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Use of prior information to stabilize a population data analysis.

When modeling new data with a complex population pharmacokinetic/pharmacodynamic model, there may not be sufficient information to obtain estimates of all parameters. In this case information from previous studies can also be used to help stabilize estimation. Using simulated data, we explored three different ways to do this. (i) Some parameter values were fixed to estimates obtained from earlier data. (ii) The earlier data were combined with the current data. (iii) The objective function based on the current data was augmented by a penalty function expressing summary information obtained from the earlier data. This last method is similar to the use of a Bayesian prior. It may be particularly useful when either the combined data set of method (ii) is very large and leads to large computation times or when the early data are not readily available. With this method, two different types of penalty functions were used. With our examples, the three methods all resulted in stabilized estimation. Methods (ii) and (iii) gave similar results for parameter and standard error estimation, especially with respect to fixed effects parameters. For hypothesis testing, results obtained with method (i) are very problematic. There are also problems with the results obtained with method (iii), but they are much less severe, and when the design for the earlier data is known, they can be corrected by using a computer-intensive simulation test procedure.

Algorithms↗

[Genetic diversity of carrion and jungle crows from RAPD-PCR analysis data].

RAPD-PCR analysis of the genetic diversity of the carrion crow (Corvus corone) and jungle crow (C. macrorhynchos) living in the continental parts of their species ranges and on some Russian and Japanese Far Eastern islands has been performed. Taxon-specific molecular markers have been found for each species. The genetic diversity of the carrion crow is considerably less than that of the jungle crow at the same genetic distance (P95 = 68.2%, DN = 0.27 and P95 = 88.4%, DN = 0.24, respectively). In both species, the genetic polymorphism of island samples is almost two times greater than that of continental samples (62 and 31.8%, respectively, for C. corone and 81.5 and 47.2%, respectively, for C. macrorhynchos). In addition, differences in genetic diversity between males and females (P95 = 55.1 and P95 = 72.1, respectively) has been found in the carrion crow but not in the jungle crow. The gene diversity of C. macrorhynchos is greater than that of C. corone: the mean numbers of alleles per locus are 2 and 1.81, effective numbers of alleles are 1.62 and 1.43, and the mean expected heterozygosities are 0.39 and 0.30, respectively. The phenograms and phylograms significantly segregate the clusters of the carrion and jungle crows. The clustering patterns of carrion crows corresponds to the intraspecies taxonomic and geographic differentiation: subspecies C. c. corone and C.c. orientalis living in the western and eastern parts of the species range, respectively, form different subclusters. The cluster of the jungle crow does not exhibit differentiation into subspecies C. m. mandshuricus and C. m. japonensis; molecular genetic differences between them are small.

Animals↗

Urine profiling using capillary electrophoresis-mass spectrometry and multivariate data analysis.

This work presents the development of a general and fast method for metabolic profiling of urine, using capillary electrophoresis-electrospray ionisation mass spectrometry (CE-ESIMS) and multivariate data analysis (DA). Human urine samples collected before and after ingestion of paracetamol were analysed at acidic and basic CE conditions, using both positive and negative ESI-MS detection. Analysis of the entire resulting data set, with no prior knowledge of the target compounds, using pair-wise 'fuzzy' correlation and eigenvalue analysis enabled the samples to be discriminated between on the basis of blank urine and urine collected after drug intake. By generating two-dimensional loadings plots, it was also possible to identify the m/z values of the substances responsible for the differentiation between control and dosed samples.

Acetaminophen↗

A procedure for data analysis of the rodent micronucleus test involving a historical control.

No standard procedure of data analysis for rodent micronucleus tests involving historical controls has been established. In the present paper, under the presumption that the distribution of the historical control is stable and reliable, a procedure with three statistical steps is proposed to analyze the frequency of micronucleated polychromatic erythrocytes (MNPCEs). In the first step, the frequencies of MNPCEs in negative and positive control groups of a current experiment of the micronucleus test are compared with the distribution of historical negative and positive controls to examine the technical validity of the current experiment. In the second step, the frequency of MNPCEs in each treatment group is compared with the distribution of the historical negative control. In the third step, the dose-response relation is tested with the Cochran-Armitage trend test. A Monte Carlo stimulation study shows that the power of this procedure is acceptable and also this procedure is robust. An application of this procedure on real data reveals that it is effective in detecting clastogenic chemicals when the probability of a type I error is nearly .01.

