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[Quality of data on folic acid content in vegetables included in several Spanish Food Composition Tables and new data on their folate content].

The relationship between adequate folate intake, adequate serum levels, and lowering the risk of suffering from cardiovascular diseases, neural tube defects, neural illness and some kind of cancers have been widely studied. Because of the expected health benefits, the consumption of foods with high folate content or enriched foods is increasing. Therefore, an adequate folate intake is important in order to reach acceptable serum levels. Reliable food composition data are necessary in order to evaluate and estimate the populations folate intake, elaborate diets and formulate recommended dietary intakes. For this reason, we revised folic acid data in Spanish Food Composition Tables (FCT). The quality of the data was evaluated and compared with other well-known international Food Composition Tables as well as with a high-resolution liquid chromatographic method (HPLC) validated in our laboratory. We evaluated all data about folate content, as well as all the information given like data origin, analytical method, sampling or original database. For the HPLC method, the food samples were incubated with hog kidney conjugase. After that, the samples were purified and concentrated by strong anion exchange (SAX), then the folate content was quantified by HPLC with a combination of two ultraviolet and fluorescence detectors. The evaluation and comparison of data was established according to some parameters, which define the quality of data, giving punctuation depending on the compliance with these parameters. The study of different sources showed that nutrients were different in definition, analysis method, units and expression of data, and that this fact could have a potential influence on TCA data values. In addition, it has been possible to show a wide variation in food number, name of these foods as well as the analysis of raw or cooked products with different composition. When the quality conditions were tested, the Spanish FCT had the lowest punctuation in folate content data. That is because the Spanish FCT did not use a validated method to quantify folic acid in foods (Direct method of FCT elaboration), but they used folate content data from others FCT (Indirect method of FCT elaboration). These data manifest the importance of getting a consensus method to determine folate content in foods with the aim to obtain a FCT with reliable folate data.

Folic Acid↗
PubMed2026

Computational metabolomics at scale: from open data to insight.

Metabolomics data are currently generated at scale thanks to the evolution of technologies that have led to marked improvements in the number of metabolites detected, spanning all chemical classes. These data are increasingly submitted to public repositories for data reuse, integration, and interpretation. Despite the availability of public resources and associated computational tools, the field still lacks a widely adopted, consistent data and analytics infrastructure capable of transforming this wealth of information into scientific insight. Indeed, the metabolomics field is just now scratching the surface of being able to harness the power of new computational technologies. In this review, we summarize discussions from the "Dagstuhl-Seminar 24181 Computational Metabolomics: Towards Molecules, Models, and their Meaning" with a focus on public data availability, open data standards, data and knowledge integration, and education. Our goal is to raise awareness and adoption of the latest open science resources while highlighting key areas needing further development.

Metabolomics↗
PubMed1995

A comparison of meta-analytic results using literature vs individual patient data. Paternal cell immunization for recurrent miscarriage.

OBJECTIVE: To compare the meta-analytic results from published literature vs those obtained from pooling original patient data. DATA SOURCES: Individual patient data from 15 completed or ongoing trials on paternal white blood cell immunization as treatment for recurrent miscarriage were obtained through the American Society for Reproductive Immunology. STUDY SELECTION: Only randomized controlled trials were selected. Within these eight selected trials, 202 patients were from four published studies, 43 were added by the same investigators after publication, and 140 were from four unpublished trials. DATA EXTRACTION: Individual patient data were collected using a standardized form and double data entry. DATA SYNTHESIS: Using the fixed treatment effect model, we found that the effect of immunization, denoted as the relative live-birth ratio (RR), was greater by pooling summary data from published articles (RR, 1.29; 95% confidence interval [CI], 1.03 to 1.60) than by pooling all individual patient data from the same investigators (RR, 1.17; 95% CI, 0.97 to 1.37) or when individual patient data were pooled from four unpublished trials (RR, 1.01; 95% CI, 0.74 to 1.28). A similar diminishing treatment effect for the same comparisons was observed using the random treatment effect model (RR, 1.38; 95% CI, 0.89 to 1.87 using published summary data; RR, 1.18; 95% CI, 0.98 to 1.42 using individual patient data; RR, 1.01; 95% CI, 0.74 to 1.28 using unpublished trials). CONCLUSIONS: Meta-analytic results may differ depending on the use of various data sources: whether the source was from summary statistics in the literature, from individual patient data provided by trialists, or from unpublished trials.

Abortion, Habitual↗
PubMed1994

Data verification in the residue laboratory.

