Goodness-of-Fit Testing for the Logistic Regression Model when the Estimated Probabilities are Small

The distribution of the Hosmer-Lemeshow chi-square type goodness-of-fit tests (?_g, ?_g) for the logistic regression model are examined via simulations designed to examine their behavior when most of the estimated probabilities are small or are expected to fall in a few deciles. The results of the simulations show statistic ?_g should be used when the two outcome groups (y = 0, 1) are not well separated, Δ≤2, where Δ² is the Mahalanobis distance. Statistic ?_g should be used when Δ ≥ 8. Either statistic may be used when 2 ≦ Δ ≦ 8. All tests should be used with caution when the proportion in the sample with y = 1 is less than 0.1.     

A Primer to Molecular Phylogenetic Analysis in Plants

Reconstructing a tree of life by inferring evolutionary history is an important focus of evolutionary biology. Phylogenetic reconstructions also provide useful information for a range of scientific disciplines such as botany, zoology, phylogeography, archaeology and biological anthropology. Until the development of protein and DNA sequencing techniques in the 1960s and 1970s, phylogenetic reconstructions were based on fossil records and comparative morphological/physiological analyses. Since then, progress in molecular phylogenetics has compensated for some of the shortcomings of phenotype-based comparisons. Comparisons at the molecular level increase the accuracy of phylogenetic inference because there is no environmental influence on DNA/peptide sequences and evaluation of sequence similarity is not subjective. While the number of morphological/physiological characters that are sufficiently conserved for phylogenetic inference is limited, molecular data provide a large number of datapoints and enable comparisons from diverse taxa. Over the last 20 years, developments in molecular phylogenetics have greatly contributed to our understanding of plant evolutionary relationships. Regions in the plant nuclear and organellar genomes that are optimal for phylogenetic inference have been determined and recent advances in DNA sequencing techniques have enabled comparisons at the whole genome level. Sequences from the nuclear and organellar genomes of thousands of plant species are readily available in public databases, enabling researchers without access to molecular biology tools to investigate phylogenetic relationships by sequence comparisons using the appropriate nucleotide substitution models and tree building algorithms. In the present review, the statistical models and algorithms used to reconstruct phylogenetic trees are introduced and advances in the exploration and utilization of plant genomes for molecular phylogenetic analyses are discussed.     

喷气燃料中污染微生物检测方法概况

微生物污染不仅降解喷气燃料,还严重威胁储存和飞行安全.喷气燃料中污染微生物的检测是有效治理微生物污染的前提.基于此,本文将喷气燃料中污染微生物检测方法分为传统法、分析生物学法以及分子生物学方法,并对三种方法优缺点进行了详细介绍.最后对喷气燃料中污染微生物检测方法进行了展望.     

测定糖尿病患者血清LDL-C水平的方法学比较

目的：比较不同方法检测糖尿病患者血清LDL-C水平,为临床诊疗提供准确可行的检验方法。方法：采用沉淀法、匀相法、电泳法及超速离心法对233例糖尿病患者和102例健康人群的血清LDL-C水平进行测定,比较各方法之间的相关性,同时分析导致结果差异的因素。结果：四种方法检测健康人群LDL-C水平,结果间无统计学差异（P〉0.05）;糖尿病组,当TG≤2.26mmol/L时,四种方法检测LDL-C结果间相关性良好。高胆红素、血红蛋白、高TG及乳糜等干扰因素存在时,与其他方法相比,电泳法和超速离心法检测血清LDL-C结果受影响较小（P〉0.05）。结论：超速离心法虽耗时、价格贵,但仍为检测LDL-C的经典方法,电泳法受高胆红素、血红蛋白、高三酰甘油等干扰因素的影响相对较小,适用于糖尿病合并高血脂患者血清LDL-C水平检测。     

测定糖尿病患者血清LDL-C 水平的方法学比较

目的:比较不同方法检测糖尿病患者血清LDL-C水平,为临床诊疗提供准确可行的检验方法。方法:采用沉淀法、匀相法、电泳法及超速离心法对233例糖尿病患者和102例健康人群的血清LDL-C水平进行测定,比较各方法之间的相关性,同时分析导致结果差异的因素。结果:四种方法检测健康人群LDL-C水平,结果间无统计学差异(P>0.05);糖尿病组,当TG≤2.26mmol/L时,四种方法检测LDL-C结果间相关性良好。高胆红素、血红蛋白、高TG及乳糜等干扰因素存在时,与其他方法相比,电泳法和超速离心法检测血清LDL-C结果受影响较小(P>0.05)。结论:超速离心法虽耗时、价格贵,但仍为检测LDL-C的经典方法,电泳法受高胆红素、血红蛋白、高三酰甘油等干扰因素的影响相对较小,适用于糖尿病合并高血脂患者血清LDL-C水平检测。     