Animals↗

Exploratory data analysis of evoked response single trials based on minimal spanning tree.

OBJECTIVE: An exploratory data analysis framework, based on minimal spanning tree, is proposed as a means to support the analysis of single trial (ST) electrophysiological signals. The core of this framework is the compact description of the input ST sample in a form of content-dependent ordered lists. Based on the established hierarchies, efficient ways to increase the SNR, extract prototypical responses, visualize possible self-organization trends in the sample and track the course of evoked response along the trial-to-trial dimension, are proposed. METHOD: Magnetoencephalographic auditory evoked responses were used for demonstrating and validating the introduced framework. RESULTS AND CONCLUSION: The results demonstrate the benefits, from this intelligent manipulation of STs, in understanding and enhancing the actual evoked signal. Specifically we find support for stimulus-induced phase-resetting hypothesis in the 3-20 Hz band, the existence of trials void of the prototypical evoked response, and an order across the single trial set hinting at an underlying process with long time scale.

Adult↗

Zherlock: an open source data analysis software.

Zherlock is an open source software that provides state-of-the-art data analysis tools to the user in an intuitive and flexible way. It is a front-end to different numerical "engines" to produce a seamless integration of algorithms written in different computer languages. Of particular interest is creating an interface to high-level scientific languages such as Octave (a Matlab clone) and R (an S-PLUS clone) to enable efficient porting of new data analytical methods. Zherlock uses advanced scientific visualization tools in 2-D and 3-D and has been extended to work on virtual reality (VR) systems. Central to Zherlock is a visual programming environment (VPE) which enables diagram based programming. These diagrams consist of nodes and connection lines where each node is an operator or a method and lines describe the flow of data between nodes. A VPE is chosen for Zherlock because it forms an effective way to control the processing pipeline in complex data analyses. The VPE is similar in functionality to other programs such as IRIS Explorer, AVS or LabVIEW.

Algorithms↗

Secondary data analysis: research method for the clinical nurse specialist.

This article presents a description of secondary data analysis and suggests that this type of research methodology may be helpful in facilitating research by the clinical nurse specialist (CNS). The article discusses the advantages and disadvantages of the use of this method specifically in relation to the CNS and offers suggestions for sources of data.

Data Collection↗

Fundamentals of cDNA microarray data analysis.

Microarray technology is a powerful approach for genomics research. The multi-step, data-intensive nature of this technology has created an unprecedented informatics and analytical challenge. It is important to understand the crucial steps that can affect the outcome of the analysis. In this review, we provide an overview of the contemporary trend on various main analysis steps in the microarray data analysis process, which includes experimental design, data standardization, image acquisition and analysis, normalization, statistical significance inference, exploratory data analysis, class prediction and pathway analysis, as well as various considerations relevant to their implementation.

Animals↗

Extreme value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression.

One important issue commonly encountered in the analysis of microarray data is to decide which and how many genes should be selected for further studies. For discriminant microarray data analyses based on statistical models, such as the logistic regression models, gene selection can be accomplished by a comparison of the maximum likelihood of the model given the real data, L(D|M), and the expected maximum likelihood of the model given an ensemble of surrogate data with randomly permuted label, L(D(0)|M). Typically, the computational burden for obtaining L(D(0)M) is immense, often exceeding the limits of available computing resources by orders of magnitude. Here, we propose an approach that circumvents such heavy computations by mapping the simulation problem to an extreme-value problem. We present the derivation of an asymptotic distribution of the extreme-value as well as its mean, median, and variance. Using this distribution, we propose two gene selection criteria, and we apply them to two microarray datasets and three classification tasks for illustration.

Chromosome Mapping↗

Techniques to identify clinical contexts during automated data analysis.

