based methods for estimating bacterial abundance on eggshells,with comments on statistical analyses

Field ornithologists have used traditional culture‐based techniques to determine the presence and abundance of microbes on surfaces such as eggshells, but culture‐independent PCR‐based methods have recently been introduced. We compared the traditional culture‐based and the real‐time PCR‐based methods for detecting and quantifying Escherichia coli on the eggshells of Eurasian Magpies (Pica pica). PCR estimates of bacterial abundance were ～10 times higher than culture‐based estimates, and the culture‐based technique failed to detect bacteria at lower densities. When both methods detected bacteria, bacterial densities determined by the two methods were positively correlated, indicating that both methods can be used to study factors affecting bacterial densities. The difference between the two methods is consistent with generally acknowledged higher sensitivity of the PCR method, but the extent of the difference in our study (10×) may have been influenced by both a PCR‐based overestimation and culture‐based underestimation of bacterial densities. Our results also illustrate that bacterial counts may sometimes produce left‐censored data (i.e., we did not detect E. coli in 62% of our samples using the culture‐based method). Specific statistical methods have been developed for analyzed left‐censored data, but, to our knowledge, have not been used by ornithologists. In future studies, investigators studying bacterial loads should provide information about the possible degree of left censoring and should justify their choice of statistical methods from the broad set of available methods, including those explicitly designed for censored data.