Microbial Biomass Estimation

ABSTRACT

The development of a fully automated on-line monitoring and control system is very important in bioprocesses. One of the most important parameters in these processes is biomass. This review discusses different methods for biomass quantification. A general definition of biomass and biovolume are presented. Interesting concepts about active but not culturable cells considerations are included as well as concepts that must be taken into account when selecting biomass quantification technology. Chemical methods have had few applications in biomass measurement to date; however, bioluminescence can selectively enumerate viable cells. Photometric methods including fluorescence and scattered light measurements are presented. Reference methods including dry and wet weight, viable counts and direct counts are discussed, as well as the physical methods of flow cytometry, impedancimetric and dielectric techniques.     

PCR detection of pirimicarb resistance in Australian field isolates of Aphis gossypii Glover (Aphididae: Hemiptera)

Aphis gossypii Glover (cotton aphid) is a major secondary pest of Australian cotton that readily develops resistance to the carbamate insecticide pirimicarb (Pirimor®) and to organophosphates generally. To test the pirimicarb resistance status of Australian strains of A . gossypii , a polymerase chain reaction (PCR) assay followed by restriction enzyme assay (REA) was designed to identify the Ace I polymorphism S431F known to be responsible for resistance. The method was tested against reference and 33 field strains collected over two consecutive seasons. Both methods confirmed pirimicarb resistance in two field strains, one from each cotton season, giving credence to the molecular technique described. The PCR assay proved specific for the Ace I gene. This PCR REA assay has the potential to replace bioassay for the routine pirimicarb resistance monitoring in A . gossypii. With the molecular assay providing results in 48 h, compared with 4–8 weeks for bioassay, such an assay could be used before insecticide control.     

A window on cyclitols: Characterization and analytics of inositols

Cyclitols are cycloalkanes with one hydroxyl group on each of three or more ring atoms, also called cycloalkane polyols or sugar alcohol which attract attention since they have numerous pharmaceutical properties and are widespread in the plants. Inositols are important cyclitols, which constitute a group of naturally occurring polyhydric alcohols and some isomers of this group can be commonly found in most plants, provided adequate methods of detection are employed. This review presents plant containing cyclitols, with emphasis put on their pharmaceutical properties. The text focuses on sample preparation, extraction and purification and on analysis of cyclitols in plants. In addition, it addresses the application of different methodologies utilized in the analysis of cyclitol compounds in plant.     

基于β-微管蛋白基因部分序列探讨灵芝属菌株的亲缘关系

PCR分别扩增了38个灵芝属菌株的β-微管蛋白基因片段,并对PCR产物进行序列测定,得到419bp的一段核苷酸系列.根据MEGA 2.1软件中的neighbour-joining methods对上述序列进行聚类分析,结果所有供试菌株被分成9个聚类组.中国栽培灵芝菌株分布于6个聚类组,其中树舌亚属、紫芝组的菌株各自聚成一组,灵芝组的菌株分成四组,但大部分灵芝组菌株均聚于同一组, 这表明树舌亚属、紫芝组和灵芝组间的遗传差异较大,灵芝组内虽然存在着一定的遗传差异,但总体上亲缘关系比较近,遗传多样性并不丰富.同时,序列分析的结果显示,β-tubulin基因序列在第三位密码子和内含子部位有高的碱基替换率,这些变异提供了丰富的系统发育信息,提示β-tubulin基因适合于灵芝属菌株的亲缘关系研究.     

Rapidly converging numerical algorithms for models of population dynamics

We propose algorithms for the approximation of the age distributions of populations modeled by the McKendrick-von Foerster and the Gurtin-MacCamy systems both in one- and two-sex versions. For the one-sex model methods of second and fourth order are proposed. For the two-sex model a second order method is described. In each case the convergence is demonstrated. Several numerical examples are given.     