The interpretation of automatically collected data to produce intelligent alarms and identify particular conditions is nearly impossible without identifying the specific context in which the data are obtained. Shifts in clinical context occur because of changes in the patient's physiologic state, or due to the passage of time, or due to changes imposed by therapeutic intervention such as surgery. Techniques to identify such changes in clinical context are discussed with particular attention to the application of cluster analysis, discriminant analysis, and statistical predictors. An example of these analyses applied to EEG data is presented, showing an unexpected hysteresis of EEG behavior in response to an hypoxic challenge.

Cluster Analysis↗

Software for temporal gait data analysis.

This study presents a computer program, developed to support a low-cost, portable telemetry system that has been designed to assess footfall timing. This software frees the user from data processing and allows concentration on data analysis. The new technique has been applied with accuracy and reliability to the analysis of the gait of orthopedic patients, athletes, mountaineers, etc. The subroutines developed for data acquisition, storage and analysis are explained in detail, and an example is presented.

Data Interpretation, Statistical↗

Multivariate exploratory tools for microarray data analysis.

The ultimate success of microarray technology in basic and applied biological sciences depends critically on the development of statistical methods for gene expression data analysis. The most widely used tests for differential expression of genes are essentially univariate. Such tests disregard the multidimensional structure of microarray data. Multivariate methods are needed to utilize the information hidden in gene interactions and hence to provide more powerful and biologically meaningful methods for finding subsets of differentially expressed genes. The objective of this paper is to develop methods of multidimensional search for biologically significant genes, considering expression signals as mutually dependent random variables. To attain these ends, we consider the utility of a pertinent distance between random vectors and its empirical counterpart constructed from gene expression data. The distance furnishes exploratory procedures aimed at finding a target subset of differentially expressed genes. To determine the size of the target subset, we resort to successive elimination of smaller subsets resulting from each step of a random search algorithm based on maximization of the proposed distance. Different stopping rules associated with this procedure are evaluated. The usefulness of the proposed approach is illustrated with an application to the analysis of two sets of gene expression data.

Algorithms↗

Comparison of Ehrlich ascites tumour and mouse liver cells by analytical subcellular fractionation combined with a sensitive computational method for data analysis.

A simple method of analytical subcellular fractionation, combined with a sensitive computational method for data analysis and presentation, has been used to reinvestigate the distribution and relative amounts of several enzymes in the cytoplasmic and plasma membranes of two different cell types: one is a neoplastic, transformed cell type (Ehrlich ascites tumour cells), the other an untransformed, highly differentiated cell type (liver hepatocytes plus Kupffer and endothelial cells). In general the distribution of the enzymes in particular membranes is similar in the two cell types, however the relative amounts differ. Ehrlich ascites tumour cells have a higher specific activity of galactosyltransferase and ouabain-sensitive (Na,K)ATPase, while liver cells have higher glucose-6-phosphatase, 5'-nucleotidase and succinate dehydrogenase activity. These differences appear to be correlated with morphological and, in some cases, functional differences between the two cell types.

5'-Nucleotidase↗

Seeing the forest despite the trees. The benefit of exploratory data analysis to program evaluation research.

In the present article, it is argued that there is a benefit to applying techniques of exploratory data analysis (EDA) to program evaluation. To exemplify this, an evaluation of a rehabilitation program for people with rheumatoid arthritis is presented. The perceived health status of patients receiving intensive rehabilitation services from a major rehabilitation institute was compared with that of patients receiving customary office-based care over an 18-month period. The data were analyzed in a conventional way (analysis of variance) and then by way of EDA techniques (graphic display of medians and boxplots). The conventional analysis suggested that all patients improved over time and that intensive rehabilitation services provided no particular benefit or harm. The exploratory analysis showed that the distribution of the outcome variable was patently nonnormal, thus casting doubt on the validity of the conventional analysis. The EDA further showed that the rehabilitation group lagged behind the comparison group for a year, with a precipitious improvement at the 18-month period. This suggests that a selection factor was operating (i.e., those in the rehabilitation group could have been sicker) or that the patients in the rehabilitation group were made more aware of their condition by the intensive health services they received. The EDA provided an important insight.

Analysis of Variance↗

A simplified method of echocardiographic data analysis.

Rapid accurate analysis of echocardiographic data is accomplished using a sonic digitizer and programmable calculator. This method allows the echocardiographer to select technically optimal areas of the recording for analysis. The resolution of the measuring device is 0.1 mm. A hardcopy printout of both measurement and calculation is provided. Instead of expensive on-line computer, an inexpensive programmable calculator is used.

