Statistical Software Application Research Articles

E0464 Clinical significance of the changes of serum TNF-α, IFN-γ, MMP-9

A variety of inflammatory factors in atherosclerosis (AS) plays a complex role, the combination of two or more of the inflammatory mediators can increase inflammatory mediators in coronary heart disease...

Validation of Putative Reference Genes for Normalization of Q-RT-PCR Data From Paraffin-embedded Lymphoid Tissue

Normalization of quantitative reverse transcription-PCR (Q-RT-PCR) data to appropriate tissue-specific reference genes is an essential part of interpreting the results. This study aimed to determine the most appropriate reference genes for normalizing gene expressions in lymphatic tissue, represented by non-neoplastic lymph nodes and diffuse large B-cell lymphomas, by using 2 statistical software applications, geNorm and NormFinder. In addition, we wanted to validate the usefulness of paraffin-embedded samples for Q-RT-PCR studies by investigating gene expressions of relevant target genes in paired frozen and paraffin-embedded samples. Moreover, we studied the impact of amplicon sizes on the efficiency of Q-RT-PCR in paraffin-embedded tissues. Six putative reference genes were tested for stability of expression in 21 pairs of snap-frozen and formalin-fixed, paraffin-embedded lymph nodes and lymphomas. The genes were ranked according to their suitability as reference genes. According to both statistical approaches, beta-glucoronidase was the single most appropriate reference gene in both snap-frozen and paraffin-embedded samples. TATA box-binding protein gene and Abelson murine leukemia viral oncogene homolog 1 gene were also highly ranked by both programs. In addition, we measured the relative expressions of 7 target genes by Q-RT-PCR, using PCR primer-probes with amplicon sizes up to 105 bases. The correlation coefficient for expression measured in matched frozen and paraffin-embedded samples was 0.93 (P<0.01) after normalization with the appropriate reference genes. Thus, we show that formalin-fixed, paraffin-embedded lymphoid samples are suitable for Q-RT-PCR when using thoroughly validated reference genes.

Three years of preanalytical errors: Quality specifications and improvement through implementation of statistical process control

Background: The objectives of this research were to show the most frequent preanalytical sample errors from two distinct patient populations and blood-drawing personnel, to calculate preanalytical quality specifications, and to demonstrate an improvement strategy for patients whose samples have been drawn in the primary health care center by means of a monthly preanalytical quality control report based on statistical process control (SPC). Material and methods: We collected preanalytical errors from the tests requested for hematology, coagulation, chemistry, and urine samples in both populations. To monitor an improvement strategy, we designed a set of indicators. The indicator results for 35 months were entered into the statistical software application, where they were statistically analyzed. The preanalytical quality specifications were calculated using the SPC control charts. The intervention consisted of the sending of a monthly preanalytical quality report to a pilot Decentralized Phlebotomy Center (DPC) and setting up a direct communication channel between the laboratory and the DPC. Results: Fewer errors were observed when the sample drawing was carried out by the laboratory personnel, showing distinct preanalytical quality specifications. Improvements were seen in the DPC after four months of the improvement strategy. Conclusions: We show a practical and effective methodology for the identification, monitoring, and reduction of preanalytical errors using the technology employed in daily total testing laboratory process.

Hawkes Learning Systems

Over the past some 20 years I have had the opportunity to informally review a number of statistical learning applications, most of which were associated with a particular software com pany. Some impressed me more than others, and a few were very well thought out systems aimed at instructing students in learning elementary statistical methods. The Hawkes Learning Systems application for statistics, however, is different from the learning systems that I have looked at in the past. It is one often learning packages developed by the company, and is not associ ated with any statistical software company or application.

Application of public-domain statistical analysis software for evaluation and comparison of comet assay data

A novel approach for statistical analysis of comet assay data (i.e.: tail moment) is proposed, employing public-domain statistical software, the R system. The analytical strategy takes into account that the distribution of comet assay data, like the tail moment, is usually skewed and do not follow a normal distribution. Probability distributions used to model comet assay data included: the Weibull, the exponential, the logistic, the normal, the log normal and log-logistic distribution. In this approach it was also considered that heterogeneity observed among experimental units is a random feature of the comet assay data. This statistical model can be characterized with a location parameter m ij , a scale parameter r and a between experimental units variability parameter θ. In the logarithmic scale, the parameter m ij depends additively on treatment and random effects, as follows: log ( m i j ) = a 0 + a 1 x i j + b i , where exp( a 0) represents approximately the mean value of the control group, exp( a 1) can be interpreted as the relative risk of damage with respect to the control group, x ij is an indicator of experimental group and exp( b i ) is the individual risk effects assume to follows a Gamma distribution with mean 1 and variance θ. Model selection is based on Akaike's information criteria (AIC). Real data coming from comet analysis of blood samples taken from the flounder Paralichtys orbignyanus (Teleostei: Paralichtyidae) and from samples of cells suspension obtained from the estuarine polychaeta Laeonereis acuta (Nereididae) were employed. This statistical approach showed that the comet assay data should be analyzed under a modeling framework that take into account the important features of these measurements. Model selection and heterogeneity between experimental units play central points in the analysis of these data.

Database production and maintenance.

The advent of computers and electronic databases have revolutionized the way that clinical research is done. If study inclusion criteria are saved in the database, creating a study population can be accomplished by constructing an electronic query. Prospectively-entered outcome data related to a particular patient population then can be accessed and exported to a statistical software application for analysis. The senior author has more than 2 decades of experience with computer-based clinical outcome databases. In the context of his personal experience, this review offers some insights related to database design and maintenance.

Statistical software packages for PCs — A market survey

The increase of statistical software applications for PCs is caused by decreasing hardware costs and dramatically enhanced PC performance. Whereas in the past the domain of statistical computing has been reserved to mainframe solutions, a great number of new software packages for PCs have come out in the last five years. Therefore, the producers of established mainframe software were also forced to offer PC-based solutions. By limiting a market analysis to products with a medium set of well known statistical methods, the immense number of available products is reduced to about fifty systems. We ordered an evaluation copy of these systems to test the numerical quality, the system speed, and the performance of several procedures. Seventeen packages were made available for an extensive examination. This paper will (1) discuss the problems and the solutions of obtaining a complete and correct datamatrix that describes the entire market and (2) present the results of a comparative market analysis.