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PubMed1979

Classification of fungi by means of pyrolysis-gas chromatography-pattern recognition.

Repetitive samples of three strains of the mould Penicillium were subjected to pyrolysis-gas chromatography (Py-GC). From the chromatograms, 26 peak heights were used in a subsequent SIMCA pattern recognition analysis. This data analysis gives a marked improvement in the classification of the samples (100% correct, 85% unique) in comparison with the traditional analysis based on the average chromatogram of each class (92% correct, 45% unique). The data analytical method is described in detail using the Py-GC data as an illustration.

Analysis of Variance↗

PubMed1983

Use of anion gap for the quality control of electrolyte analyzers.

A simple model for the simulation of patient Na, CO2, Cl, and anion gap was formulated from patient electrolyte data. Analytical error, either random or systematic, was incorporated into the simulation of the electrolyte data and allowed study of the response of anion gap to error. Power functions, plots of probability of error detection vs. size of analytical error, were constructed and indicated a low probability of error detection when single patient specimens with abnormal anion gaps were reanalyzed. These power functions showed that pooling of the anion gap data by averaging consecutive anion gaps resulted in a high probability for detecting systematic error. We recommend, as a useful quality control procedure, averaging at least eight consecutive anion gaps and testing for a significant difference between the average and the established mean gap.

Acid-Base Equilibrium↗

PubMed1995

Standard reference materials and data quality assurance: the lesson from the analysis of trace elements.

The problem of having accurate and precise analytical data of the concentrations of trace elements and compounds in bioclinical studies is of fundamental importance. This can be conveniently faced if appropriate standard reference materials, with known concentrations of the analyte object of study, are available. This paper reviews the present situation of these standard materials in the field of trace element analysis in biological specimens. The most important requirements in the preparation and in the application of these materials are presented and discussed.

Evaluation Studies as Topic↗

PubMed1990

Epidemiology of adenocarcinoma of the cervix.

There is general evidence that the incidence of adenocarcinoma of the cervix has been rising, particularly among younger women. The determinants of these trends, however, remain largely unknown. We have reviewed the epidemiology of adenocarcinoma of the cervix using descriptive data from cancer registration and clinical series and two main sources of analytical data: clinical studies comparing cervical adenocarcinoma (AC) and squamous carcinoma (SC) and formal case-control and cohort epidemiological studies. In both the United States and northern Europe there is evidence of the rising frequency of AC in absolute and relative terms as compared to SC. These trends are generally restricted to younger women: under-age-35 AC incidence approximately doubled from the early 1970s to the early 1980s. Available data, although scanty, consistently show that the frequency of cervical adenocarcinoma rises with the number of partners and with decreasing age at first intercourse, suggesting a potential role for sexually transmitted (viral) factors. In clinical series, nulliparity was reported more frequently in AC than in SC cases but an inconsistent association was found in three formal epidemiological studies. Similarities with the epidemiology of endometrial cancer are also suggested from the association with overweight, while a possible relation with hypertension and diabetes is based on clinical series only and hence more difficult to interpret. Thus, adenocarcinoma of the cervix appears to share epidemiological characteristics with both adenosquamous cancer of the cervix and adenocarcinoma of the endometrium, although uncertainties in classification and registration leave several questions unanswered.

Adenocarcinoma↗

PubMed1986

Modifications of lipid structure and their influence on mesomorphism in model membranes: the influence of hydrocarbon chains.

The influence of hydrocarbon chains on the temperature (TG-LC) of the gel to liquid-crystalline phase transition of model membranes has been investigated over an extensive variety of phosphatidylcholines (PC). The TG-LC is dependent upon the length of the hydrocarbon chains, on whether or not the chains are saturated or have been modified in some way, and on the position of any modification along the chain. For PC having two different acyl chains (heteroacid PC) in the sn-1 and sn-2 positions, the TG-LC is dependent on the chain position and on the inequivalence of chain penetration into the bilayer. Positional isomers of PC have different TG-LC. The first two double bonds introduced in each chain of a PC cause a much greater reduction in TG-LC and in the enthalpy change of the transition than does the subsequent introduction of additional double bonds. Dipolyunsaturated PC have uncooperative (broad) transitions that occur at low temperatures and have small enthalpy changes. While each PC has unique transitional characteristics, there are a number of patterns in the TG-LC which emerge on consideration of all the available data. One such pattern may be useful in predicting TG-LC from analytical data on the composition and positions of acyl chains of various lipids.

Chemical Phenomena↗

PubMed1990

Evaluation of criteria for the acceptance of bioanalytical data.