Computers↗

A consultation system constructor for medical data analysis.

MAD is a system that helps an expert data analyst in a specific application domain (like epidemiology or image analysis) to build reasoning models aimed at fulfilling specific tasks. These models may be subsequently used to guide doctors in the analysis of a set of data referring to a specific ground domain. Expert knowledge is represented at various levels: a general description of an application domain and various models that formalize the reasoning followed to perform specific tasks within a defined application domain. Reasoning models are represented as rules of propositional calculus, and a meta-knowledge permits to support knowledge acquisition. During the consultation, different external programs may be run when needed, without the doctor having to learn how to use them. MAD is written in Golden Common LISP and may be linked to any external software for data analysis, provided it runs under MS-DOS and does not require more than 192 Kb. Examples of application of the system to epidemiology and image analysis are given.

Computer Simulation↗

Benign brain tumours and psychiatric morbidity: a 5-years retrospective data analysis.

OBJECTIVE: To examine the psychiatric comorbidity in benign brain tumours. METHOD: A retrospective (5 years) data analysis at our 500 bed teaching hospital. The diagnoses of benign brain tumours were based on the record of final diagnoses in the case records confirmed by either CT or MRI scans. Case records of patients with clearly documented history of psychiatric symptoms of several weeks to several months duration were identified only if such symptoms had antedated a diagnosis of the brain tumour. Using a specially designed proforma, two psychiatrists rated the symptoms together. We also collected data on age, gender and CT/MRI findings. Consensus was reached on all cases in regard to the psychiatric phenomenology. The symptoms were divided according to their presentation into purely neurological or psychiatric symptoms. RESULTS: A total of 79 patients were identified as having a primary diagnosis of benign brain tumour. There were 56 female patients and 23 male patients. Seventy-two of these had meningiomas. Fifteen (21%) of 72 meningioma cases, eight men and seven women, presented with psychiatric symptoms in the absence of neurological symptoms. Affective disorders were a common presentation. There was no correlation between brain laterality and the psychiatric comorbidity. CONCLUSIONS: Psychiatric symptoms may be the only initial manifestations of meningiomas of the brain in a significant number of cases occurring in the fifth decade of life. Such patients must be investigated by brain imaging studies even if there are no neurological signs or symptoms.

Adult↗

A pooled data analysis on the use of intermittent cyclical etidronate therapy for the prevention and treatment of corticosteroid induced bone loss.

OBJECTIVE: To conduct a pooled data analysis in a group of patients defined by sex, menopausal status, and underlying disease in order to examine the effect of intermittent cyclical etidronate in the prevention and treatment of corticosteroid induced osteoporosis. METHODS: We selected 5 randomized, placebo controlled studies that examined the efficacy of intermittent cyclical etidronate therapy in which the raw data were available for analysis. Three were prevention studies and 2 treatment studies. The primary outcome was the difference between treatment groups in the percentage change from baseline in lumbar spine bone density. Secondary outcomes included the difference between treatment groups in the percentage change from baseline in femoral neck and trochanter bone density, and vertebral fracture rates. RESULTS: Results are separately pooled for the prevention and treatment studies. The prevention studies had significant mean differences (95% CI) between groups in mean percentage change from baseline in lumbar spine, femoral neck, and trochanter bone density of 3.7 (2.6 to 4.7), 1.7 (0.4 to 2.9), and 2.8% (1.3 to 4.2) after one year of treatment, in favor of the etidronate group. The treatment studies displayed a mean difference between groups in mean percentage change from baseline in lumbar spine bone density of 4.8 (2.7 to 6.9) and 5.4% (2.5 to 8.4) after one and 2 years of therapy. In the prevention studies, a reduced fracture incidence was observed in the etidronate group compared with the placebo group (relative risk 0.50; CI 0.21 to 1.19). CONCLUSION: Etidronate therapy was effective in preventing bone loss in the prevention studies and in preventing or slightly increasing bone mass in the treatment studies. A fracture benefit was observed in postmenopausal women treated with etidronate in the prevention studies.

Adult↗