Residue analysis frequently presents a challenge to the quality assurance (QA) auditor due to the sheer volume of data to be audited. In the face of multiple boxes of raw data, some process must be defined that assures the scientist and the QA auditor of the quality and integrity of the data. A program that ensures that complete and appropriate verification of data before it reaches the Quality Assurance Unit (QAU) is presented. The "Guidelines for Peer Review of Data" were formulated by the Residue Analysis Business Center at Ricerca, Inc. to accommodate efficient use of review time and to define any uncertainties concerning what are acceptable data. The core of this program centers around five elements: Study initiation (definitional) meetings, calculations, verification, approval, and the use of a verification checklist.

Chemistry Techniques, Analytical↗
PubMed1991

Structural classification of carbohydrates in glycoproteins by mass spectrometry and high-performance anion-exchange chromatography.

A general strategy has been developed for determining the structural class (oligomannose, hybrid, complex), branching types (biantennary, triantennary, etc.), and molecular microheterogeneity of N-linked oligosaccharides at specific attachment sites in glycoproteins. This methodology combines mass spectrometry and high-performance anion-exchange chromatography with pulsed amperometric detection to take advantage of their high sensitivity and the capability for analysis of complex mixtures of oligosaccharides. Glycopeptides are identified and isolated by comparative HPLC mapping of proteolytic digests of the protein prior to, and after, enzymatic release of carbohydrates. Oligosaccharides are enzymatically released from each isolated glycopeptide, and the attachment site peptide is identified by fast atom bombardment mass spectrometry (FAB-MS) of the mixture. Part of each reaction mixture is then permethylated and analyzed by FAB-MS to identify the composition and molecular heterogeneity of the carbohydrate moiety. Fragment ions in the FAB mass spectra are useful for detecting specific structural features such as polylactosamine units and bisecting N-acetylhexosamine residues, and for locating inner-core deoxyhexose residues. Methylation analysis of these fractions provides the linkages of monomers. Based on the FAB-MS and methylation analysis data, the structural classes of carbohydrates at each attachment site can be proposed. The remaining portions of released carbohydrates from specific attachment sites are preoperatively fractionated by high-performance anion-exchange chromatography, permethylated, and analyzed by FAB-MS. These analyses yield the charge state and composition of each peak in the chromatographic map, and provide semiquantitative information regarding the relative amounts of each molecular species. Analytically useful data may be obtained with as little as 10 pmol of derivatized carbohydrate, and fmol sensitivity has been achieved. The combined carbohydrate mapping and structural fingerprinting procedures are illustrated for a recombinant form of the CD4 receptor glycoprotein.

Amino Acid Sequence↗
PubMed2002

Crystal structure and dimerization equilibria of PcoC, a methionine-rich copper resistance protein from Escherichia coli.

PcoC is a soluble periplasmic protein encoded by the plasmid-born pco copper resistance operon of Escherichia coli. Like PcoA, a multicopper oxidase encoded in the same locus and its chromosomal homolog CueO, PcoC contains unusual methionine rich sequences. Although essential for copper resistance, the functions of PcoC, PcoA, and their conserved methionine-rich sequences are not known. Similar methionine motifs observed in eukaryotic copper transporters have been proposed to bind copper, but there are no precedents for such metal binding sites in structurally characterized proteins. The high-resolution structures of apo PcoC, determined for both the native and selenomethionine-containing proteins, reveal a seven-stranded beta barrel with the methionines unexpectedly housed on a solvent-exposed loop. Several potential metal-binding sites can be discerned by comparing the structures to spectroscopic data reported for copper-loaded PcoC. In the native structure, the methionine loop interacts with the same loop on a second molecule in the asymmetric unit. In the selenomethionine structure, the methionine loops are more exposed, forming hydrophobic patches on the protein surface. These two arrangements suggest that the methionine motifs might function in protein-protein interactions between PcoC molecules or with other methionine-rich proteins such as PcoA. Analytical ultracentrifugation data indicate that a weak monomer-dimer equilibrium exists in solution for the apo protein. Dimerization is significantly enhanced upon binding Cu(I) with a measured delta(deltaG degrees )<or=-8.0 kJ/mole, suggesting that copper might bind at the dimer interface.

Amino Acid Motifs↗
PubMed2001

Comparison of different immunoassays for CA 19-9.