Results from bioanalytical analyses for registration of a new drug entity are used to define its pharmacokinetics and bioavailability/bioequivalence. Whilst analytical data may be derived from the application of a validated method, it is essential to apply mathematical criteria to its acceptance, in order that the analyst can be assured that the assay is performing within defined limits and to its validated specification. Parameters evaluated for acceptability are the batch calibration curve, the minimum quantifiable concentration and the quality control (QC) sample acceptability. Specifically, six QC samples per analytical batch are used, two samples at each of three concentrations. The rationale for the definition of these criteria is evaluated together with a consideration of their applications and limitations. The relevance and use of Shewhart and Cusum plots to monitor assay performance is illustrated.

Biological Availability↗

PubMed1991

Advances in data assessment. Application to the etiology of nausea reported during chemotherapy, concerns about significance testing, and opportunities in clinical trials.

Typical inferential statistical procedures, such as the t-test and analysis of variance, compare differences in mean values of variables. This approach can sometimes obscure rather than illuminate research data. Here we present and discuss alternative data analytic techniques. Potential advantages of box plots over conventional t-tests for understanding data are shown by comparing the area under high and low frequencies from spectral curves of autonomic changes following chemotherapy treatment. Typical t-tests provide information regarding statistical significance in terms of the differences in group means; box plots and related exploratory techniques provide information regarding the characteristics of the distributions within the groups as well as examination of potential outliers. Multivariate analysis of variance (MANOVA) and other multivariate techniques are commonly used to deal with potentially complex data sets with multiple outcome measures. The potential advantages of visual clustering techniques such as star plots, Chernoff faces, and Andrew's Function Plots are demonstrated by examining changes in facial pallor caused by chemotherapy-induced nausea and vomiting. Typical MANOVA approaches can identify potential differences in mean values between groups; visual clustering approaches do this by graphically presenting complex interrelationships for individual cases. This approach enhances the visual interpretation of potential interactions that would be obscured by simply focusing on overall mean values. Preliminary data from a meta-analysis on the effect of metoclopramide on chemotherapy-induced vomiting demonstrates the potential uses and advantages of this summary technique over simple tabular summaries. We found significant relationships between the effect size of the drug and variables such as the year of study publication and whether the publication was an article or an abstract. While none of these techniques are meant to replace traditional inferential statistics, they offer advantages in terms of data exploration and understanding relationships within data sets that are not clearly addressed by other methods. They are potentially valuable alternatives worthy of exploration. Finally, we discuss issues of interim analyses and multiple endpoint assessment for clinical trials.

Antineoplastic Agents↗

PubMed1986

Novel sulfur-containing microbial metabolite of primaquine.

Microbial metabolism studies of the antimalarial drug primaquine, using Streptomyces roseochromogenus (ATCC 13400) have produced an N-acetylated metabolite and a methylene-linked dimeric product, both of which have been previously reported, and a novel sulfur-containing microbial metabolite. The structure of the metabolite as a sulfur-linked dimer was proposed on the basis of spectral and chemical data. The molecular formula C34H44N6O4S was established from field-desorption mass spectroscopy and analytical data. The 1H- and 13C-nuclear magnetic resonance spectral data firmly established that the novel metabolite was a symmetrically substituted dimer of primaquine N-acetate with a sulfur atom linking the two units at C-5. The metabolite has been shown to be a mixture of stereoisomers which can equilibrate in solution. This observation was confirmed by microbial synthesis of the metabolite from optically active primaquine.

Chemical Phenomena↗

PubMed1994

Employing simulated data to illustrate an important cause of the 'steepling' effect in breath alcohol analysis.

The 'steepling' effect (large excursions in analytical data over time) is a debated issue in forensic breath alcohol analysis with various explanations being postulated. Simulated breath alcohol data was generated according to a hypothetical kinetic model where single random samples as well as means of duplicate random samples were plotted with respect to time at 0.2 hour intervals. In addition, the simulated data was compared when both two or more digit treatment was employed. Results showed the occurrence of significant noise or 'steepling' when single, two-digit breath alcohol samples were employed as compared to a four-digit mean computed from three-digit duplicates. The magnitude of variability was quantified by means of nonlinear regression resulting in the residual sum of squares (RSS) = 0.00202 for the single analysis and RSS = 0.00053 for the mean of duplicates. The method of data collection and treatment appears to contribute significantly to the 'steepling' phenomenon. Intuitively, replicate analyses reduce variability and allow for more accurate kinetic modelling employing breath alcohol analysis.

Alcoholic Intoxication↗

PubMed1988

Elemental microanalysis of biological specimens.

