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PubMed1999

Amino acid biosynthesis in the halophilic archaeon Haloarcula hispanica.

Biosynthesis of proteinogenic amino acids in the extremely halophilic archaeon Haloarcula hispanica was explored by using biosynthetically directed fractional 13C labeling with a mixture of 90% unlabeled and 10% uniformly 13C-labeled glycerol. The resulting 13C-labeling patterns in the amino acids were analyzed by two-dimensional 13C,1H correlation spectroscopy. The experimental data provided evidence for a split pathway for isoleucine biosynthesis, with 56% of the total Ile originating from threonine and pyruvate via the threonine pathway and 44% originating from pyruvate and acetyl coenzyme A via the pyruvate pathway. In addition, the diaminopimelate pathway involving diaminopimelate dehydrogenase was shown to lead to lysine biosynthesis and an analysis of the 13C-labeling pattern in tyrosine indicated novel biosynthetic pathways that have so far not been further characterized. For the 17 other proteinogenic amino acids, the data were consistent with data for commonly found biosynthetic pathways. A comparison of our data with the amino acid metabolisms of eucarya and bacteria supports the theory that pathways for synthesis of proteinogenic amino acids were established before ancient cells diverged into archaea, bacteria, and eucarya.

Acetyl Coenzyme A↗
PubMed1986

Mathematical coupling of data: correction of a common error for linear calculations.

The need frequently arises in the scientific environment to investigate the relationship between quantities that are calculated from a common set of directly measured variables. However, the presence of error in the common set of measured variables distorts the relationship among the calculated quantities and can lead to incorrect conclusions. This article presents a method of correcting for such distortions in the Pearson correlation coefficient and in the linear regression coefficient for linear calculations involving two measured variables. The errors considered may be either independent of, or proportional to, the value of the variable being measured. Tests to determine whether these popular coefficients have values significantly different from zero are presented. An example from the physiology literature is presented to illustrate these techniques.

Mathematics↗
PubMed2000

Avoiding common pitfalls in qualitative data collection and transcription.

The subjective nature of qualitative research necessitates scrupulous scientific methods to ensure valid results. Although qualitative methods such as grounded theory, phenomenology, and ethnography yield rich data, consumers of research need to be able to trust the findings reported in such studies. Researchers are responsible for establishing the trustworthiness of qualitative research through a variety of ways. Specific challenges faced in the field can seriously threaten the dependability of the data. However, by minimizing potential errors that can occur when doing fieldwork, researchers can increase the trustworthiness of the study. The purpose of this article is to present three of the pitfalls that can occur in qualitative research during data collection and transcription: equipment failure, environmental hazards, and transcription errors. Specific strategies to minimize the risk for avoidable errors will be discussed.

Data Collection↗
PubMed2003

Initiation into qualitative data analysis.

Qualitative data analysis may be daunting to nursing graduate students and other novice qualitative researchers. This article describes a qualitative research project required in a graduate nursing research course that was desired to guide students through their first qualitative data analysis. Common pitfalls novice researchers may encounter, such as data shuffling, premature closure, and overly delayed closure, also are discussed. The project reported in this article not only decreased students' anxiety concerning qualitative data analysis but also helped students gain respect for the amount of time, effort, and creativity this process entails.

Comprehension↗
PubMed1992

Strengthening some common multiple test procedures for discrete data.

This paper proposes modification of some commonly used multiple test procedures for testing problems that arise when the underlying distributions are discrete. These procedures have been shown as conservative because the exact nominal levels are unattainable. The amended procedures can achieve actual type I errors much closer to the nominal levels, thus giving rise to more powerful tests.

Animals↗
PubMed2000

Obtaining marginal estimates from conditional categorical repeated measurements models with missing data.

The most commonly used models for categorical repeated measurement data are log-linear models. Not only are they easy to fit with standard software but they include such useful models as Markov chains and graphical models. However, these are conditional models and one often also requires the marginal probabilities of responses, for example, at each time point in a longitudinal study. Here a simple method of matrix manipulation is used to derive the maximum likelihood estimates of the marginal probabilities from any such conditional categorical repeated measures model. The technique is applied to the classical Muscatine data set, taking into account the dependence of missingness on previous observed values, as well as serial dependence and a random effect.

Adolescent↗
PubMed2002

A comparison of imputation techniques for handling missing data.

Researchers are commonly faced with the problem of missing data. This article presents theoretical and empirical information for the selection and application of approaches for handling missing data on a single variable. An actual data set of 492 cases with no missing values was used to create a simulated yet realistic data set with missing at random (MAR) data. The authors compare and contrast five approaches (listwise deletion, mean substitution, simple regression, regression with an error term, and the expectation maximization [EM] algorithm) for dealing with missing data, and compare the effects of each method on descriptive statistics and correlation coefficients for the imputed data (n = 96) and the entire sample (n = 492) when imputed data are inculded. All methods had limitations, although our findings suggest that mean substitution was the least effective and that regression with an error term and the EM algorithm produced estimates closest to those of the original variables.

