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PubMed1990

Isocratic high performance liquid chromatographic analysis of S-adenosylmethionine and S-adenosylhomocysteine in animal tissues: the effect of exposure to nitrous oxide.

A simple isocratic high performance liquid chromatographic method for the simultaneous measurement of S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) in animal tissues is described. The direct injection of perchloric acid tissue extracts and rapid resolution of both compounds in a single run reduces any sampling and analytical errors in determining the SAM/SAH ratio, a measure of methylation reactions. The method has been used to determine changes in brain SAM/SAH ratios after exposure of rats to nitrous oxide.

Animals↗
PubMed2004

Diagnosis of gastrointestinal tract lesions by endoscopic ultrasound-guided fine-needle aspiration biopsy.

BACKGROUND: Endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNA) allows detailed imaging of both intramural and extramural structures of the gastrointestinal (GI) tract and also allows tissue samples to be obtained from masses and lesions in the GI tract. The objective of the current study was to determine the diagnostic utility of EUS-FNA in evaluating intramural and extramural GI tract lesions. METHODS: The authors evaluated all EUS-FNA specimens of GI tract lesions obtained over a 30-month period (from August 2000 to February 2003). Samples of pancreatic and intrabdominal/mediastinal lymph nodes were excluded from the study. A single endosonographer performed all procedures. An attending cytopathologist also was present on site to assess specimen adequacy. Cytologic diagnoses were analyzed for correlations with final diagnoses, which were based on histologic examination of biopsied/resected pathology materials and/or clinical follow-up findings. RESULTS: Sixty-two EUS-FNA specimens of intramural and extramural GI tract lesions were obtained from a total of 60 patients. The mean patient age was 58.8 years (standard deviation, 15.3 years). Thirty-six patients (60%) were male, and 24 (40%) were female. Twenty-eight patients had surgical pathologic evaluation of the corresponding lesions. The remaining 32 patients were followed clinically for a mean duration of 9.5 months (standard deviation, 7.7 months). The anatomic sites of the lesions were as follows: esophagus in 23 patients (37%), stomach in 13 patients (21%), duodenum in 15 patients (24%), and rectum/sigmoid in 11 patients (18%). It is noteworthy that 29 patients (43%) previously had experienced unsuccessful attempts at tissue diagnosis by endoscopic forceps biopsy. Of the 62 EUS-FNA specimens, 43, 4, and 15 were reported as being positive for a neoplasm, suspicious, and benign, respectively. Neoplastic lesions included carcinoma (n = 24), gastrointestinal stromal tumor (GIST; n = 18), neuroendocrine neoplasm (n = 2), and lymphoma (n = 1). There were two cases of endometriosis, three foregut duplication cysts, and one case of diverticulosis. There were two lesions that yielded false-negative findings (one gastric lymphoma and one GIST) secondary to sampling or interpretive error. There also were three cases that yielded false-positive findings (one case of endometriosis, one case of duodenal diverticula with smooth muscle hyperplasia, and one case of normal pancreas, which presented as a periduodenal mass). The sensitivity, specificity, and diagnostic accuracy of EUS-FNA in diagnosing GI tract neoplastic lesions were 89%, 88%, and 89%, respectively. CONCLUSIONS: EUS-FNA provides accurate tissue diagnosis in a wide variety of extraintestinal mass lesions and intramural GI tumors, particularly in patients for whom previous endoscopic forceps biopsy was unsuccessful in establishing a diagnosis.

Abdominal Neoplasms↗
PubMed1991

First-trimester genetic diagnosis in multiple pregnancy: principles and potential pitfalls.

Both the principles of first-trimester genetic diagnosis in multiple pregnancy and the special considerations required to avoid potential diagnostic pitfalls are presented. The experience consisted of 65 cases of twins and one case of quadruplets. Dichorionic twins were recognized by sonography in 54 cases. Transabdominal aspiration was generally preferred to transcervical for obtaining chorionic tissue, although in two cases both approaches were used. Diagnostic error following erroneous sampling was reported in 3 out of 54 sets of dichorionic twins (5.5 per cent). When like-sex dichorionic twins cannot be differentiated by cytogenetic or DNA polymorphism studies, amniocentesis should be recommended to confirm the reliability of the result on chorionic tissue.

Adult↗
PubMed2004

Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.