Although X-ray microanalysis in the electron microscope is the most common method for microanalysis of biological specimens, other methods of elemental microanalysis (electron energy loss spectroscopy, scanning Auger microanalysis, and proton, ion, and laser microprobe analysis) may provide important complementary information and help overcome some of the limitations of electron probe X-ray microanalysis. Despite differences in physical principles and instrumentation, the various microanalytical methods have much in common with regard to specimen preparation, quantitative analysis, and interpretation of analytical data. A common approach to microanalytical problems in the biological sciences, irrespective of the analytical techniques used, seems therefore indicated.

Electron Probe Microanalysis↗

PubMed1992

Clinical pathology: preanalytical variation in preclinical safety assessment studies--effect on predictive value of analyte tests.

Significant differences in concentrations of analytes in samples may be introduced before samples enter analyzers. These differences are known as preanalytical variation and are part of the overall variation in analytical data. Preanalytical variation is caused by factors that operate during animal preparation prior to sampling, sample collection, sample processing, and sample storage prior to measurement. Preanalytical variation is important because it detracts from the predictive value of analyte measurements. Preanalytical variation may permanently damage data. Because its effects are difficult to quantitate it should be minimized in safety assessment studies. Sources of preanalytical variation are actions performed on animals prior to sample collection and actions performed on the specimen prior to analysis. Preanalytical variation produces a range of artefacts in experimental data. Consequences of preanalytical variation are loss of confidence in the data, obfuscation of real test article effects, false effects, and possibly the expense of repeating a study. To limit preanalytical variation, its sources must be identified, the effects documented, and measures devised to eliminate its sources. Predictive value (likelihood of actual disease) of appropriate clinical pathology tests in toxicology is inversely dependent on preanalytical variation: uncontrolled variation produces data with low predictive values, and controlled variation produces data with high predictive values.

Animals↗

PubMed2025

Evaluation of sequencing reads at scale using rdeval.

MOTIVATION: Large sequencing datasets are being produced and deposited into public archives at unprecedented rates. The availability of tools that can reliably and efficiently generate and store sequencing read summary statistics has become critical. RESULTS: As part of the effort by the Vertebrate Genomes Project (VGP) to generate high-quality reference genomes at scale, we sought to address the community's need for efficient sequence data evaluation by developing rdeval, a standalone tool to quickly compute and interactively display sequencing read metrics. Rdeval can either run on the fly or store key sequence data metrics in tiny read 'snapshot' files. Statistics can then be efficiently recalled from snapshots for additional processing. Rdeval can convert fa*[.gz] files to and from other popular formats including BAM and CRAM for better compression. Overall, while CRAM achieves the best compression, the gain compared to BAM is marginal, and BAM achieves the best compromise between data compression and access speed. Rdeval also generates a detailed visual report with multiple data analytics that can be exported in various formats. We showcase rdeval's functionalities using long-read data from different sequencing platforms and species, including human. For PacBio long-read sequencing, our analysis shows dramatic improvements in both read length and quality over time, as well as the benefit of increased coverage for genome assembly, though the magnitude varies by taxa. AVAILABILITY AND IMPLEMENTATION: Rdeval is implemented in C++ for data processing and in R for data visualization. Precompiled releases (Linux, MacOS, Windows) and commented source code for rdeval are available under MIT license at https://github.com/vgl-hub/rdeval. Documentation is available on ReadTheDocs (https://rdeval-documentation.readthedocs.io). Rdeval is also available in Bioconda and in Galaxy (https://usegalaxy.org). An automated test workflow ensures the consistency of software updates.

Software↗

PubMed1983

Analytical versus food table values for vitamin C in foods: the effect on calculated vitamin C intake of elderly subjects.

During a longitudinal study of vitamin C nutrition in 23 healthy elderly people, samples of cooked vegetables and liver, canned meats, canned vegetables and fruit drinks were analysed for vitamin C content. The analytical data are presented here and the effect on calculated daily intake of vitamin C of using the analytical values in place of food table values is assessed. For cooked foods the analysed values were close to food table values; exceptions were spring cabbage, cauliflower and canned potatoes. Fortified fruit drinks contained 20-60 mg vitamin C per 100 ml and made an important contribution to intake. Canned meats contained 0.3-61.4 mg per 100 g (mean 14.9 mg), but their contribution to intake was considered small. The difference between daily intakes calculated using analytical and food table values was greater than 5 mg in 37 per cent of 1-day periods and in 17 per cent of 7-day periods. These differences were not sufficient to significantly alter the correlations between intake and biochemical indices found in the original study. Nevertheless, given the discrepancies between calculated and analysed vitamin C intakes reported in the literature, analytical work is probably essential in studies of vitamin C nutrition.

Aged↗

PubMed1981

Physico-chemical and analytical studies on plafibride.

