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At least 127 records · Page 7Linked to original sources
PubMed1994

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.

The ratio of expected variance to mean, R(t), of numbers of DNA base substitutions for contemporary sequences related by a "star" phylogeny is widely seen as a measure of the adherence of the sequences' evolution to a Poisson process with a molecular clock, as predicted by the "neutral theory" of molecular evolution under certain conditions. A number of estimators of R(t) have been proposed, all predicted to have mean 1 and distributions based on the chi 2. Various genes have previously been analyzed and found to have values of R(t) far in excess of 1, calling into question important aspects of the neutral theory. In this paper, I use Monte Carlo simulation to show that the previously suggested means and distributions of estimators of R(t) are highly inaccurate. The analysis is applied to star phylogenies and to general phylogenetic trees, and well-known gene sequences are reanalyzed. For star phylogenies the results show that Kimura's estimators ("The Neutral Theory of Molecular Evolution," Cambridge Univ. Press, Cambridge, 1983) are unsatisfactory for statistical testing of R(t), but confirm the accuracy of Bulmer's correction factor (Genetics 123: 615-619, 1989). For all three nonstar phylogenies studied, attained values of all three estimators of R(t), although larger than 1, are within their true confidence limits under simple Poisson process models. This shows that lineage effects can be responsible for high estimates of R(t), restoring some limited confidence in the molecular clock and showing that the distinction between lineage and molecular clock effects is vital.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of Variance↗
PubMed1985

Statistical analysis of growth limitations in Paracoccus denitrificans: an experiment with a completely randomized two-way factorial design with replications.

Cultivation of microorganisms under growth limitation is a widely used technique in microbiology. The relevant investigations, though seemingly based on straightforward experiments, have generated conflicting results, e.g., concerning molar growth yields. The purpose of this paper is to show that discrepancies in the literature could be solved if more attention were paid to methodology, especially statistics. New experimental results, concerning growth limitations in Paracoccus denitrificans, will exemplify this. They include the following items. Two limitations, one of them being succinate limitation, were established in the present study. Molar growth yields on succinate were 41 g X mol-1 for succinate limitation (95% confidence limits were 38 and 44) and 32 g X mol-1 for the other limitation (95% confidence limits were 29 and 35). The latter result is compatible with sulphate limitation, but the present experimental design does not really permit this conclusion.

Analysis of Variance↗
PubMed1997

Frequencies of the defective CYP2C19 alleles responsible for the mephenytoin poor metabolizer phenotype in various Oriental, Caucasian, Saudi Arabian and American black populations.

The 4'-hydroxylation of S-mephenytoin is polymorphic in man. The poor metabolizer (PM) phenotype exhibits a lower frequency in Caucasians (2-5%) compared to Oriental populations (13-23%). Previous studies from our laboratory have described two mutations (CYP2C19m1 and CYP2C19m2) which account for approximately 100% of Oriental and approximately 85% of Caucasian PM alleles. The present study examined whether the genotype predicted the phenotype in Japanese, Filipino and Saudi Arabian populations, and compared the frequencies of the defective CYP2C19 alleles in these populations with those found in European-Americans, Chinese-Taiwanese, and African-Americans from North Carolina. Among 53 Japanese, 15% were PMs and among 52 Filipinos 23% were PMs. Among 97 Saudi Arabians, only two were PMs. There was a complete concordance between genotype and phenotype in all three populations. The incidence of CYP2C19m1 was 0.23 (95% confidence limits 0.15-0.31) in Japanese, 0.39 (95% confidence limits 0.29-0.48) in Filipinos, 0.32 (95% confidence limits 0.26-0.38) in Chinese-Taiwanese, 0.15 (95% confidence limits 0.10-0.20) in Saudi Arabians, 0.13 (95% confidence limits 0.08-0.17) in European-Americans, and 0.25 in African-Americans from North Carolina (95% confidence limits (0.14-0.31). The incidence of CYP2C19m1 in Saudi Arabians was similar to that found in European-Americans, and significantly lower than that found in Oriental populations or African-Americans (p < 0.05). CYP2C19m2 was not found in European-Americans, Saudi Arabians or African-Americans (95% confidence limits 0-0.014). The incidence of CYP2C19m2 in the three Oriental populations ranged from 0.10 (95% confidence limits 0.05-0.17) in Japanese and 0.08 (95% confidence limits 0.03-0.13) in Filipinos to 0.06 (95% confidence limits 0.03-0.08) in Chinese-Taiwanese.

Alleles↗
PubMed2005

Survival, Pb-uptake and behaviour of three species of earthworm in Pb treated soils determined using an OECD-style toxicity test and a soil avoidance test.

Mature (clitellate) Eisenia andrei Bouché (ultra epigeic), Lumbricus rubellus Hoffmeister (epigeic), and Aporrectodea caliginosa (Savigny) (endogeic) earthworms were placed in soils treated with Pb(NO(3))(2) to have concentrations in the range 1,000 to 10,000 mg Pb kg(-1). After 28 days LC50(-95%confidence limit)(+95%confidence limit) values were E. andrei 5824(-361)(+898) mg Pb kg(-1), L. rubellus 2867(-193)(+145) mg Pb kg(-1) and A. caliginosa2747(-304)(+239) mg Pb kg(-1) and EC50s for weight change were E. andrei2841(-68)(+150) mg Pb kg(-1), L. rubellus1303(-201)(+240) mg Pb kg(-1) and A. caliginosa1208(-206)(+212) mg Pb kg(-1). At any given soil Pb concentration, Pb tissue concentrations after 28 days were the same for all three earthworm species. In a soil avoidance test there was no difference between the behaviour of the different species. The lower sensitivity to Pb exhibited by E. andrei is most likely due to physiological adaptations associated with the modes of life of the earthworms, and could have serious implications for the use of this earthworm as the species of choice in standard toxicological testing.