A subnanomolar inhibitor of human immunodeficiency virus type 1 (HIV-1) protease, designated QF34, potently inhibits the wild-type and drug-resistant enzyme. To explain its broad activity, the binding of QF34 to the wild-type HIV-1 protease is investigated by molecular dynamics simulations and compared to the binding of two inhibitors that are used clinically, saquinavir (SQV) and indinavir (IDV). Analysis of the flexibility of protease residues and inhibitor segments in the complex reveals that segments of QF34 were more mobile during the dynamics studies than the segments of SQV and IDV. The dynamics of hydrogen bonding show that QF34 forms a larger number of stable hydrogen bonds than the two inhibitors that are used clinically. Absolute binding free energies were calculated with molecular mechanics-generalized Born surface area (MM-GBSA) methodology using three protocols. The most consistent results were obtained using the single-trajectory approach, due to cancellation of errors and inadequate sampling in the separate-trajectory protocols. For all three inhibitors, energy components in favor of binding include van der Waals and electrostatic terms, whereas polar solvation and entropy terms oppose binding. Decomposition of binding energies reveals that more protease residues contribute significantly to the binding of QF34 than to the binding of SQV and IDV. Moreover, contributions from protease main chains and side chains are balanced in the case of QF34 (52:48 ratio, respectively), whereas side chain contributions prevail in both SQV and IDV (main-chain:side-chain ratios of 41:59 and 45:55, respectively). The presented results help explain the ability of QF34 to inhibit multiple resistant mutants and should be considered in the design of broad-specificity second-generation HIV-1 protease inhibitors.

Drug Design↗
PubMed2001

Analysis of failure time hierarchical data in the presence of competing risks with application to oral contraceptive pill use in Egypt.

Problems of practical interest in the analysis of data on contraceptive use, from Demographic and Health Surveys (DHS), include the estimation of the cause-specific probability of discontinuation by time t (the cumulative incidence function), in the presence of other competing causes and the evaluation of the effect of covariates on the cause-specific hazards of discontinuation. Methods of analysis of failure time data with competing risks are by now fairly well developed in the case of a simple random sample. However, the data from the DHS are clustered by geographical areas and include multiple episodes per woman. For a marginal (population average) approach, we propose using methods developed for simple random samples with standard errors calculated using a double bootstrap to take account of the clustered hierarchical nature of the data. In the conditional approach, the cause-specific hazards are modelled as log-linear functions of the covariates conditional on random effects of clusters and women, using a three-level multinomial discrete-time logit model. The methods are applied to data from Egypt 1992 DHS on the oral contraceptive pill use.

Adolescent↗
PubMed2005

An appraisal of methods for the analysis of longitudinal categorical data with MAR drop-outs.

A number of methods for analysing longitudinal ordinal categorical data with missing-at-random drop-outs are considered. Two are maximum-likelihood methods (MAXLIK) which employ marginal global odds ratios to model associations. The remainder use weighted or unweighted generalized estimating equations (GEE). Two of the GEE use Cholesky-decomposed standardized residuals to model the association structure, while another three extend methods developed for longitudinal binary data in which the association structures are modelled using either Gaussian estimation, multivariate normal estimating equations or conditional residuals. Simulated data sets were used to discover differences among the methods in terms of biases, variances and convergence rates when the association structure is misspecified. The methods were also applied to a real medical data set. Two of the GEE methods, referred to as Cond and ML-norm in this paper and by their originators, were found to have relatively good convergence rates and mean squared errors for all sample sizes (80, 120, 300) considered, and one more, referred to as MGEE in this paper and by its originators, worked fairly well for all but the smallest sample size, 80.

Biometry↗
PubMed1993

Characterization of absorption and scattering properties of small-volume biological samples using time-resolved spectroscopy.

With time-resolved spectroscopy, we develop an experimental approach by sample substitution to measure the absorption (mu a) and reduced scattering (mu's) coefficients of small-volume biological samples. To investigate the method, small-volume control samples are substituted into a large-size host medium during increases in the absorber (or scatterer) concentration of the host. By characterizing the deviation of the spectra taken with and without the sample, we determine the matching points where the sample and surrounding medium are optically identical. We show that this method can result in correct values of the mu a and mu's for the sample within 6% error if the matching conditions for both the mu a and mu's are fully realized. The results also indicate that this method can give approximate values of the mu a and mu's in a reasonable range if either the mu a or the mu's matching between the two media is realized. This method has been applied to the studies of absorption properties of a human finger and of scattering properties of yeast.

Absorption↗
PubMed1993

Automated ribosomal DNA fingerprinting by capillary electrophoresis of PCR products.