Physico-chemical and analytical studies on N-2-(p-chlorophenoxy)-isobutyryl)-N'-morpholinomethylurea (plafibride, ITA 104) are reported. Besides the usual analytical data, spectral (UV, IR, NMR, MS) and chromatographic (HPLC, TLC) properties are described. As to chemico-analytical procedures, ITA 104 is detectable by titrimetric and spectralphotometric methods and by thin-layer chromatography.

Chemical Phenomena↗

PubMed1988

Genetic changes across language boundaries in Europe.

By means of three different methods we investigated whether 59 allele frequencies and ten cranial variables show increased change at 29 language-family boundaries in Europe. The quadrat-variance method compares variances of map quadrats crossed by language-family boundaries to variances of quadrats that are not crossed. The rate-of-change method examines the directional derivative of surfaces of the variables perpendicular to a language-family boundary and compares these derivatives to the same quantities obtained by randomly placing the language boundaries on the map of Europe. The difference method tests whether these variables differ more across language-family boundaries than across randomly placed boundaries. These special data-analytic techniques had to be developed to avoid the problem of spatial autocorrelation of both language and biological data. All three methods indicate increased genetic change at language-family boundaries. Clearer and more pronounced results are obtained by the first two methods than by the difference method. Thirteen language-family boundaries show significant gene frequency change by at least one of the methods. Changes are more marked in gene frequencies than in cranial variables. Different allele frequencies mark the increased change at different language boundaries. A model, based on the known history of each language-family boundary, was constructed to predict whether given boundaries should exhibit increased genetic change. The model is in good agreement with the observed results.

Alleles↗

PubMed1989

[LATINFOODS].

Food Composition Tables should be considered as national wealth and as valuable tools for utilization in food and nutrition, in nutritional therapy, in agricultural planning and production, in food guides, and in the food industry for the formulation of information on the product that appears in the label. They should, therefore, be considered as national wealth because they chemically describe the food resources of a country at a very high price, and are considered valuable tools due to their multiple applications. The countries present Tables were published between 1935 and 1961, with analytical data available at that time. So far the Tables have met their purpose, but due to changes that have occurred in raw materials, in analytical methodology, in the new knowledge acquired in nutrition, and in the relationships between food and diseases, in November 1986, representative groups of the Latin American and the Caribbean countries decided to create LATINFOODS. The objective of the program is to promote the development of data banks of foods of the Latin American countries, creating national multidisciplinary groups interested in data production, compilement, publication and utilization, and that eventually, may be homogeneously united to form a data bank for Latin America and the Caribbean Region. During the meeting in favor of the creation of LATINFOODS, detection was made of the constraints of the Food Composition Tables now used as well as the measures needed to correct such problems. These included the number of samples collected as well as the analytical methods used, and the number of nutrients. Due to the observed increase in production and distribution of new food products by the food industry, and to the increased association between foods and diseases, the food industry must participate not only in the generation of data, but in their utilization for food identification, nutrient contribution and nutritional education. Likewise, academic programs in Food Technology should extend the concepts of Food Science with special emphasis on food nutrient contents, to reach an adequate nutritional and health status for the Latin American population.

Databases, Factual↗

PubMed1995

Commentary and opinion: I. Principal component analysis, variance partitioning, and "functional connectivity".

We briefly review the need for careful study of "variance partitioning" and "optimal model selection" in functional positron emission tomography (PET) data analysis, emphasizing the use of principal component analysis (PCA) and the importance of data analytic techniques that allow for heterogeneous spatial covariance structures. Using an [15O]water dataset, we demonstrate that--even after data processing--the intrasubject signal component of primary interest in baseline activation studies constitutes a very small fraction of the intersubject variance. This small intrasubject variance component is subtly but significantly changed by using analysis of covariance instead of scaled subprofile model processing before applying PCA. Finally, we argue that the concept of "functional connectivity" should be interpreted very generally until the relative roles of inter- and intrasubject variability in both disease and normal PET datasets are better understood.

Analysis of Variance↗

PubMed1987

Validity of calculating fatty acid intake from mixed diets.

One hundred and seventy six weighed duplicate diets were collected over 16 consecutive days from 11 subjects. Analyses of their fatty acid composition were used to asses the validity of food composition tables. Four different calculating techniques were employed. Using the published data produced correlation coefficients of 0.29 between analysed and calculated polyunsaturated/saturated fatty acid ratios, whilst the addition of new analytical data and recoding fried foods produced a correlation coefficient of 0.56. The latter method also decreased the mean difference between analysed and calculated polyunsaturated/saturated consumption, when compared with the standard procedure.

Adult↗