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At least 271 records · Page 15Linked to original sources
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↗
PubMedDate not supplied

Processing and classification of protein mass spectra.

Among the many applications of mass spectrometry, biomarker pattern discovery from protein mass spectra has aroused considerable interest in the past few years. While research efforts have raised hopes of early and less invasive diagnosis, they have also brought to light the many issues to be tackled before mass-spectra-based proteomic patterns become routine clinical tools. Known issues cover the entire pipeline leading from sample collection through mass spectrometry analytics to biomarker pattern extraction, validation, and interpretation. This study focuses on the data-analytical phase, which takes as input mass spectra of biological specimens and discovers patterns of peak masses and intensities that discriminate between different pathological states. We survey current work and investigate computational issues concerning the different stages of the knowledge discovery process: exploratory analysis, quality control, and diverse transforms of mass spectra, followed by further dimensionality reduction, classification, and model evaluation. We conclude after a brief discussion of the critical biomedical task of analyzing discovered discriminatory patterns to identify their component proteins as well as interpret and validate their biological implications.

Algorithms↗
PubMed2001

Techniques for long-term multisite neuronal ensemble recordings in behaving animals.

Advances in our understanding of neural systems will go hand in hand with improvements in the experimental techniques used to study these systems. This article describes a series of methodological developments aimed at enhancing the power of the methods needed to record simultaneously from populations of neurons over broad regions of the brain in awake, behaving animals. First, our laboratory has made many advances in electrode design, including movable bundle and array electrodes and smaller electrode assemblies. Second, to perform longer and more complex multielectrode implantation surgeries in primates, we have modified our surgical procedures by employing comprehensive physiological monitoring akin to human neuroanesthesia. We have also developed surgical implantation techniques aimed at minimizing brain tissue damage and facilitating penetration of the cortical surface. Third, we have integrated new technologies into our neural ensemble, stimulus and behavioral recording experiments to provide more detailed measurements of experimental variables. Finally, new data analytical techniques are being used in the laboratory to analyze increasingly large quantities of data.

Animals↗
PubMed1997

Limitations of the coupling of amino acid mixtures for the preparation of equimolar peptide libraries.

The standard method of peptide library synthesis involves coupling steps in which a single amino acid is reacted with a mixture of resin-bound amino acids. The more recently described positional scanning strategy (in which each position in the peptide sequence is occupied in turn by a single residue) is different since it involves the coupling of mixtures of amino acids to mixtures of resin-bound amino acids. In the present study, we analyze the compounds produced under these conditions measuring coupling rates and amounts of formed products, using mainly UV, HPLC, LC/MS and MS/MS techniques. Our data do not permit to conclude that the resulting libraries are complete. Indeed, our analytical data indicate that a large part of the di-, tri- and tetrapeptides synthesized with this method are not present in the final mixture. Although chemical compensation (in which poor coupling kinetics is compensated by a larger excess of the incoming amino acid) has been thought to counterbalance these biases, our experiments show that the compensation method does not take into account the crucial influence of the resin-bound amino acid and that even the dipeptide libraries obtained in this way are far from completeness. The present work provides strong evidence that the coupling of mixtures of amino acids to resin-bound residues, which is required by the positional scanning strategy, results in incomplete and/or non-equimolar libraries. It also clearly confirms that coupling rates in solid-phase peptide synthesis are dependent on the nature of both the incoming and the immobilized amino acid.

Amino Acids↗
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↗
PubMed2001

Multivariate data analysis of quality parameters in drinking water.

The quality of water destined for human consumption has been treated as a multivariate property. Since most of the quality parameters are obtained by applying analytical methods, the routine analytical laboratory (responsible for the accuracy of analytical data) has been treated as a process system for water quality estimation. Multivariate tools, based on principal component analysis (PCA) and partial least squares (PLS) regression, are used in the present paper to: (i) study the main factors of the latent data structure and (ii) characterize the water samples and the analytical methods in terms of multivariate quality control (MQC). Such tools could warn of both possible health risks related to anomalous sample composition and failures in the analytical methods.

Multivariate Analysis↗
PubMed2005

Ecotoxicological evaluation of diesel-contaminated soil before and after a bioremediation process.