We compared six routinely employed immunoassay kits: Architect i2000 and AxSYM, Abbott Laboratories; Elecsys 2010, Roche Diagnostics; ELSA, CIS-BioInternational; Immulite 1, Diagnostic Products Corporation; and IRMA-mat, Byk-Sangtec Diagnostica. Using all analytical systems, we measured identical groups of clinical samples completed with selected control samples. The repeatability of measurements (coefficient of variation) ranged from 2.1% (Elecsys 2010) to 6.7% (ELSA). The parameters of Passing-Bablok regression show significant systematic differences among analytical systems. Data from a Bland-Altman diagram suggest that these differences project onto other, still more significant individual differences among individual samples. Though the cut-off values differ between various systems, no similar clinical efficacy appears to be attained. The behavior of individual systems is quite different for identical control materials and does not necessarily duplicate the calibration for biological samples. The results of determining CA 19-9 cannot be extrapolated from one analytical technique to another, even in cases where the same monoclonal antibody is used. Standardization of CA 19-9 measurement systems is necessary to allow use of the results for the purposes of evidence-based medicine.

CA-19-9 Antigen↗
PubMed2005

Modeling the electrophoretic mobility of beta-blockers in capillary electrophoresis using artificial neural networks.

Artificial neural networks were used for modeling the mobility of five beta-blockers (i.e., labetalol atenolol, practolol, timolol and propranolol) in running buffer with ternary solvent background electrolyte systems containing 80 mM acetate buffer dissolved in water, methanol, ethanol and their ternary mixtures. The volume fractions of two solvents (f(2), f(3)) and cologarithm of electrophoretic mobilities in pure solvents (i.e., -Lnmu(1), -Lnmu(2) and -Lnmu(3)) were used as inputs and cologarithm of the mobility in mixed solvents was the output of the networks. The number of neurons in hidden layer, learning rate, momentum and the number of epochs were optimized, in which two neurons in hidden layer, 0.2, 0.9 and 20000 were found the optimized values for learning rate, momentum and number of epochs, respectively. Mean percentage deviations (MPD) between calculated and experimental mobilities were computed as an accuracy criterion. To assess the correlative ability of the model, all data points in each set were used as training set and the mobilities were back-calculated by the trained networks, in which the overall MPD (OMPD)+/- standard deviation (SD) for correlative study was 3.1+/- 2.3. To evaluate the prediction capability of the proposed ANN model, the network was trained using 15 data points for each analyte and the remaining data points were predicted. The obtained OMPD (+/-SD) for this analysis was 3.6+/-3.0. To further investigate on the applicability of ANN, a generalized network was trained with 10 data points from each beta-blocker and then the network was employed to predict the mobilities of the analytes in ternary solvent electrolyte systems. The MPDs for predicted mobilities were 3.6%, 3.6%, 3.9%, 3.7% and 2.9% respectively for labetalol, atenolol, practolol, timolol and propranolol.

Adrenergic beta-Antagonists↗
PubMed1981

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↗
PubMed1996

An Attempt to Interpret the Spread of Element Concentration in Antarctic Surface Snow: The Same Element in a Given Test Field, Several Elements in Different Sampling Fields

Sampling surface snow on a large test field always leads to a spread of analyte concentration data which partly follows a Gaussian distribution and partly a rectangular one as can be observed from the analysis of literature data. The spread depends on the nonuniformity of the air-snow interface in the field and on the extent of reproducibility of all the procedures used from sampling to analysis. Consequently a sample relevant to a restricted surface might be poorly representative of the surrounding area. Contamination of the sample during the gathering and storing steps is assumed to be the main source of nonrandom results (outliers). Using various statistical tools we were able to evaluate which part of the spread was due to the snow surface nonuniformity in the case of many samples collected in the same test field. In the case of samples gathered in different geographical areas, the possibility of finding correlations among points is greatly enhanced when three or more analytes are considered for each sample. When the same correlation is found for some analytes and a variable tentatively tested, information can be gained about the source of chemical content of snow samples. The use of UV pretreatment of snow samples has been proven to cut down the interference of organics on the electrochemical process in DPASV, allowing one to obtain accurate and reproducible data.

Journal Article↗
PubMed1993

Competitive solid-phase enzyme immunoassay for melatonin in human and rat serum and rat pineal gland.