Capillary electrophoresis (CE) provides a rapid and automated technique for the analysis of subnanogram amounts of DNA fragments generated by the polymerase chain reaction (PCR). Here we describe the implementation of size-selective CE for DNA profiling and restriction fragment length polymorphism analysis of amplified polymorphic spacers of ribosomal DNA from fungi. Separations of unpurified and isopropanol-precipitated PCR-amplified DNA fragments in the size range of 20-1600 base pairs were achieved in less than 20 min with the use of hydroxypropyl methylcellulose as a sieving medium. The amplified internal transcribed spacer (ITS) and intergenic spacer (IGS) of RNA genes could be sized by coelectrophoresing a standard size ladder mixed with every sample, thereby eliminating errors in size estimation. This, together with the strictly controlled conditions of CE, permit the discrimination of amplified rDNA fragments differing only a few base pairs in length. Inter- and intraspecific variation in the size and number of restriction sites of the amplified rDNA spacers from the ectomycorrhizal basidiomycetes Laccaria laccata and Laccaria bicolor was observed and most strains could thus be reliably genotyped by PCR-CE. Multiple amplified IGS fragments of heterogeneous size were detected in several strains. This polymorphism is due to the occurrence of 5S rDNA subrepeats (i.e., multiple annealing of primer) within IGS. With CE, in contrast to slab gel electrophoresis, run times are short, the capillary can be reused, and full automation is feasible. Data acquisition and analysis are computer-controlled, which facilitates the locus identification and reduces error especially when large numbers of PCR products must be analyzed.(ABSTRACT TRUNCATED AT 250 WORDS)

Autoanalysis↗
PubMed1998

Evolution of mate-choice copying: a dynamic model.

Mate-choice copying has recently been demonstrated in several species. Two, not mutually exclusive, explanations for copying have been proposed: it reduces sampling costs and/or error of mate choice. In guppies, Poecilia reticulata, and black grouse, Tetrao tetrix, young females seem most likely to copy. Therefore, copying may teach inexperienced females what attractive males look like. I developed a 2-year dynamic model, to investigate under which conditions a mate-copying strategy might first evolve. An original population of pure choosers was assumed, which was invaded by a mutant female, able to copy during her first mating season, thereby instantly improving her ability to assess male quality. Alternatively, she could either wait and learn by observing males, just as non-copiers may do, but incurring some time costs, or choose, relying on her own abilities. The degree to which copying occurred among these mutant, young, inexperienced females increased with an increasing proportion of old, experienced females in the population, and with decreasing time left until the end of the season. The model demonstrates that mate-choice copying may evolve, when young females are poor at discrimination and need to learn what high-quality males look like. Male quality proved to be unimportant for copying to evolve, as long as there are sufficient differences in quality for mate choice to be meaningful. As with previous models, time constraints are an important assumption for copying to be advantageous over non-copying. Copyright 1998 The Association for the Study of Animal Behaviour. Copyright 1998 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1991

Therapeutic monitoring of cyclosporin--an update.

The success of organ transplantation is closely related to clinical use of the immunosuppressive drug cyclosporin (CsA). The dosage of CsA is complicated by the large intra- and interindividual variability in its pharmacokinetics, as well as by the narrow concentration range between insufficient immunosuppression and toxicity. Potential sources of error in the sampling procedure and the advantages and disadvantages of the available analytical methods are discussed. Traditionally, 12 or 24 hour trough concentrations of CsA are monitored. Recently, peak concentrations or estimation of AUCs by a limited sampling strategy have been tried to improve the relatively weak concentration-effect and concentration-toxicity relationships found with trough CsA concentration monitoring. Studies of the CsA concentration-effect relationships for various treatment indications are reviewed.

Blood Specimen Collection↗
PubMed1995

Colour Doppler and duplex sonography and angiography of the carotid artery bifurcations. Prospective, double-blind study.

We undertook a prospective double-blind study of 128 carotid artery bifurcations using colour Doppler and duplex sonography and angiography. Sixty-four patients with cerebrovascular events were admitted for angiography. All underwent sonography within 24 h of angiography. Standard duplex sonography and colour Doppler imaging without spectral analysis were performed, on the same device, by two sonographers, using defined morphological and haemodynamic criteria. Digital radiological data on vessel diameter were interpreted independently by two radiologists. The two sonographic methods gave similar grading of stenosis, compared to angiography, with an accuracy ranging from 96% in severe to 83% in minor stenoses. Colour Doppler studies gave better area measurements than standard duplex sonography, except for major stenoses. Discrepancies between ultrasonography and angiography were due mainly to minor stenoses and large plaques of calcification on the vessel walls, which masked very segmental 70% stenoses in 2 cases. Angiography is limited by its own resolution, does not show uncalcified vessel walls and does not give cross-sectional data. It would therefore be inappropriate for showing small plaques, the full extent of ectasia or for defining the carotid bulb accurately. The advantages of colour methods were in investigating sinuous or deep vessels and hypoechoic plaques. Analysis of the residual lumen of a stenosis and its extent could be determined more rapidly. Haemodynamic quantification of stenoses by standard duplex sonography may be difficult because of limited sample volume and error in estimation of angle, whereas colour Doppler allows semiquantitative estimation of haemodynamics.(ABSTRACT TRUNCATED AT 250 WORDS)

