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At least 613 records · Page 34Linked to original sources
PubMed1981

EPA health and environmental effects data analysis system.

This paper discusses the development of a system to organize, store, retrieve, and correlate data pertaining to chemicals and their biological and environmental effects. The particular problems of data identification, acquisition, classification, and automation are discussed in relation to existing data sources and methods of data collection and analysis. The problems of computer software development are also addressed, and a design overview of the system is presented.

Animals↗
PubMed2005

Handling outliers in brain tumour MRS data analysis through robust topographic mapping.

Uncertainty is inherent in medical decision making and poses a challenge for intelligent technologies. This paper focuses on magnetic resonance spectra (MRS) for discrimination of brain tumour types and grades. Modelling of this type of high-dimensional data is commonly affected by uncertainty caused by the presence of outliers. Multivariate data clustering and visualization of MRS data is proposed using the GTM framework with basis functions comprising Student t-distributions in order to minimize the negative impact on the model from outliers. The effectiveness of this model on the MRS data is demonstrated empirically.

Brain↗
PubMed2006

Metabonomics and biomarker discovery: LC-MS metabolic profiling and constant neutral loss scanning combined with multivariate data analysis for mercapturic acid analysis.

In the field of metabonomics, 1H NMR and full scan mass spectrometry methods have usually been combined with principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) to detect patterns in biofluids that correspond to specific effects, usually a toxic site effect of a compound. Confounders together with great interindividual variation complicate such analysis in humans, and therefore, metabonomic data are almost restricted to animals. In our study, a constant neutral loss (CNL) scan on a linear ion trap demonstrated increased sensitivity and specificity compared to a full scan approach and was performed to detect mercapturic acids (MA), a class of effect markers. The method was applied to human volunteers administered 50 and 500 mg of acetaminophen (AAP), a model compound known to form MAs. Using a new algorithm to prepare the CNL data for chemometrics, discrimination of control and postdose samples could be performed using PCA and PLS-DA. The loadings plots clearly revealed AAP-MA as a marker, even at low-dose levels. Orthogonal signal correction (OSC) was carried out to investigate background information that is not due to exposure. Surprisingly, the OSC data provided a classification of male and female subjects showing the performance of the new approach.

Acetylcysteine↗
PubMed1998

A software system for data analysis in automated DNA sequencing.

Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and GelImager, is described. BaseFinder is a framework for trace processing, analysis, and base-calling. BaseFinder is highly extensible, allowing the addition of trace analysis and processing modules without recompilation. Powerful scripting capabilities combined with modularity and multilane handling allow the user to customize BaseFinder to virtually any type of trace processing. We have developed an extensive set of data processing and analysis modules for use with the program in fluorescence-based sequencing. GelImager is a framework for gel image manipulation. It can be used for gel visualization, lane retracking, and as a front end to the Washington University Getlanes program. The programs were designed using a cross-platform development environment, currently allowing them to run in Windows NT, Windows 95, Openstep/Mach, and Rhapsody. Work is ongoing to deploy the software on additional platforms, including Solaris, Linux, and MacOS. This software has been thoroughly tested and debugged in the analysis of >2 million bp of raw sequence data from human chromosome 19 region q13. Overall sequencing accuracy was measured using a significant subset of these data, consisting of approximately 600 sequences, by comparing the individual shotgun sequences against the final assembled contigs. Also, results are reported from experiments that analyzed the accuracy of the software and two other well-known base-calling programs for sequencing the M13mp18 vector sequence. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF025422]

Algorithms↗
PubMed2006

Evaluation of the influence of protein precipitation prior to on-line SPE-LC-API/MS procedures using multivariate data analysis.

Matrix effects on mass spectrometry (MS) response were investigated with three atmospheric pressure ionization (API) sources after on-line solid-phase extraction (SPE) of human plasma. On-line SPE was evaluated with one restricted access material (RAM), two large particle supports (LPS) and one monolith. A sample protein precipitation (PP) with acetonitrile (2:1) and a direct injection were tested. Principal component analysis (PCA) was performed to simplify data presentation and interpretation. Protein precipitation was found to be mandatory for reducing signal modification. Regarding sensitivity towards matrix effects after PP, atmospheric pressure photoionization (APPI) was globally the least sensitive ionization mode while electrospray ionization ESI was the most sensitive.

