A Graphical Approach for Quality Control of Oligonucleotide Array Data

Abstract

In studies of quality control of oligonucleotide array data, one objective is to screen out ineligible arrays. Incomparable arrays (one type of ineligible arrays) arise as the experimental factors are poorly controlled. Due to the high volume of data in gene arrays, examination of array comparability requires special treatments to reduce data dimension without distortion. This paper proposes a graphical approach to address these issues. The proposed approach uses percentile methods to group data, and applies the 2D image plot to display the grouped data. Moreover, an invariant band is employed to quantify degrees of array comparability. We use two publicly available oligonucleotide array datasets from Affymetrix GeneChip System for evaluation. The results demonstrate the utility of our approach to examine data quality and also as an exploratory tool to verify differentially expressed genes selected by vigorous statistical methods.     

规范化疼痛教育对创伤患者围手术期疼痛控制的影响探讨

目的研究创建疼痛护理小组对创伤患者进行规范化疼痛教育,取得患者主动配合疼痛控制治疗,有效控制围手术期疼痛,让患者更舒适地渡过围手术期.方法将2009年6月收治的患者112例,随机分为研究组65例和对照组47例,两组患者均给予常规镇痛治疗,研究组由疼痛护理小组进行规范化疼痛教育,对照组则由责任护士进行常规疼痛教育,比较两组患者的疼痛评分掌握率、疼痛控制配合度、疼痛控制效果及满意度.结果研究组疼痛评分掌握率及疼痛控制配合度均为100%,对照组分别为76%与86%.研究组疼痛控制效果及满意度明显优于对照组,差异有统计学意义（P〈0.01）.结论规范化疼痛教育能提高患者依从性,有效控制了围手术期疼痛,提高了患者满意度.     

Chromosomal integrity of human preimplantation embryos at different days post fertilization

Introduction

In order to investigate the dynamics of genomic alterations that occur at different developmental stages in vitro, we examined the chromosome content of human preimplantation embryos by molecular-cytogenetic techniques at the single-cell level, up to 13 days post fertilization.

Methods

The embryos were genetically analyzed several times during their development in culture; each embryo was first analyzed by FISH at ‘Day 3’ post fertilization, than during its growth in vitro and the third analysis was performed at development arrest, then the entire blastocyst was analyzed by comparative genomic hybridization (CGH/aCGH).

Results

We found that while on ‘Day 3’ only 31 % of the embryos were detected as normal, on ‘Day 5–6’, 44 % of the embryos were classified as normal and on ‘Day 7’, 57 % were normal. On ‘Days 8–13’, 52 % of the embryos were classified as chromosomally normal. One third of the embryos that were chromosomally abnormal on ‘Day 3’, were found to be normal at development arrest point.

Discussion

These dynamic changes that occur at early developmental stages suggest that testing a single blastomere at ‘Day 3’ post fertilization for PGD might inaccurately reflect the embryo ploidy and increase the risk of false aneuploidy diagnosis. Alternatively, blastocyst stage diagnosis may be more appropriate.     

Development of a multiple-run high-resolution melting assay for Salmonella spp. genotyping HRM application for Salmonella spp. subtyping

A quick and robust Salmonella spp. differentiation method based on high-resolution DNA melting (HRM) was developed. DNA samples from 134 Salmonella spp. strains and 20 serotypes were tested. Each serotype was represented by at least 2 strains. All raw data were derived on the Rotor-Gene 65H0-100 system using the designed 8 primer pairs. The reference samples for HRM error evaluation between runs were applied. Raw data error minimization and fluorescence normalization between runs were carried out by application of the proposed calculations. The data analysis showed that repetitive sequence targets are much more informative than the nonrepetitive ones. The method possesses a high potential and can be adopted for further subtyping analyses.     

推拿治疗腰椎间盘突出症手法规范化与疗效量化标准的研究

目的制定一套行之有效推拿治疗腰椎间盘突出症的规范化手法,同时为推拿手法治疗本病引入量化的疗效评价标准。方法应用回顾性研究方法对已有的五年文献进行整理,结合全国中医推拿重点专科的临床分析,制定腰椎间盘突出症的中医推拿手法方案。选取腰椎间盘突出症患者60例,按年龄分为二组,每组30例,应用该方案进行前瞻性研究,选用VAS评分、ODI评分作为观察指标对疗效进行量化评定。结果推拿治疗后二组患者VAS评分改善和ODI指数改善均有统计学意义,并且二者之间密切相关。二组治疗均有效,治愈率存在统计学差异(P0.05)。结论中医推拿治疗腰椎间盘突出症临床疗效显著。推拿治疗不同年龄段的腰椎间盘突出症患者临床疗效存在差异。可以量化评估推拿治疗腰椎间盘突出症临床疗效。     

