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Biomedical subjects

P D Bridge

Publications and source records attributed to P D Bridge.

At least 37 records · Page 2Linked to original sources

Increasing physicians' awareness of the impact of statistics on research outcomes: comparative power of the t-test and and Wilcoxon Rank-Sum test in small samples applied research.

To effectively evaluate medical literature, practicing physicians and medical researchers must understand the impact of statistical tests on research outcomes. Applying inefficient statistics not only increases the need for resources, but more importantly increases the probability of committing a Type I or Type II error. The t-test is one of the most prevalent tests used in the medical field and is the uniformally most powerful unbiased test (UMPU) under normal curve theory. But does it maintain its UMPU properties when assumptions of normality are violated? A Monte Carlo investigation evaluates the comparative power of the independent samples t-test and its nonparametric counterpart, the Wilcoxon Rank-Sum (WRS) test, to violations from population normality, using three commonly occurring distributions and small sample sizes. The t-test was more powerful under relatively symmetric distributions, although the magnitude of the differences was moderate. Under distributions with extreme skews, the WRS held large power advantages. When distributions consist of heavier tails or extreme skews, the WRS should be the test of choice. In turn, when population characteristics are unknown, the WRS is recommended, based on the magnitude of these power differences in extreme skews, and the modest variation in symmetric distributions.

Epidemiologic Studies↗

Measurement of airway resistance using the interrupter technique in preschool children in the ambulatory setting.

This study describes the feasibility, repeatability, and interrater reliability of the measurement of airway resistance by the interrupter technique (Rint) in children 2-5 yrs of age, and examines whether reversibility to bronchodilator can be demonstrated in wheezy children. The mean of six Rint values was taken as a measurement. If subjects could complete one measurement and then a second 15 min after bronchodilator, baseline testing and reversibility testing were considered feasible. To measure repeatability, two measurements 30 s apart and measurements before and 15 min after placebo bronchodilator were compared. Measurements by two testers were compared for interrater reliability. Change in Rint in wheezy children was measured after bronchodilator. Fifty-six per cent of 2-3-yr-olds (n=79), 81% of 3-4-yr-olds (n=104) and 95% of 4-5-yr-olds (n=88) completed baseline testing, and 53%, 71% and 91% completed reversibility testing. Baseline measurements were 0.47-2.56 kPa x L(-1) x s. Repeatabilities (2 SD of the mean differences between measurements) at 30 s in the three age bands were 0.21, 0.17 and 0.15 kPa x L(-1) x s and 0.19 kPa x L(-1) x s after placebo. Using 0.21 kPa x L(-1) x s as the threshold for reversibility, reversibility was demonstrated in most wheezy children. Interrater reliability was 0.15 kPa x L(-1) x s. Preschool children can undertake measurements of airway resistance by the interrupter technique in ambulatory settings and reversibility to bronchodilator in wheezy children can be demonstrated. This technique promises to be a useful clinical and research tool.

Airway Resistance↗

Presence of a 20 bp insertion/deletion in the ITS1 region of Verticillium lecanii.

Polymerase chain reaction (PCR) amplification of the complete ribosomal RNA internally transcribed spacer (ITS) region of 36 isolates of Verticillium lecanii and related species gave a single 620 bp product in 31 isolates. Five isolates received as V. lecanii, however, gave a single product of 600 bp. Restriction fragment analysis of the PCR products from all isolates gave consistent patterns for the 31 isolates with a 620 bp product. The five isolates with the 600 bp product showed only minor discrepancies to these, generally related to the size of only one restriction fragment. The total ITS region was sequenced from 10 typical 620 bp isolates and one 600 bp isolate. Sequence variation between the isolates varied from 0 to 14.5%, and the 20 bp size discrepancy was found to relate to an insertion or deletion in the centre of the ITS1 region.

Base Sequence↗

Physiological and biochemical characterization of Trichoderma harzianum, a biological control agent against soilborne fungal plant pathogens.

Monoconidial cultures of 15 isolates of Trichoderma harzianum were characterized on the basis of 82 morphological, physiological, and biochemical features and 99 isoenzyme bands from seven enzyme systems. The results were subjected to numerical analysis which revealed four distinct groups. Representative sequences of the internal transcribed spacer 1 (ITS 1)-ITS 2 region in the ribosomal DNA gene cluster were compared between groups confirming this distribution. The utility of the groupings generated from the morphological, physiological, and biochemical data was assessed by including an additional environmental isolate in the electrophoretic analysis. The in vitro antibiotic activity of the T. harzianum isolates was assayed against 10 isolates of five different soilborne fungal plant pathogens: Aphanomyces cochlioides, Rhizoctonia solani, Phoma betae, Acremonium cucurbitacearum, and Fusarium oxysporum f. sp. radicis lycopersici. Similarities between levels and specificities of biological activity and the numerical characterization groupings are both discussed in relation to antagonist-specific populations in known and potential biocontrol species.