Alanine↗
PubMed1984

Computerized patient visit data analysis for the outpatient department of Jeddah General Hospital.

Hospitals play a vital role in the service of any community. In order that they may provide good quality service efficiently and at a reasonable cost, it is essential that they be properly managed. The development of a management information system (MIS) is a sine qua non for fulfilling this kind of need. With the above realization in mind, a computerized MIS is being developed for the Jeddah General Hospital, which was started only a few years ago. This paper describes the computerized analysis of the outpatient department's data so as to report it to the management as a part of the overall MIS. First, statistics such as number of patients/clinic/day, new and follow-up cases, male and female patients, time per patient, absentees, etc., are generated. These are then analyzed by using computers and are incorporated in the reports to be presented to the management on a periodic basis. The computer programming is in BASIC language so that mini-computers may be used for this purpose. The paper also discusses the possibilities of future enlargement of this work.

Appointments and Schedules↗
PubMedDate not supplied

Advances in proteomics data analysis and display using an accurate mass and time tag approach.

Proteomics has recently demonstrated utility for increasing the understanding of cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled with high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced.

Animals↗
PubMed1988

Objective comparison of exon and intron sequences by means of 2-dimensional data analysis methods.

Here we advocate the use of 2-dimensional data representation in the context of the informational approach of sequence analysis (Claverie & Bougueleret (1986) Nucleic Acids Research 14, 179-196) by applying these methods to the problem of intron/exon discrimination. Two main findings are reported: i) oligonucleotide patterns complementary to the Ul small nuclear RNA are specifically avoided in exon sequences, ii) vertebrate intron sequences, to the exclusion of other eukaryotic phyla, are characterized by a peculiar distribution of CpG containing patterns.

Algorithms↗
PubMed2003

Within-case and across-case approaches to qualitative data analysis.

The generalizations developed by qualitative researchers are embedded in the contextual richness of individual experience. Qualitative data management strategies that depend solely on coding and sorting of texts into units of like meaning can strip much of this contextual richness away. To prevent this, some authors have recommended treating individual accounts as whole cases or stories, but whole cases are difficult to compare with one another when the goal of the research is to develop generalizations that represent multiple accounts. In this article, the authors describe the ways in which three different qualitative researchers combined across-case coding and sorting with a variety of within-case data management and analysis techniques to produce contextually grounded, generalizable findings.

Caregivers↗
PubMed2006

Graphical comparison of image analysis and laser diffraction particle size analysis data obtained from the measurements of nonspherical particle systems.

The purpose of this paper is to describe results from the use of a set of Excel macros written to facilitate the comparison of image analysis (IA) and laser diffraction (LD) particle size analysis (psa) data. Measurements were made on particle systems of differing morphological characteristics including differing average aspect ratios, particle size distribution widths and modalities. The IA and LD psa data were plotted on the same graph treating both the weighting and the size unit of the LD psa data as unknowns. Congruency of the IA and LD plots was considered to indicate successful experimental determination of the weighting and size unit .The weighting of the resulting LD psa data (so-called volume-weighted) is shown to be better correlated with IA area-weighted data. The size unit of LD psa data is shown to be a function of particle shape. In the case of high aspect ratio particles characterized by approximately rectangular faces the LD psa data is shown to be a function of multiple particle dimensions being related to IA size descriptors through a simple variation of the law of mixtures. The results demonstrate that successful correlations between IA and LD psa data can be realized in the case of non-spherical particle systems even in the case of high aspect ratio particles; however, the inappropriateness of the application of the Equivalent Spherical Volume Diameter and the Random Particle Orientation assumptions to the interpretation of the LD psa results must first be acknowledged. Correlation permits cross validation of IA and LD psa results increasing confidence in the accuracy of the data from each orthogonal technique.

Humans↗
PubMed2006

Reproducibility of intravascular ultrasound radiofrequency data analysis: implications for the design of longitudinal studies.