We describe a solid-phase competitive enzyme immunoassay for determination of melatonin in serum. The detection limit of the assay is 1.0 fmol/well. Low cross-reactivity of the antiserum with other indoles, parallel serum extract dilution and melatonin standard curves, good analytical recovery, and within- and between-assay CVs of 6.4-14.4% provide validation of the assay. Linear regression analysis of melatonin concentrations measured with this assay (y) and with a commercial 3H RIA (x) in 88 sera yielded the relation y = 0.62 x - 0.76, Sy/x = 0.03. Values for melatonin in serum samples from healthy subjects are lower during the day than during the night. Melatonin response in rat serum and pineal gland to isoproterenol injection is similar to published RIA data. The analytical procedure is also simple. Thus, the assay should have practical applications in investigation of pineal function in both clinical and basic studies.

Animals↗
PubMed2005

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).

The spring workshop of the HUPO-PSI convened in Siena to further progress the data standards which are already making an impact on data exchange and deposition in the field of proteomics. Separate work groups pushed forward existing XML standards for the exchange of Molecular Interaction data (PSI-MI, MIF) and Mass Spectrometry data (PSI-MS, mzData) whilst significant progress was made on PSI-MS' mzIdent, which will allow the capture of data from analytical tools such as peak list search engines. A new focus for PSI (GPS, gel electrophoresis) was explored; as was the need for a common representation of protein modifications by all workers in the field of proteomics and beyond. All these efforts are contextualised by the work of the General Proteomics Standards workgroup; which in addition to the MIAPE reporting guidelines, is continually evolving an object model (PSI-OM) from which will be derived the general standard XML format for exchanging data between researchers, and for submission to repositories or journals.

Mass Spectrometry↗
PubMed2004

Sorption and desorption by ideal two-compartment systems: unusual behavior and data interpretation problems.

This paper examines the current practices of fitting curves to sorption, desorption, and equilibrium data obtained from laboratory experiments. Systems of equations incorporating Freundlich isotherms and first-order kinetics for two different idealized sorbents, one "fast" and one "slow," were solved numerically to produce "data". Two-compartment curves were then fit to the data by nonlinear regression, and the parameters computed by the regression are compared with the original parameters used to produce the data. The results show that a sorbent with fast kinetics will not steadily accumulate sorbate until it reaches the equilibrium value but will overshoot equilibrium, accumulating an excess of sorbate. This overshoot will cause the sorption rates for both sorbents and the distribution between the fast and slow sorbents to be estimated incorrectly. The system may appear to be at equilibrium by external measures, but sorbate will slowly be redistributing from the fast to the slow sorbent. An isotherm constructed from data acquired during this process will have an incorrect coefficient and exponent. Consequently, the meaning of the results obtained by curve fitting may often be questionable and may say little about the phenomena occurring within the sorbate-sorbent-liquid system. Possible physical explanations for the effects observed are offered.

Absorption↗
PubMed1997

Analytic approaches to longitudinal caries data in adults.

The objective of this paper is to consider current methods for analyzing longitudinal caries data in adults. To illustrate these methods, we used data from the Piedmont dental study, a prospective investigation of the oral health of older adults. Longitudinal dental data sets comprise repeated observations of an outcome (often clustered within randomly selected primary sampling units), and a set of covariates for each of many subjects, in whom clustering can occur as a result of measuring teeth, or surfaces, within people. One objective of statistical analysis is to predict the outcome variable as a function of the covariates, while accounting for the correlation among the repeated observations for a given subject and the effect of clustering within subjects, as well as between subjects within primary sampling units, such as communities, schools, hospitals, or other such units. We considered two statistical approaches: generalized estimating equations and survey regression models. We also examined the impact of varying diagnostic criteria for caries estimation between epidemiologists and clinicians. One approach is to perform the usual time(x) exam score minus time0 score analysis for the baseline and final examinations, while an alternative is to analyze trends among interim examinations. Finally, because caries studies in which the onset of the disease is the endpoint face the problem of censoring due to subject attrition and/or tooth loss, we recommend the incidence density (time-to-event) analytic strategy to address this problem. This approach was found to be most suitable for longitudinal studies of older adults since it accounts for the time each surface remains at risk for the event of interest, making use of interim exam data until the moment the subject and/or the tooth are no longer available for examination. We also included a discussion on biases that occur upon application of the usual methods of estimating caries experience in missing teeth and crowns, which often ignore the classification error in the estimation. We propose a method to adjust for misclassification of the M-component of the DMFS index. In the case where one can observe true reversals or remineralization of caries lesions, we recommend an adjustment formula to account for reversals that are most likely due to examiner misclassification. We provide examples to demonstrate the applicability of the methods for covariates subject to outcome misclassification.