Antibiosis↗

A portable device based on the interrupter technique to measure bronchodilator response in schoolchildren.

A new device for measuring airway resistance following brief airflow interruption (Microlab 4000; Micromedical Ltd, UK) was evaluated in 25 asthmatic school children in comparison with well-established methods. Airway resistance was measured during brief airflow interruption (Rint), before and after administration of salbutamol 200 micrograms by metered-dose inhaler, and in the spirometric parameters, forced expiratory volume in one second (FEV1) and peak expiratory flow (PEF), and total respiratory system resistance at 6 Hz (Rrs,6) measured by the forced oscillation technique (FOT). The sensitivity index (SI) (mean change/baseline standard deviation) was calculated for each subject. At baseline, interrupter conductance, the reciprocal of Rint, correlated well with FEV1 (r = 0.837; p < 0.001) and PEF (r = 0.773; p < 0.001), and Rint correlated highly with Rrs,6 (r = 0.942; p < 0.001). The median intrasubject coefficient of variation of the interrupter method was higher than the FOT or either spirometric parameter; Rint 11%, Rrs,6 9%, FEV1 5% and PEF 5%. However, the sensitivity to detect change after bronchodilator, expressed as the median SI, did not differ significantly between measurements: Rint 3.5, Rrs,6 3.6, FEV1 2.4 and PEF 3.0. A significant response (SI > 2) was shown by the interrupter in 22 of the subjects compared with 16 by FEV1. The interrupter technique is useful for assessing changes in airway calibre in asthmatic school children, with a sensitivity at least as good as standard methods. Such a device could be of particular value in those too young to perform spirometry.

Airway Resistance↗

Rapid mitochondrial probes for analysis of polymorphisms in Fusarium oxysporum special forms.

A method is described for the production of simple mitochondrial DNA probes from filamentous fungi for the partial characterization of mitochondrial DNA without the need for cloning, gradient centrifugation or PCR amplification. A probe (P449) consisting of a 3.38 kb mitochondrial fragment from an isolate of Fusarium oxysporum special form cubense was used to determine RFLPs in restriction digests of total DNA from 28 isolates of F. oxysporum from a variety of hosts and locations. The probe showed mtDNA polymorphisms within and between different special forms.

Blotting, Southern↗

Pneumocystis carinii shows DNA homology with the ustomycetous red yeast fungi.

Pneumocystis carinii causes life-threatening pneumonia in T-lymphocyte-immunodeficient subjects in transplant and oncology units or with acquired immune deficiency syndrome (AIDS). Recent DNA homology studies show P. carinii to be a fungus. To investigate the biology and epidemiology of this parasite further, we elected to determine for it a more precise taxonomic assignment within the fungal kingdom. We screened a wide range of organisms representing the major orders of fungi using DNA amplification and subsequently sequenced a portion of the mitochondrial gene encoding the large subunit ribosomal RNA. Our data show that the opportunistic pulmonary pathogen P. carinii is closely related to the ustomycetous red yeast fungi, a group which includes organisms that are extensively distributed throughout the environment and which release many widely dispersed airborne spores.

Animals↗

An integrated approach to Phoma systematics.

Physiological and morphological characters were recorded from 55 strains of 17 Phoma taxa and one Pyrenochaeta. The results were subjected to numerical analysis and UPGMA dendrograms produced. The full results were compared with TLC profiles of secondary metabolites. Seven distinct clusters were recovered from dendrograms based on full and partial character sets and the grouping of strains within each cluster discussed. The new combination Phoma sambuci-nigrae (Sacc.) Monte, Bridge & Sutton is proposed for P. herbarum f. sambuci-nigrae Sacc.

Animals↗

Stability of classification of filamentous fungi under changes in character coding strategy.

The characteristics of a number of filamentous fungal cultures were obtained from two previously published numerical taxonomic studies on Penicillium and Phoma. The coding strategies for some of the physiological and morphological properties employed in the original studies were re-examined and the data was re-coded by combining sets of characters into single ordered multistate characters. The different coding procedures were compared by generating average linkage (UPGMA) dendrograms which were in turn compared by calculating correlation coefficients between the final similarity matrices implied by these dendrograms. The character conversions had no significant effect on the final outcome of the clustering.

Mitosporic Fungi↗

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. I. Numerical taxonomy.

Three-hundred-and-forty-eight strains representing the major species of terverticillate penicillia, and including representatives of other closely and distantly related species, were included in a numerical taxonomic study. One-hundred characters were derived from morphological features, physiological and biochemical activities and SEM micrographs. Strains were compared by both Gower's coefficient and Pattern difference, and clustered using the average linkage algorithm. Thirty-seven species or species-complex clusters were recovered at approximately 70% similarity; they generally corresponded to existing taxonomic concepts. Several species were shown to contain variants or chemotypes which were often supported by differences in conidial shape and ornamentation. The use of different types of characters enabled a number of new and previously accepted species to be shown to be either variants or deteriorated examples of other species. Variation in properties both between and within species was considered, particularly in relation to strain stability.