Physicochemical characterization of deflazacort: thermal analysis, crystallographic and spectroscopic study

The solid state properties of deflazacort (1-(1beta,16alpha)-21-(acetyloxy)-11-hydroxy-2'-methyl-5'H-pregna-1,4-dieno[17,16-d]oxazole-3,20-dione, 1) were investigated using differential scanning calorimetry (DSC), thermogravimetry (TG), single-crystal X-ray diffraction, solid and liquid nuclear magnetic resonance spectroscopy ((13)C NMR), Fourier transform infrared and Raman spectroscopy (FTIR and FT Raman). From the trends observed in the crystal structure and spectral data some conclusions can be made about hydrogen bonding, molecular conformation and crystal packing. Compound 1 crystallizes in an orthorhombic cell, space group P2(1)2(1)2(1) and the following lattice parameters: a=11.2300(5), b=12.8161(8), c=16.171(1)A, V: 2327.4(2)A(3), D(c): 1.260g/cm(3), R1=0.0479, wR2=0.1012. The crystal structure is stabilized by intra and intermolecular interactions, which provides for a very closely packed form. The NMR data indicated that 1 shows a similar conformation in solid and liquid state; while, thermal data revealed that 1 follows a monophasic pattern with a DSC melting peak at 258.4 degrees C (DeltaH 99.7Jg(-1), n=3), indicating that 1 is thermally stable as solid; but, as liquid is unstable to undergo a thermal decomposition reaction. The reactivity of 1 toward light and moisture was examined via DSC and TLC. The data indicated that 1 do not interact with water to give hydrated forms or decomposition products; however, light degrades 1.     

Spatial autocorrelation invalidates the Dow-Cheverud test

Dow and Cheverud (Am. J. Phys. Anthropol. 68:367–373, 1985) have published a statistical test for comparing any three similarity matrices. Using both simulations and analytical arguments, I establish that the presence of spatial autocorrelation, a common feature of geographically based anthropological and biological data, causes this test to reject too often. Increasing the spatial autocorrelation increases the spurious rejection rate. About 20% of the papers that reference Dow and Cheverud's paper have used their test with spatially autocorrelated data. Mantel's (Cancer Res. 27:209–220, 1967) method, when used as a test of spatial autocorrelation, is unaffected by these considerations, since its null hypothesis is that the data are uncorrelated. © 1992 Wiley-Liss, Inc.     

幽门螺杆菌诊断的最新进展

幽门螺杆菌(Helicobacter pylori,H.pylori)是一种常见的引起多种胃肠道疾病的病原体。临床中通常利用具有不同灵敏度和特异性的侵入性或非侵入性诊断方法来检测H.pylori的感染。目前,诊断H.pylori的方法包括尿素呼气试验、粪便抗原试验、血清学、内镜检查、胃活检组织学、快速尿素酶试验、培养、分子生物学方法等。在实际临床实践中,考虑不同的医疗条件、医生的专业水平、检测成本、敏感性和特异性等多方面因素,如何合理地选择一种或多种方法来诊断H.pylori感染进而指导临床预防和治疗,是一项重要的临床研究课题。本文将对H.pylori感染诊断方法的最新进展、不同方法的优缺点以及其在临床实践中的应用作一综述。     

Multimodal Observation Method of Digital Accessibility for Elderly People

This article presents a new methodological framework for multimodal observation of digital technologies. It is based on the use of mixed methods developed in the interdisciplinary MAN project founded by CNRS. It focuses on the digital accessibility of older people. The originality of the method lies in the implementation of a method combining qualitative and quantitative measurement to determine relevant indicators. These indicators characterize the person's behavior when using a technology and its usability. We show how these indicators are built, based on the cross-referencing of data. We present the different tools (questionnaire, interviews and technological data recording tools) used in the MAN method in a living laboratory environment controlled with four volunteers. Two use scenarios are proposed to illustrate the method in assessing the accessibility of a tactile application for older people without a digital divide and without disabilities. We present the recorded qualitative and quantitative data and illustrate by an example the unrelatedness of these data through a specific annotation tool.     