Adult↗
PubMed1998

The solution structure of human coagulation factor VIIa in its complex with tissue factor is similar to free factor VIIa: a study of a heterodimeric receptor-ligand complex by X-ray and neutron scattering and computational modeling.

Factor VIIa (FVIIa) is a soluble four-domain plasma serine protease coagulation factor that forms a tight complex with the two extracellular domains of the transmembrane protein tissue factor in the initiating step of blood coagulation. To date, there is no crystal structure for free FVIIa. X-ray and neutron scattering data in solution for free FVIIa and the complex between FVIIa and soluble tissue factor (sTF) had been obtained for comparison with crystal structures of the FVIIa-sTF complex and of free factor IXa (FIXa). The solution structure of free FVIIa as derived from scattering data is consistent with the extended domain arrangement of FVIIa seen in the crystal structure of its complex with sTF, but is incompatible with the bent, less extended domain conformation seen in the FIXa crystal structure. The FVIIa scattering curve is also compatible with a subset of 317 possible extended structures derived from a constrained automated conformational search of 15 625 FVIIa domain models. Thus, the scattering data support extended domain models for FVIIa free in solution. Similar analyses showed that the solution scattering derived and crystal structures of the FVIIa-sTF complex were in good agreement. An automated constrained search for allowed structures for the complex in solution based on scattering curves showed that only a small family of compact models gave good agreement, namely those in which FVIIa and sTF interact closely over a large surface area. The general utility of this approach for structural analysis of heterodimeric complexes in solution is discussed. Analytical ultracentrifugation data and the modeling of these data were consistent with the scattering results. It is concluded that in solution FVIIa has an extended or elongated domain structure, which allows rapid interaction with sTF over a large surface area to form a high-affinity complex.

Amino Acid Sequence↗
PubMed2004

Algorithm-assisted elucidation of disulfide structure: application of the negative signature mass algorithm to mass-mapping the disulfide structure of the 12-cysteine transforming growth factor beta type II receptor extracellular domain.

The power of an algorithm-driven method for interpreting disulfide mass-mapping data is demonstrated in the context of determining the disulfide structure of the extracellular domain of the transforming growth factor beta type II receptor, a 14-kDa cystinyl protein containing 12 cysteines in the form of six disulfide bonds. The disulfide mass-mapping methodology is based on partial reduction and cyanylation-induced cleavage of the cystinyl protein. Because the multiplicity of possible disulfide structures that must be considered grows rapidly with the number of cysteines, as does the difficulty in physically isolating each of the partially reduced and cyanylated isoforms of the analyte, manual data interpretation for disulfide mapping a cystinyl protein containing more than eight cysteines becomes unmanageable. Recently, we introduced the concept of a "negative signature mass algorithm" (NSMA) to determine the disulfide structure of a cystinyl protein by processing an input of its amino acid sequence and mass spectral data from analysis of its associated cyanylation-induced cleavage products. Here, we present experimental results to validate the NSMA concept. A key advantage of the NSMA, in addition to convenience and automation, is its capacity to interpret mass spectra from mixtures of cyanylation-induced cleavage fragments without separating the partially reduced isoforms of the cystinyl protein and without knowledge of the extent of partial reduction.

Algorithms↗
PubMed1998

Determination of reference ranges for elements in human scalp hair.

Expected values, reference ranges, or reference limits are necessary to enable clinicians to apply analytical chemical data in the delivery of health care. Determination of references ranges is not straightforward in terms of either selecting a reference population or performing statistical analysis. In light of logistical, scientific, and economic obstacles, it is understandable that clinical laboratories often combine approaches in developing health associated reference values. A laboratory may choose to: 1. Validate either reference ranges of other laboratories or published data from clinical research or both, through comparison of patients test data. 2. Base the laboratory's reference values on statistical analysis of results from specimens assayed by the clinical reference laboratory itself. 3. Adopt standards or recommendations of regulatory agencies and governmental bodies. 4. Initiate population studies to validate transferred reference ranges or to determine them anew. Effects of external contamination and anecdotal information from clinicians may be considered. The clinical utility of hair analysis is well accepted for some elements. For others, it remains in the realm of clinical investigation. This article elucidates an approach for establishment of reference ranges for elements in human scalp hair. Observed levels of analytes from hair specimens from both our laboratory's total patient population and from a physician-defined healthy American population have been evaluated. Examination of levels of elements often associated with toxicity serves to exemplify the process of determining reference ranges in hair. In addition the approach serves as a model for setting reference ranges for analytes in a variety of matrices.

Adolescent↗