Blood Flow Velocity↗
PubMed2003

The conservation of redundancy in genetic systems: effects of sexual and asexual reproduction.

The relationship between probability of survival and the number of deleterious mutations in the genome is investigated using three different models of highly redundant systems that interact with a threatening environment. Model one is a system that counters a potentially lethal infection; it has multiple identical components that act in sequence and in parallel. Model two has many different overlapping components that provide threefold coverage of a large number of vital functions. The third model is based on statistical decision theory: an ideal detector, following an optimum decision strategy, makes crucial decisions in an uncertain world. The probability of a fatal error is reduced by a redundant sampling system, but the chance of error rises as the system is impaired by deleterious mutations. In all three cases the survival profile shows a synergistic pattern in that the probability of survival falls slowly and then more rapidly. This is different than the multiplicative or independent survival profile that is often used in mathematical models. It is suggested that a synergistic profile is a property of redundant systems. Model one is then used to study the conservation of redundancy during sexual and asexual reproduction. A unicellular haploid organism reproducing asexually retains redundancy when the mutation rate is very low (0.001 per cell division), but tends to lose high levels of redundancy if the mutation rate is increased (0.01 to 0.1 per cell division). If a similar unicellular haploid organism has a sexual phase then redundancy is retained for mutation rates between 0.001 and 0.1 per cell division. The sexual organism outgrows the asexual organism when the above mutation rates apply. If they compete for finite resources the asexual organism will be extinguished. Variants of the sexual organism with increased redundancy will outgrow those with lower levels of redundancy and the sexual process facilitates the evolution of more complex forms. There is a limit to the extent that complexity can be increased by increasing the size of the genome and in asexual organisms this leads to progressive accumulation of mutations with loss of redundancy and eventual extinction. If complexity is increased by using genes in new combinations, the asexual form can reach a stable equilibrium, although it is associated with some loss of redundancy. The sexual form, by comparison, can survive, with retention of redundancy, even if the mutation rate is above one per generation. The conservation and evolution of redundancy, which is essential for complexity, depends on the sexual process of reproduction.

Genome↗
PubMed1994

Enhanced sensitivity for the determination of selenium by INAA.

A working analytical procedure for selenium determinations by INAA, using gamma spectrometry with a germanium well-type detector, is presented. The spectral line at 400.7 keV is employed, enhanced with the effect of energy summing in true coincidence of cascade photons. The main advantage of the method is high efficiency and reliable, interference-free results; potential drawbacks are increases in input count rate and pile-up losses, decrease in resolution, and sensitivity to errors in sample-to-detector geometry. The procedure is applied to certification analysis of reference materials, large-area biomonitoring by oak leave samples, and determination of separated proteins.

Animals↗
PubMed2005

Sampling the soil in long-term forest plots: the implications of spatial variation.

Long-term monitoring of forest soils as part of a pan-European network to detect environmental change depends on an accurate determination of the mean of the soil properties at each monitoring event. Forest soil is known to be very variable spatially, however. A study was undertaken to explore and quantify this variability at three forest monitoring plots in Britain. Detailed soil sampling was carried out, and the data from the chemical analyses were analysed by classical statistics and geostatistics. An analysis of variance showed that there were no consistent effects from the sample sites in relation to the position of the trees. The variogram analysis showed that there was spatial dependence at each site for several variables and some varied in an apparently periodic way. An optimal sampling analysis based on the multivariate variogram for each site suggested that a bulked sample from 36 cores would reduce error to an acceptable level. Future sampling should be designed so that it neither targets nor avoids trees and disturbed ground. This can be achieved best by using a stratified random sampling design.

Carbon↗
PubMed2005

Fast assignment of 15N-HSQC peaks using high-resolution 3D HNcocaNH experiments with non-uniform sampling.