Evaluation of contaminated sites is usually performed by chemical analysis of pollutants in soil. This is not enough either to evaluate the environmental risk of contaminated soil nor to evaluate the efficiency of soil cleanup techniques. Information on the bioavailability of complex mixtures of xenobiotics and degradation products cannot be totally provided by chemical analytical data, but results from bioassays can integrate the effects of pollutants in complex mixtures. In the preservation of human health and environment quality, it is important to assess the ecotoxicological effects of contaminated soils to obtain a better evaluation of the healthiness of this system. The monitoring of a diesel-contaminated soil and the evaluation of a bioremediation technique conducted on a microcosm scale were performed by a battery of ecotoxicological tests including phytotoxicity, Daphnia magna, and nematode assays. In this study we biostimulated the native microflora of soil contaminated with diesel by adding nutrients and crop residue (corn straw) as a bulking agent and as a source of microorganisms and nutrients; in addition, moisture was adjusted to enhance diesel removal. The bioremediation process efficiency was evaluated directly by an innovative, simple phytotoxicity test system and the diesel extracts by Daphnia magna and nematode assays. Contaminated soil samples were revealed to have toxic effects on seed germination, seedling growth, and Daphnia survival. After biostimulation, the diesel concentration was reduced by 50.6%, and the soil samples showed a significant reduction in phytotoxicity (9%-15%) and Daphnia assays (3-fold), confirming the effectiveness of the bioremediation process. Results from our microcosm study suggest that in addition to the evaluation of the bioremediation processes efficiency, toxicity testing is different with organisms representative of diverse phylogenic levels. The integration of analytical, toxicological and bioremediation data is necessary to properly assess the ecological risk of bioremediation processes.

Animals↗
PubMed1998

Elimination profile of methylthiouracil in cows after oral administration.

In addition to methods for the determination of residues, there is an important need for knowledge of the fate and excretion of growth promoting substances in fattening animals. In court, often simple questions are asked, such as, over what period of time can the drug be detected?, is it possible to find residues after 2 months, etc. These questions can only be answered by conducting animal experiments. Data on excretion and distribution of thiouracils in cows are rather scarce. At the beginning of the 1980s, animal experiments with methylthiouracil (MTU) were carried out in the Laboratory of Chemical Analysis. These experiments showed that treatment of cows with MTU results in the rapid appearance of the drug in plasma, urine and milk, whereas MTU selectively accumulates in the thyroid gland. The results of these experiments were only published in media with limited access (thesis, abstracts) and also there has been a considerable improvement in data handling with computer programs in the last 15 years. This investigation reinterprets the 'old' analytical data from animal experiments using a pharmacokinetic software package.

Administration, Oral↗
PubMed2007

MIPSPlantsDB--plant database resource for integrative and comparative plant genome research.

Genome-oriented plant research delivers rapidly increasing amount of plant genome data. Comprehensive and structured information resources are required to structure and communicate genome and associated analytical data for model organisms as well as for crops. The increase in available plant genomic data enables powerful comparative analysis and integrative approaches. PlantsDB aims to provide data and information resources for individual plant species and in addition to build a platform for integrative and comparative plant genome research. PlantsDB is constituted from genome databases for Arabidopsis, Medicago, Lotus, rice, maize and tomato. Complementary data resources for cis elements, repetive elements and extensive cross-species comparisons are implemented. The PlantsDB portal can be reached at http://mips.gsf.de/projects/plants.

Arabidopsis↗
PubMed1993

Pesticide residue control in the years 1988-1989 in Italy.

The paper reports the monitoring for pesticide residue contamination of foodstuffs carried out in the years 1988-1989 by the Italian peripheral laboratories officially commissioned for the task. The tables show the analytical data for each class of substrate versus the limits in force at the time. 2506 food samples and 555 samples from the environment were analysed and a total of 16,259 determinations made. The residues were absent in 90% of the cases; the percentage of irregularities was 1.52%. These results confirm the data obtained in previous years, which is particularly significant considering the much larger number of analytical determinations performed this time. It has been deemed convenient to survey specific types of foodstuffs (for example, cereals and animal products) by examining a larger number of samples.

Edible Grain↗
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↗
PubMedDate not supplied

Characterization and identification of local defects in glass.

The most relevant defects in glasses are categorized and investigated by appropriate microanalytical techniques. Since these defects very often present a real challenge because of complex chemical and mineralogical properties, a multimethod approach is necessary to supplement or confirm the findings from scanning techniques. The combination of electron probe microanalysis/energy-dispersive x-ray (EPMA/EDX) and laser ablation inductively coupled plasma mass spectroscopy (LA-ICP-MS) allows the determination of element trace concentrations in a knot, a glassy defect, thus finally enabling the identification of a special source of the defect from otherwise nondistinguishable refractories. The type of crystals can be determined exactly by the use of EPMA and x-ray dispersion (XRD), stones (a crystalline agglomerate) are analyzed by EPMA/EDX pointing to a possible source for this defect; results on metallic inclusions, "filled bubbles," and surface defects are reported and defect sources are discussed. Since close cooperation with the production departments and knowledge of production techniques and conditions are necessary for the diagnosis to take appropriate countermeasures, an approach is presented which systematically accumulates all information into a data base. The structure of such "expert systems" is described, which leads to correlation of appearance, analytical data, and source of the defects for even more accurate diagnosis and faster reaction.