Algorithms↗
PubMed2006

Analytical performances of FT-IR spectrometry and imaging for concentration measurements within biological fluids, cells, and tissues.

FT-IR spectrometry has proved to be a useful tool for determining a series of plasma molecular concentrations. Dedicated experiments were first performed to test the analytical performance that could be obtained by FT-IR spectrometry using a synthesized N3-peptide exhibiting a -N3 absorption centered at 2110 cm(-1), a spectral region where no organic material of biological samples absorbs. Further, we investigated whether this technology was able to allow quantification of metabolic parameters (glucose and lactic acid) within plasma, cells, and tissues as an alternative method to the "classical" biochemical approaches, which require sophisticated biological material treatment and expensive reagents. For this purpose we used a series of plasma samples to determine glucose and lactic acid concentrations, which are common markers of cancer growth. We compared the results of the main spectral data treatments commonly achieved for FT-IR data analysis, such as univariate (Beer-Lambert) or multivariate (PLS) calibrations, as well as the deconvolution of the spectral interval of interest (1200-900 cm(-1)). No significant differences were found regarding the analytical performances of these methods. Spectral deconvolution was finally undertaken on cultured and on xenografted cells (U87 glial cells implied in human gliomas) to determine glucose and lactic acid concentrations. In this case, qualification was allowed by FT-IR imaging on the cellular models since biochemical approaches are not efficient to reach metabolic concentrations at the cellular level while keeping tissue organization.

Biomarkers↗
PubMed2003

Neutrality tests using DNA polymorphism from multiple samples.

The polymorphism of a gene or a locus is studied with increasing frequency by multiple laboratories or the same group at different times. Such practice results in polymorphism being revealed by different samples at different regions of the locus. Tests of neutrality have been widely conducted for polymorphism data but commonly used statistical tests cannot be applied directly to such data. This article provides a procedure to conduct a neutrality test and details are given for two commonly used tests. Applying the two new tests to the chemokine-receptor gene (CCR5) in humans, we found that the hypothesis that all mutations are selectively neutral cannot explain the observed pattern of DNA polymorphism.

Chromosome Mapping↗
PubMed2005

The tissue microarray data exchange specification: a document type definition to validate and enhance XML data.

BACKGROUND: The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness. RESULTS: A document type definition (DTD) that governs the allowed common data elements (CDE) in TMA DES export XML files was written, tested and evolved and is in routine use by the ACSR. This DTD defines TMA DES CDEs which are implemented in an external file that can be supplemented by internal DTD extensions for locally defined TMA data elements (LDE). CONCLUSION: ACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a DTD to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application. Improvements to the specification have additionally been suggested by our experience in importing other institution's exported TMA data. Enhancements to TMA DES to remove ambiguous situations and clarify the data should be considered. Better specified identifiers and hierarchical relationships will make automatic use of the data possible. Our tool can be used to reorder data and add identifiers; upgrading data for changes in the specification can be automatically accomplished. Using a DTD (optionally reflecting our proposed enhancements) can provide stronger validation of exported TMA data.

AIDS-Related Complex↗
PubMed1991

[Criteria of the operability of patients with a common arterial trunk based on hemodynamic data].

Criteria of operability of patients with a common arterial trunk were evaluated from a complex of hemodynamic, clinical, and morphological data. The patients were divided into 2 main groups according to the value of the pulmonary blood flow (PBF): group 1 with the pulmonary to systemic blood flow ratio (PBF/SBF) greater than 1; group 2 with PBF/SBF less than 1. The indications for operation in group 1 depended on the degree of PBF increase. For instance, an operation was indicated for patients with marked increase of PBF (PBF/SBF greater than 2); in cases with moderate PBF growth [formula: see text] the indications for operation were determined only after additional lung biopsy. The operation was not indicated for group 2 patients (PBF/SBF less than 1.0) because of the severity of their condition due to obstructive pulmonary vascular disease.

Adolescent↗
PubMed2004

Increment definitions for scale-dependent analysis of stochastic data.

It is common for scale-dependent analysis of stochastic data to use the increment Delta(t,r) =xi(t+r)-xi(t) of a data set xi(t) as a stochastic measure, where r denotes the scale. For joint statistics of Delta(t,r) and Delta(t, r') the question of how to nest the increments on different scales r, r' is investigated. Here we show that in some cases spurious correlations between scales can be introduced by the common left-justified definition. The consequences for a Markov process are discussed. These spurious correlations can be avoided by an appropriate nesting of increments. We demonstrate this effect for different data sets and show how it can be detected and quantified. The problem allows to propose a unique method to distinguish between experimental data generated by a noiselike or a Langevin-like random-walk process, respectively.

Journal Article↗