Review of established and innovative detection methods for carbapenemase‐producing Gram‐negative bacteria

The minimal antibiotic options for carbapenemase‐producing Gram‐negative bacteria necessitate their rapid detection. A literature review of a variety of phenotypic and genotypic methods is presented. Advances in culture methods and screening media are still subject to long incubation hours. Biochemical methods have shorter turnaround times and higher sensitivities and specificities, but cannot differentiate between various types and variants. Spectrophotometric methods are cheap and efficient, but are uncommon in many clinical settings, while the MALDI‐TOF MS is promising for species identification, typing and resistance gene determination. Although next generation sequencing (NGS) technologies provide a better platform to detect, type and characterize carbapenem‐resistant bacteria, the different NGS platforms, the large computer memories and space needed to process and store genomic data and the nonuniformity in data analysis platforms are still a challenge. The sensitivities, specificities and turnaround times recorded in the various studies reviewed favours the use of the biochemical tests (Carba NP or Rapid Carb screen tests) for the detection of putative carbapenemase‐producing isolates. MALDI‐TOF MS and/or molecular methods like microarray, loop‐mediated isothermal amplification and real‐time multiplex PCR assays could be used for further characterization in a reference laboratory. NGS may be used for advanced epidemiological and molecular studies.     

协同系统发生的研究方法

协同系统发生研究生态上相关群体的系统发生间的关系,其研究方法主要分为两类：基于事件法和整体拟合法.基于事件法包括布鲁克斯简约分析、组分分析、协调树分析等,此类方法考虑进化情境,逻辑性强,但分析结果过多,较难选择;整体拟合法考虑了系统发生的误差,提供较好的关系一致性,但缺乏联系进化情境.本文详细比较了两类方法下各种分析软件的优劣,提出了整合两类方法的可能性,以便更好地理解协同系统发生.     

陆地生态系统碳平衡主要研究方法评述

陆地生态系统碳平衡是全球变化科学中的核心问题之一,目前也是生态科学中的前沿与热点问题,而陆地生态系统的复杂性与不确定性决定了对陆地生态系统碳平衡估测的复杂性和不确定性。为研究这一复杂性问题,已发展了许多研究方法。可分为“自下而上”与“自上而下”两种,各种方法都有其自身的优势和劣势。相关方向也已经有了大量的研究报道,但是,不同的研究由于在方法、时间与空间尺度等存在的差异,使得许多研究结果和预测很难被有效的整合或适用于大范围甚至全球水平。综述了陆地碳平衡的主要研究方法,分析和比较了各方法的特点,指出在研究中对不同方法的结果进行分析和比较,以及采用综合方法的必要性。     

Optimizing Controlled Environment Assessment of Levels of Resistance to Yam Anthracnose Disease Using Tissue Culture-derived Whole Plants

Studies were conducted to determine the timing and frequency of disease assessment required to effectively identify levels of resistance to yam anthracnose using tissue culture‐derived whole plant inoculation assay. The effects of inoculation methods (paint brush and spray), and disease scoring methods [individual leaf area (ILA) and whole plant area (WPA)] were also assessed. Spray inoculation resulted in rapid infection and higher variations among yam genotypes, leading to earlier discrimination of genotypes than with the paintbrush method. Both the ILA and WPA scoring methods showed variation among yam genotypes, and association between the two methods gave a high positive correlation (r > 0.90). However, the WPA was faster and had the advantage of detecting differences in reactions of yam genotypes to less aggressive pathogen isolates to which the ILA method showed no variation. A single disease evaluation at 7 days after inoculation was as good as the area under the disease progress curve (AUDPC) and the disease progress rate (R_d) derived from multiple evaluations. However, a significant time–genotype interaction, suggests a need for more than a single assessment for effective comparison of genotypes. AUDPC derived from two assessments (5 and 7 DAI) was better than AUDPC from three assessments (5, 7 and 9 DAI) in separating genotypes reactions to a less aggressive pathogen isolate. This study showed that the use of spray inoculation method, the WPA scoring method, and AUDPC derived from two assessments (5 and 7 DAI) provided best conditions for evaluating yam genotypes for levels of anthracnose resistance with the tissue culture‐derived whole plant assay.     

Physicochemical mechanisms of histological silver staining and their utilization for rendering individual silver methods selective and reliable

Staining morphological or chemical constituents of biological tissues, cells and microorganisms with silver proceeds via different reaction routes. In this paper, I put their physicochemical mechanisms into a coherent system and discuss how these can be controlled and separated from each other, thereby permitting selective, sensitive and reliable demonstration of individual tissue constituents.