OBJECTIVES: The purpose of this study was to assess in vivo the reproducibility of tissue characterization using spectral analysis of intravascular ultrasound (IVUS) radiofrequency data (IVUS-VH). BACKGROUND: Despite the need for reproducibility data to design longitudinal studies, such information remains unexplored. METHODS AND RESULTS: IVUS-VH (Volcano Corp., Rancho Cordova, USA) was performed in patients referred for elective percutaneous intervention and in whom a non-intervened vessel was judged suitable for a safe IVUS interrogation. The IVUS catheters used were commercially available catheters (20 MHz, Volcano Corp., Rancho Cordova, USA). Following IVUS-VH acquisition, and after the disengagement and re-engagement of the guiding catheter, an additional acquisition was performed using a new IVUS catheter. Fifteen patients with 16 non-significant lesions were assessed by 2 independent observers. The relative inter-catheter differences regarding geometrical measurements were negligible for both observers. The inter-catheter relative difference in plaque cross-sectional area (CSA) was 3.2% for observer 1 and 0.5% for observer 2. The limits of agreement for (observer 1 measurements) lumen, vessel, plaque and plaque burden measurements were 0.82, -1.10 mm(2); 0.80, -0.66 mm(2); 1.08, -0.66 mm(2); and 5.83, -3.89%; respectively. Limits of agreement for calcium, fibrous, fibrolipidic and necrotic core CSA measurements were 0.22, -0.25 mm(2); 1.02, -0.71 mm(2); 0.61, -0.65 mm(2); and 0.43, -0.38 mm(2) respectively. Regarding the inter-observer agreement, the limits of agreement for lumen, vessel, plaque and plaque burden measurements were 2.61, -2.09 mm(2); 2.20-3.03 mm(2); 1.70, -3.04 mm(2); and 9.16, -16.41%; respectively, and for calcium, fibrous, fibrolipidic and necrotic core measurements of 0.08, -0.09 mm(2); 0.89, -1.28 mm(2); 0.74, -1.06 mm(2); and 0.16, -0.20 mm(2); respectively. CONCLUSIONS: The present study demonstrates that the geometrical and compositional output of IVUS-VH is acceptably reproducible.

Coronary Disease↗
PubMed2000

Two-compartment model for whole-cell data analysis and transient compensation.

Recording and analysis of neuronal patch-clamp data involve many assumptions about membrane properties and cell morphology. Some of these assumptions introduce large errors or oversimplifications into the results. In particular, dendritic branching with high intracellular resistance leads to difficulty with capacitance calculation and transient subtraction, and may significantly distort measured currents. A two-compartment model, presented in detail here, provides a simple method of reducing many of these problems for the relatively simple case of cultured neurons studied with whole-cell patch electrodes. Some passive membrane properties may be accurately calculated, and the results may be used to correct recorded currents for resulting series resistance, intracellular resistance, and capacitive transient errors. The model may be tailored to particular cell types or experimental conditions. Programs to implement the algorithms are available from http://www.its.caltech.edu/ approximately nadeau/Rscomp.html.

Animals↗
PubMed1994

Current techniques for measuring dental fluorosis: issues in data analysis.

The currently popular scoring systems used to diagnosis fluorosis use different measurement units, evaluate variable numbers of sites per person, and involve non-comparable groupings of clinical symptoms. Although none of these factors is related to the level of fluoride exposure in the examined population, their combined effect produces fluorosis prevalence values for a population which vary considerably among and within these scoring systems. Intrinsic factors for a scoring system include the inclusion of a questionable category, the minimal level of fluorotic involvement, and the number of affected sites within a subject required for case definition. Thus, a case definition of fluorosis for each scoring system, although not mandatory, would certainly be desirable so that dental epidemiologists and clinical investigators can interpret fluorosis scores relative to risk assessment. On the other hand, ratios of fluorosis prevalence magnitudes, as evidenced by odds ratios, can be more stable between scoring systems when groups with different fluoride exposure levels are compared. There is a strong correlation between extent and specific measures of fluorosis severity for Dean's Index (DI) and the Tooth Surface Index of Fluorosis (TSIF) scoring system, as well as within each scoring system separately. Parallel patterns in fluorosis severity were found among groups with different fluoride exposure on severity levels of fluorosis may be better understood by using relative measures rather than by using differences in severity levels.

Analysis of Variance↗