对医药企业在营销活动中道德建设的探索

目的使企业的在医药市场中的行为由"被监管,被规范"向着"自律"的方向转变。方法从道德建设的角度出发,探索规范企业营销手段的新思路。结果与结论当前医药企业营销活动道德缺失现象非常严重,给医药市场造成十分不利的影响,必须规范。     

The use of total protein stains as loading controls: an alternative to high-abundance single-protein controls in semi-quantitative immunoblotting

Western blots are used to estimate the relative concentrations of proteins of interest based on staining by specific antibodies. Quantitative measurements are often subject to error due to overloading of the loading control and over-reliance on normalization. We have found that at the protein concentrations normally used to quantify most low-abundance proteins of interest, frequently used single-protein loading controls, such as glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin, do not accurately reflect differences in protein concentration. Two total protein stains, SYPRO Ruby and Amido Black, were compared and found to be acceptable alternatives to single-protein controls. Although we cannot prove that high-abundance loading controls are inaccurate under all possible conditions, we conclude that the burden of proof should lie with the researcher to demonstrate that their loading control is reflective of quantitative differences in protein concentration.     

豚鼠眼形觉剥夺后恢复期的生物学参数变化规律探讨

目的探讨豚鼠眼球形觉剥夺后恢复期的生物学参数变化规律。方法普通级2～3周龄豚鼠30只,随机分为两组:①实验组:20只,右眼采用半透明眼罩遮盖进行形觉剥夺4周,随后去遮盖3周,左眼作为自身对照;②正常对照组:10只,双眼不进行任何干预,开放饲养7周。形觉剥夺前、形觉剥夺4周后及去遮盖后第2、6、10、14和21天,测量豚鼠双眼生物学参数:睫状肌麻痹后行带状光检影测量屈光度;A超测量前房深度、晶体厚度和眼轴长度,计算出玻璃体腔长度。结果经过4周形觉剥夺,实验组豚鼠右眼向近视漂移,屈光度为(-2.88±2.30) D,诱导了(-5.50±1.9) D相对近视。去遮盖后,豚鼠右眼重新正视化,屈光度恢复的快速期发生在6 d内,14 d时双眼屈光度差值差异无显著性(t=-2.049,P=0.080),为(-0.18±0.26) D;右眼玻璃体腔长度缩短,14 d时双眼玻璃体腔长度差值差异无显著性(t=1.652,P=0.14),为(0.0234±0.0400) mm;右眼眼轴长度缩短,14 d时双眼眼轴长度差值差差异无显著性(t=1.443,P=0.192),为(0.0183±0.0359) mm。与正常对照组右眼相比,去遮盖6 d,屈光度差异为(-0.48±0.36) D,差异无显著性 (t=-1.325,P=0.206),而2 d时玻璃体腔和眼轴长度差异分别为(0.0961±0.0630) mm、(0.0621±0.0386) mm,差异无显著性(t=1.652,P=0.14;t=1.607,P=0.125)。结论2～3周龄豚鼠去除形觉剥夺后可以重新进行正视化,伴随玻璃体腔和眼轴长度缩短;去遮盖6 d内为眼生物学参数恢复的主要时期。     

On the use of continuous relative phase: Review of current approaches and outline for a new standard

Background

In this paper we review applications of continuous relative phase and commonly reported methods for calculating the phase angle. Signals with known properties as well as empirical data were used to compare methods for calculating the phase angle.

Findings

Our results suggest that the most valid, robust and intuitive results are obtained from the following steps: 1) centering the amplitude of the original signals around zero, 2) creating analytic signals from the original signals using the Hilbert transform, 3) calculating the phase angle using the analytic signal and 4) calculating the continuous relative phase.

Interpretations

The resulting continuous relative phase values are free of frequency artifacts, a problem associated with most normalization techniques, and the interpretation remains intuitive. We propose these methods for future research using continuous relative phase in studies and analyses of human movement coordination.     

Using documents to investigate links between implementation and sustainability in a complex community intervention: the PRISM study

The increasing imperative to find what works in health services has meant a rise in research trialing interventions deemed 'complex'. While the strength of these interventions comes from taking a 'whole of problem' approach using multiple and inter-linking strategies, ways of examining implementation are under-explored. Building sustainability is an important part of implementing complex intervention research, but this too has received little exploration in the implementation literature. This paper explores issues of implementation and sustainability by examining the case of PRISM (Program of Resources, Information and Support for Mothers), a community randomised trial in Victoria, Australia aimed at improving maternal health and wellbeing. It examines documents placed on the project website. Three groups of documents relating to implementation of the intervention were examined - implementation reports, media reports and community newsletters. Analysing these documents allowed a focus on the 'work' of the intervention - who does the work and what activities comprise the work - in order to examine implementation as it relates to sustainability. Document analysis provides a useful way of considering implementation and sustainability of complex intervention research. It can 'value add' to findings from process evaluation and extend our understanding of an intervention beyond outcome measures. Analysis of the documents in this case provides insights into why sustainability of an intervention may be difficult to achieve during implementation.