Adaptation, Physiological↗
PubMed1994

Fludarabine improves the therapeutic ratio of radiotherapy in mouse tumors after single-dose irradiation.

PURPOSE: Fludarabine, an adenine nucleoside analogue, and an effective inhibitor of chromosome repair, was previously shown to synergistically enhance radiation-induced regrowth delay in three murine tumors. The purpose of this study was to assess whether fludarabine can increase the therapeutic ratio of radiotherapy in murine tumors, that is, to increase local tumor control without significantly modifying the radiation-induced normal tissue response. METHODS AND MATERIALS: Mice bearing 8-mm tumors in the right thigh (SA-NH sarcoma and MCA-K mammary carcinoma) were given 800 mg/kg fludarabine IP 3 h or 24 h before single doses of photon irradiation. Local tumor control was assessed by the TCD50 assay 100 days after treatment. Acute normal tissue toxicity was assessed in the skin (degree of epilation 30 days after irradiation) and in the jejunum (crypt regeneration assay), and late normal tissue toxicity was assessed by a leg contracture assay 120 days after treatment. RESULTS: In both tumors and with both drug schedules, fludarabine enhanced radiation-induced local tumor control (dose modification factors (DMF) of 1.24 (95% confidence limits 1.19-1.31) and 1.26 (95% confidence limits 1.20-1.32) for SA-NH, and 1.38 (95% confidence limits 1.25-1.50) and 1.35 (95% confidence limits 1.22-1.16) for MCA-K tumors). When given 3 h before radiation, fludarabine offered a slight protection from skin toxicity (DMF = 0.83, 95% confidence limits 0.77-0.86) but enhanced jejunum toxicity (DMF = 1.53). When fludarabine was given 24 h before irradiation, the reverse trend was observed (DMF = 1.11 (95% confidence limits 1.07-1.16) and 0.89, respectively). No enhancement of leg contracture was observed for either fludarabine schedule. CONCLUSION: The data presented here demonstrate that fludarabine can potentiate local tumor control induced by single-dose irradiation. While jejunum sensitization limited the relative effectiveness when fludarabine was administered 3 h before irradiation, a therapeutic ratio greater than one was always achieved when fludarabine was given 24 h before irradiation.

Animals↗
PubMed1994

Reproducibility of retinal nerve fiber layer evaluation by dynamics scanning laser ophthalmoscopy.

Scanning laser ophthalmoscopy is a laser-based image acquisition technique, which greatly improves the quality of the examination of the fundus and the retinal nerve fiber layer. To assess retinal nerve fiber layer imaging by scanning laser ophthalmoscopy and evaluate intra- and interobserver reproducibility in the classification of retinal nerve fiber layer defects, three independent observers evaluated on two separate occasions the videotaped images of 150 eyes of 80 consecutive patients with ocular hypertension or glaucoma. Ophthalmoscopy was performed using argon blue light (488 nm), confocal apertures of 3 to 1 mm, and 40-degree and 20-degree field angles. Of 150 eyes, 20 (13.3%) were excluded from the study because of the poor quality of the images (clinically significant cataract or myopic peripapillary atrophy). The retinal nerve fiber layer was evaluated qualitatively according to a standard classification: normal pattern, slit, wedge, and diffuse defects. Intraobserver reproducibility, evaluated by kappa statistic, was excellent (> or = 0.75): observer A = 0.78 (95% confidence limits, 0.67-0.88); observer B = 0.84 (95% confidence limits, 0.72-0.96); and observer C = 0.79 (95% confidence limits, 0.67-0.91). Interobserver reproducibility was also excellent in all cases: observers A-B = 0.84 (95% confidence limits, 0.71-0.98); observers A-C = 0.76 (95% confidence limits, 0.65-0.87); and observers B-C = 0.80 (95% confidence limits, 0.69-0.92). Kappa values ranged between 0.59 and 0.69 for intraobserver reproducibility and between 0.55 and 0.69 for interobserver reproducibility when using only those eyes in which abnormalities were noted by at least one observer.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2004

Lipid screening in HIV-infected veterans.

BACKGROUND: Lipid screening is recommended for patients taking protease inhibitors (PIs). METHODS: We examined data from the Veterans Administration Immunology Case Registry to assess lipid screening among HIV-infected veterans who received PIs for at least 6 consecutive months during 1999 and 2001. We estimated crude and adjusted associations between lipid screening and patient characteristics (age, gender, HIV exposure, and race/ethnicity), comorbidities (AIDS, cardiovascular disease, diabetes, hypertension, smoking, and hyperlipidemia), and facility characteristics (urban location, case management, guidelines, and quality improvement programs). RESULTS: Among 4065 patients on PIs, clinicians screened 2395 (59%) for lipids within 6 months of initiating treatment. Adjusting for patient characteristics, comorbidities, facility traits, and clustering, lipid screening was more common among patients who were cared for in urban areas (relative risk [RR] = 1.3, confidence limits: 1.0-1.5), diabetic (RR = 1.2, confidence limits: 1.1-1.3), or previously hyperlipidemic (RR = 1.4, confidence limits: 1.3-1.5) and less common among patients with a history of intravenous drug use (IVDU) (RR = 0.90, confidence limits: 0.79-1.0) or unknown HIV risk (RR = 0.85, confidence limits: 0.75-0.95). CONCLUSIONS: Six in 10 patients taking PIs receive lipid screening within 6 months of PI use. Systemic interventions to improve overall HIV quality of care should also address lipid screening, particularly among patients with unknown or IVDU HIV risk and those cared for in nonurban areas.

Adolescent↗