几种数量综述方法的介绍与比较

综述是科学研究中的一种重要方法,数量综述较传统的叙述性综述有许多优多,文章介绍并比较了目前在科学研究中比较流行的几数量综述方法.     

Advances in Statistical Methods to Map Quantitative Trait Loci in Outbred Populations

Statistical methods to map quantitative trait loci (QTL) in outbred populations are reviewed, extensions and applications to human and plant genetic data are indicated, and areas for further research are identified. Simple and computationally inexpensive methods include (multiple) linear regression of phenotype on marker genotypes and regression of squared phenotypic differences among relative pairs on estimated proportions of identity-by-descent at a locus. These methods are less suited for genetic parameter estimation in outbred populations but allow the determination of test statistic distributions via simulation or data permutation; however, further inferences including confidence intervals of QTL location require the use of Monte Carlo or bootstrap sampling techniques. A method which is intermediate in computational requirements is residual maximum likelihood (REML) with a covariance matrix of random QTL effects conditional on information from multiple linked markers. Testing for the number of QTLs on a chromosome is difficult in a classical framework. The computationally most demanding methods are maximum likelihood and Bayesian analysis, which take account of the distribution of multilocus marker-QTL genotypes on a pedigree and permit investigators to fit different models of variation at the QTL. The Bayesian analysis includes the number of QTLs on a chromosome as an unknown.     

Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application

Genome-wide association studies (GWAS) have rapidly become a standard method for disease gene discovery. A substantial number of recent GWAS indicate that for most disorders, only a few common variants are implicated and the associated SNPs explain only a small fraction of the genetic risk. This review is written from the viewpoint that findings from the GWAS provide preliminary genetic information that is available for additional analysis by statistical procedures that accumulate evidence, and that these secondary analyses are very likely to provide valuable information that will help prioritize the strongest constellations of results. We review and discuss three analytic methods to combine preliminary GWAS statistics to identify genes, alleles, and pathways for deeper investigations. Meta-analysis seeks to pool information from multiple GWAS to increase the chances of finding true positives among the false positives and provides a way to combine associations across GWAS, even when the original data are unavailable. Testing for epistasis within a single GWAS study can identify the stronger results that are revealed when genes interact. Pathway analysis of GWAS results is used to prioritize genes and pathways within a biological context. Following a GWAS, association results can be assigned to pathways and tested in aggregate with computational tools and pathway databases. Reviews of published methods with recommendations for their application are provided within the framework for each approach.     

Review of the Methods Frequently Used to Estimate the Abundance of Orthoptera in Grassland Ecosystems

Ecologists have quantified Orthoptera (grasshoppers and crickets) density in a wide variety of conservation studies. Objective determination of Orthoptera population size is possible using mark-release recapture techniques but these are time-consuming and of little use for all but the smallest scale studies. Therefore, a wide range of sampling techniques have been devised to quantify population density and the most commonly used methods include sweep netting and quadrat counts. It is the aim of this paper to critically review studies that have used these techniques and to provide useful suggestions for non-specialists on which method may be most applicable to their study site. This paper reviews a selection of the extensive literature reporting studies estimating the abundance of grasshoppers (Acrididae) in a wide range of grassland ecosystems. Where possible, studies on bush-crickets (Tettigoniidae) and crickets (Gryllidae) are included reflecting their overall contribution to assemblage diversity in grassland ecosystems and to highlight the need for further investigations of sampling efficiency on these two under-researched families.The most rapid and inexpensive sampling methods, such as quadrat and transect counts, involve ‘flushing’ grasshoppers from the sward. These techniques are fairly accurate in short, open swards (<50 cm sward height) where grasshopper densities are low (<2 adults per m²). At higher population densities (>2 adults per m²), methods which require the capture of grasshoppers such as box quadrats and sweep netting may be more appropriate. Sampling grasshopper populations in taller vegetation (>50 cm sward height) is more problematic as the efficiency of many techniques may be reduced by vegetation structure. Methods such as timed counts can be used at low densities (<2 adults per m²) and night trapping might be most applicable where high numbers of grasshoppers are present (>2 adults per m²).There is an urgent need for development of a standardised sampling technique that can produce comparable data from studies with a wide variety of observers in grasslands with differing vegetation structures and grasshopper densities.     

A Study of Statistical Methods for Function Prediction of Protein Motifs

Automatic discovery of new protein motifs (i.e. amino acid patterns) is one of the major challenges in bioinformatics. Several algorithms have been proposed that can extract statistically significant motif patterns from any set of protein sequences. With these methods, one can generate a large set of candidate motifs that may be biologically meaningful. This article examines methods to predict the functions of these candidate motifs. We use several statistical methods: a popularity method, a mutual information method and probabilistic translation models. These methods capture, from different perspectives, the correlations between the matched motifs of a protein and its assigned Gene Ontology terms that characterise the function of the protein. We evaluate these different methods using the known motifs in the InterPro database. Each method is used to rank candidate terms for each motif. We then use the expected mean reciprocal rank to evaluate the performance. The results show that, in general, all these methods perform well, suggesting that they can all be useful for predicting the function of an unknown motif. Among the methods tested, a probabilistic translation model with a popularity prior performs the best.     

A Statistical Review of Carcinoma of the Lip

Among 3166 patients with microscopically confirmed squamous cell carcinoma of the lip registered at The Ontario Cancer Treatment and Research Foundation''s Regional Clinics in 1938-1955, the five-year crude survival rate was 65%, and the five-year net survival rate 89%. Survival was influenced by age, site and size of primary lesion, local and regional invasion, long delay, and treatment method. The initial treatment appeared to control the primary lesion in 84% of cases and involved lymph nodes in 58%. The net survival rates improved over the survey period. Findings confirm the usefulness of the proposed TNM staging.     