We describe an efficient NMR triple resonance approach for fast assignment of backbone amide resonance peaks in the 15N-HSQC spectrum. The exceptionally high resolutions achieved in the 3D HncocaNH and hNcocaNH experiments together with non-uniform sampling facilitate error-free sequential connection of backbone amides. Data required for the complete backbone amide assignment of the 56-residue protein GB1 domain were obtained in 14 h. Data analysis was vastly streamlined using a 'backbone NH walk' method to determine sequential connectivities without the need for 13C chemical shifts comparison. Amino acid residues in the sequentially connected NH chains are classified into two groups by a simple variation of the NMR pulse sequence, and the resulting 'ZeBra' stripe patterns are useful for mapping these chains to the protein sequence. In addition to resolving ambiguous assignments derived from conventional backbone experiments, this approach can be employed to rapidly assign small proteins or flexible regions in larger proteins, and to transfer assignments to mutant proteins or proteins in different ligand-binding states.

Isotope Labeling↗
PubMed1993

Modeling vehicle accidents and highway geometric design relationships.

The statistical properties of four regression models--two conventional linear regression models and two Poisson regression models--are investigated in terms of their ability to model vehicle accidents and highway geometric design relationships. Potential limitations of these models pertaining to their underlying distributional assumptions, estimation procedures, functional form of accident rate, and sensitivity to short road sections, are identified. Important issues, such as the treatment of vehicle exposure and traffic conditions, and data uncertainties due to sampling and nonsampling errors, are also discussed. Roadway and truck accident data from the Highway Safety Information System (HSIS), a highway safety data base administered by the Federal Highway Administration (FHWA), have been employed to illustrate the use and the limitations of these models. It is demonstrated that the conventional linear regression models lack the distributional property to describe adequately random, discrete, nonnegative, and typically sporadic vehicle accident events on the road. As a result, these models are not appropriate to make probabilistic statements about vehicle accidents, and the test statistics derived from these models are questionable. The Poisson regression models, on the other hand, possess most of the desirable statistical properties in developing the relationships. However, if the vehicle accident data are found to be significantly overdispersed relative to its mean, then using the Poisson regression models may overstate or understate the likelihood of vehicle accidents on the road. More general probability distributions may have to be considered.

Accidents, Traffic↗
PubMed1996

Quantitation of protein, creatinine, and urea in urine by near-infrared spectroscopy.

OBJECTIVES: To determine the feasibility of near-infrared analysis for quantitating urea, creatinine, and protein in urine. Practical advantages of this method include ease of sample presentation and the absence of reagents or disposables. DESIGN AND METHODS: The near-infrared methods were developed by first measuring the spectra of 123 different urine samples and, using independent clinical analyses, determining the protein, creatinine, and urea levels in each. Calibration models relating near-infrared spectroscopic features to those independently determined concentrations were optimized, and each model then validated using a set of 50 additional samples. RESULTS: Standard errors of calibration were 14.4 mmol/L, 0.66 mmol/L, and 0.20 g/L, and standard errors of prediction 16.6 mmol/L, 0.79 mmol/L, and 0.23 g/L, respectively, for urea, creatinine, and protein. CONCLUSIONS: Near-infrared urea quantitation is as accurate as the reference method, enzymatic (urease) conductivity, used here for calibration. Creatinine analysis is slightly less accurate relative to the reference (Jaffe rate) method; however, these errors can be minimized by careful attention to factors affecting precision. The accuracy of the near-infrared protein analysis cannot approach that of the reference method; nevertheless, the technique is potentially useful for coarse screening and for quantifying protein levels above 0.3 g/L.

Calibration↗
PubMed1985

Detection by HPLC-EC of primary amines recovered in aqueous push-pull perfusates from cat cuneate nucleus.

A method is described for the quantitative detection of primary amines - particularly free amino acids - recovered in aqueous push-pull perfusates obtained from the cat cuneate nucleus. Isoindole derivatives of primary amine groups are formed by precolumn reaction with o-phthalaldehyde and mercaptoethanol. Derivatized sample components are separated and detected using HPLC with electrochemical detection. Of 22 amino acids standards studied individually, 12 were detectable under the conditions described. Variability of elution times and detector output peak heights were less than 2% and less than 10%, respectively. Concentration curves were linear to the 10 picomole order of magnitude. For cuneate nucleus perfusates, samples recovered during continuous peripheral somatosensory stimulation contained detectable derivative levels elevated above those of control samples. Sources of error in data interpretation are discussed.

Amino Acids↗