Journal Article↗
PubMed2005

Quality of life related to type 1 Gaucher disease: Spanish experience.

UNLABELLED: The impact of type 1 Gaucher disease and its therapy on health-related quality of life (QOL) was investigated and the results were compared with a Spanish adult normative group. PATIENTS AND METHODS: Between January 1998 and December 2002, a prospective clinical QOL trial was conducted by application of a Spanish version of the Health Survey SF-36 questionnaire. Patients receiving ERT (69 cases) filled in the questionnaire two times, prior to starting ERT and after two years under ERT. The patients were stratified by gender and age group. Clinical and X-ray data to assess bone disease were obtained from the Spanish Gaucher Register. Demographic, clinical, genotype and analytical data and the response to therapy were evaluated. Four grades of severity were established according to bone disease (no symptoms = 0, moderate bone pain = 1, severe bone crisis = 2, fracture/necrosis = 3). Correlation analysis was made between QOL score and grade of bone disease. RESULTS: Mean age+/-SD 33.6+/-11.7 (range 18-66), M/F,ratio 33/36; bone disease: 0 in 27 patients (47.3%), 1 in 11 (19.3%), 2 in 5 (8.8%) and 3 in 14 (24.5%). Physical activity: 11 patients (19.3%) showed severe restriction and 41 patients (71.9%) were only limited for strenuous activities. The mean score for QOL questionnaire was 11.9+/-10.4 (range 2-46). Correlation between score and bone disease was significant only for 1 and 3 grades (p = 0.02). Improvement in self perception of global health was observed ranging from 34.3% before ERT to 91.4% after ERT (p = 0.001). Nevertheless physical activity remained unsatisfactory in 24.5% of patients due mainly to bone sequelae. COMMENTS: Physical activities and bone disease grade 1 and 3 are negatively related to QOL. Nevertheless no correlation was found with bone pain crisis, possibly due to the transitory character of this event. In spite of the improvement induced by ERT, a quarter of patients remained with physical limitations related to bone disease as well as in need of orthopaedic correction of bone sequelae. In order to improve the QOL an accurate evaluation of bone disease to define therapeutic approaches must be considered.

Exercise↗
PubMed2006

Does the Rayleigh equation apply to evaluate field isotope data in contaminant hydrogeology?

Stable isotope data have been increasingly used to assess in situ biodegradation of organic contaminants in groundwater. The data are usually evaluated using the Rayleigh equation to evaluate whether isotope data follow a Rayleigh trend, to calculate the extent of contaminant biodegradation, or to estimate first-order rate constants. However, the Rayleigh equation was developed for homogeneous systems while in the subsurface, contaminants can migrate at different velocities due to physical heterogeneity. This paper presents a method to quantify the systematic effect that is introduced by applying the Rayleigh equation to field isotope data. For this purpose, the travel time distribution between source and sampling point is characterized by an analytical solution to the advection-dispersion equation. The systematic effect was evaluated as a function of the magnitude of physical heterogeneity, geometry of the contaminant plume, and degree of biodegradation. Results revealed that the systematic effect always leads to an underestimation of the actual values of isotope enrichment factors, the extent of biodegradation, or first-order rate constants, especially in the dispersion-dominant region representing a higher degree of physical heterogeneity. A substantial systematic effect occurs especially for the quantification of first-order rate constants (up to 50% underestimation of actual rate) while it is relatively small for quantification of the extent of biodegradation (< 5% underestimation of actual degree of biodegradation). The magnitude of the systematic effect is in the same range as the uncertainty due to uncertainty of the analytical data, of the isotope enrichment factor, and the average travel time.

Biodegradation, Environmental↗
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↗
PubMed1996

The interpretation of daydreams, I.

There is a notable lack of interest in the daydream, whether in clinical work, in the literature, or in psychoanalytic teaching, compared with the attention received by nocturnal dreams, fantasy activity, and other psychoanalytic material. This neglect of daydreams may be related to the apparent infrequency with which patients report them in analytic treatment. Possible explanations for the unavailability of daydreams as analytic material are examined. The paper offers detailed clinical material that will provide some of the necessary analytic data with which to begin an exploration of the nature of daydreams and their role in the analytic process.

Adult↗