Cluster Analysis↗

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. II. Identification.

The data from an integrated numerical classification was used to construct identification schemes for some fasciculate penicillia. The identification schemes were presented as a synoptic key and a frequency matrix for computer-assisted identification. Statistical testing of the frequency matrix showed that although character separation values were generally low, only four pairs of taxa showed overlap greater than that expected for a rectangular distribution. The identification schemes were tested practically with 52 previously studied strains and 51 further cultures. A synoptic key based on 10 and 90% cutoff limits was used to correctly identify 44 of the 51 additional strains, although this proved very sensitive to single test discrepancies. The frequency matrix was used to correctly identify 45 of the additional strains with a Willcox probability score and this was compared to identifications based on the modal likelihood fraction.

Numerical Analysis, Computer-Assisted↗

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. III. An evaluation of pectinase and amylase isoenzymes for species characterization.

Polyacrylamide gel electrophoresis of extracellular pectinase and amylase isozymes of 170 mainly terverticillate Penicillium strains was undertaken. The data were coded and subjected to numerical analysis. Variation in intensity of isozymes was observed in repeat analyses of some strains, although most were consistent. Variation was also observed between some representative strains of species. P. viridicatum was more variable than P. brevicompactum and P. hordei for intensity of pectinase activity. There was a correlation between the grouping of the strains on the basis of the isozymes and the species concepts only in some cases. The method proved useful for the identification of strains producing intense activity which provided clear patterns, for example, P. brevicompactum and P. chrysogenum and to a lesser extent P. solitum var. crustosum and P. hordei. The method was also exclusionary in that some species were restricted to a particular cluster or subcluster. Amylase patterns confirmed that strains referred to as single species are not all homogeneous genetically, and that some strains are not simply haploid homokaryons. The genetic heterogeneity of the strains explains some of the problems in the systematics of the terverticillate penicillia.

Amylases↗

Investigation of variation in phenotype and DNA content between single-conidium isolates of single Penicillium strains.

Variation in phenotypic properties was examined in three strains of closely related fasciculate species of Penicillium using 114 morphological, physiological, and biochemical characters. Thirty-six of these characters showed variation within single-conidium isolates of the same strain. Conidial sizes and nuclear DNA contents were compared using flow microfluorimetry; these results suggested that significant differences in conidial DNA content are associated with phenotypic variation. The taxonomic significance of the results is discussed.

DNA, Fungal↗

Source and avoidance of the "nothing dehydrogenase" effect, a spurious band produced during polyacrylamide gel electrophoresis of dehydrogenase enzymes from yeasts.

During a study of the distribution of several NAD-linked dehydrogenase enzymes in various yeasts, in which polyacrylamide gel electrophoresis, followed by activity staining with phenazine methosulfate and a tetrazolium was used, a band was frequently detected, the production of which appeared to be independent of any added substrate (the "nothing dehydrogenase" effect). It has been shown that this effect is caused by alcohol dehydrogenase acting on traces of ethanol inadvertently introduced into the system. Two sources of ethanol were identified. They were (i) the enzyme extracts, which could be freed from ethanol by gel filtration, and (ii) the acrylamide used to prepare the gel, which could be freed from ethanol by recrystallization from ethanol-free chloroform. It is suggested that the use of commercial chloroform (stabilized with ethanol) as a recrystallizing solvent is the source of ethanol contamination in commercial preparations of acrylamide.

Acrylamide↗

Problems and prospects for the taxonomy of Penicillium.

Classification of the economically important sections of the genus Penicillium requires clarification as species concepts based primarily on morphology differ. A multidisciplinary study using physiological characters, biochemistry of metabolites, ultrastructure, and traditional morphology has been initiated. The results will be subjected to cluster analysis techniques.

Multivariate Analysis↗

Numerical taxonomy of Streptococcus.

A numerical taxonomic study of strains of Streptococcus, together with representatives of allied genera, showed 28 reasonably distinct phenons. The major areas, with their phenons, were: (a) enterococcal species group (S. faecalis, S. faecium, 'S. avium' and a proposed new species 'S. gallinarum'); (b) paraviridans species group (S. bovis, S. equinus, S. salivarius, 'S. casseliflavus', S. mutans, S. raffinolactis and an unidentified Oral Group I); (c) lactic species group (S. lactis including S. cremoris); (d) thermophilic species group (S. thermophilus); (e) viridans species group (S. mitis, S. sanguis, a proposed new species 'S. oralis' and 'S. milleri'); (f) pyogenic species group (S. agalactiae, S. pyogenes, S. equi, 'S. equisimilis' including 'S. zooepidemicus, and a cluster of Lancefield Group B strains of human origin); (g) parapyogenic species group (S. uberis, 'S. dysgalactiae', and a cluster of strains of Lancefield Groups R, S and T). Species of Aerococcus, Gemella, Leuconostoc and Pediococcus are very closely related to the streptococci.

Enterococcus faecalis↗