Applications of the Repeatability of Quantitative Imaging Biomarkers: A Review of Statistical Analysis of Repeat Data Sets

Repeat imaging data sets performed on patients with cancer are becoming publicly available. The potential utility of these data sets for addressing important questions in imaging biomarker development is vast. In particular, these data sets may be useful to help characterize the variability of quantitative parameters derived from imaging. This article reviews statistical analysis that may be performed to use results of repeat imaging to 1) calculate the level of change in parameter value that may be seen in individual patients to confidently characterize that patient as showing true parameter change, 2) calculate the level of change in parameters value that may be seen in individual patients to confidently categorize that patient as showing true lack of parameter change, 3) determine if different imaging devices are interchangeable from the standpoint of repeatability, and 4) estimate the numbers of patients needed to precisely calculate repeatability. In addition, we recommend a set of statistical parameters that should be reported when the repeatability of continuous parameters is studied.     

Biosorption with Algae: A Statistical Review

ABSTRACT

The state of the art in the field of biosorption using algae as biomass is reviewed. The available data of maximum sorption uptake (q_max) and biomass-metal affinity (b) for Cd^{2 +}, Cu^{2 +}, Ni^{2 +}, Pb^{2 +} and Zn^{2 +} were statistically analyzed using 37 different algae (20 brown algae, 9 red algae and 8 green algae). Metal biosorption research with algae has used mainly brown algae in pursuit of treatments, which improve its sorption uptake. The information available in connection with multimetallic systems is very poor. Values of q_max were close to 1 mmol/g for copper and lead and smaller for the other metals. Metal recovery performance was worse for nickel and zinc, but the number of samples for zinc was very small. All the metals except lead present a similar affinity for brown algae. The difference in the behavior of lead may be due to a different uptake mechanism. Brown algae stand out as very good biosorbents of heavy metals. The best performer for metal biosorption is lead.     

Epidermolysis Bullosa: A Review of the Tissue-Engineered Skin Substitutes Used to Treat Wounds

Molecular Diagnosis & Therapy - Skin wound healing is a crucial process for regenerating healthy skin and avoiding the undesired consequences associated with open skin wounds. For epidermolysis...     

Statistical Mechanics and the Evolution of Polygenic Quantitative Traits

The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ > 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection.     

A Review of Size at Maturity in Male Tanner (Chionoecetes bairdi) and King (Paralithodes camtschaticus) Crabs and the Methods Used to Determine Maturity

This paper reviews existing studies on the size of sexual maturityfor male Tanner or snow crab (Chionoecetes bairdi), a brachyuran,and the anomuran red king crab (Paralithodes camtschaticus).In this report the term sexual maturity is denned as the abilityto reproduce. A variety of indirect and direct methods thathave been used to determine maturity are reviewed. Examiningthe vas deferens for the presence of spermatophores was usefulin determining the size at which males first become mature.Breeding experiments in the laboratory demonstrated that mostmales, from both species, that produced spermatophores couldbreed with soft-shelled mates. Males of both species can breedat smaller sizes than do females. Morphometric techniques basedon reproductive tract weights and chela morphometry overestimatedthe sizes at which males mature in both species. Previous experimentsfor Tanner crab, which have internal fertilization, suggestsmall mature males can fertilize two to five females. Breedingexperiments showed recently matured red king crab do not appearto be able to fertilize more than one female per breeding season,while males nearing harvestable size can fertilize more thanone female. Breeding experiments and in situ observations of grasping pairsappear to be the most feasible methods for identifying malesize at maturity for these species. The value of morphometricestimations for determining when males mature is questionable.     

Statistical Inference Methods for Two Crossing Survival Curves: A Comparison of Methods

A common problem that is encountered in medical applications is the overall homogeneity of survival distributions when two survival curves cross each other. A survey demonstrated that under this condition, which was an obvious violation of the assumption of proportional hazard rates, the log-rank test was still used in 70% of studies. Several statistical methods have been proposed to solve this problem. However, in many applications, it is difficult to specify the types of survival differences and choose an appropriate method prior to analysis. Thus, we conducted an extensive series of Monte Carlo simulations to investigate the power and type I error rate of these procedures under various patterns of crossing survival curves with different censoring rates and distribution parameters. Our objective was to evaluate the strengths and weaknesses of tests in different situations and for various censoring rates and to recommend an appropriate test that will not fail for a wide range of applications. Simulation studies demonstrated that adaptive Neyman’s smooth tests and the two-stage procedure offer higher power and greater stability than other methods when the survival distributions cross at early, middle or late times. Even for proportional hazards, both methods maintain acceptable power compared with the log-rank test. In terms of the type I error rate, Renyi and Cramér—von Mises tests are relatively conservative, whereas the statistics of the Lin-Xu test exhibit apparent inflation as the censoring rate increases. Other tests produce results close to the nominal 0.05 level. In conclusion, adaptive Neyman’s smooth tests and the two-stage procedure are found to be the most stable and feasible approaches for a variety of situations and censoring rates. Therefore, they are applicable to a wider spectrum of alternatives compared with other tests.     

Methods Used to Monitor the Microbial Load of Returned Lunar Material

Methods employed to prepare lunar soil samples and procedures used to detect viable microorganisms are described.