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R J Cook

Publications and source records attributed to R J Cook.

At least 91 records · Page 5Linked to original sources
PubMed1997

A logistic model for trend in 2 x 2 x kappa tables with applications to meta-analyses.

There recently has been an increased interest in examining the relationship between the baseline (control) risk of an adverse outcome and the magnitude of the treatment effect (Brand and Kragt, 1992, Statistics in Medicine 11, 2077-2082; Davey Smith, Song, and Sheldon, 1993, The British Medical Journal 306, 1367-1373; Senn, 1994, Statistics in Medicine 13, 293-294). To facilitate such an examination, we propose a logistic model in which the relationship between the treatment effect, as measured by the log odds ratio, and the baseline risk is specified parametrically. This procedure is founded on a product-binomial likelihood and generates maximum likelihood estimates of the baseline event rates and two parameters characterizing the trend in the treatment effect. We fit this model to data from a meta-analysis involving the treatment of women at risk of preterm labor and contrast our findings with those of an earlier analysis.

Biometry↗
PubMed1997

A logistic-bivariate normal model for overdispersed two-state Markov processes.

We describe a logistic-bivariate normal mixture model for a two-state Markov chain in which each individual makes transitions between states according to a subject-specific transition probability matrix. The use of the bivariate normal mixing distribution facilitates inferences regarding the correlation of the random effects and hence provides insight as to the nature of the subject-to-subject variability in the transition probabilities. Tests regarding the correlation can be based on likelihood ratio, score, or Wald statistics. Estimates of the transition intensities of a latent continuous time conditionally Markov process may also be computed. We illustrate this methodology by application to a parasitic infection field study and contrast our findings with those previously published on this data set.

Biometry↗
PubMed1996

Effect of calcium supplementation on pregnancy-induced hypertension and preeclampsia: a meta-analysis of randomized controlled trials.

OBJECTIVE: To review the effect of calcium supplementation during pregnancy on blood pressure, preeclampsia, and adverse outcomes of pregnancy. DATA SOURCE: We searched MEDLINE and EMBASE for 1966 to May 1994. We contacted authors of eligible trials to ensure accuracy and completeness of data and to identify unpublished trials. STUDY SELECTION: Fourteen randomized trials involving 2459 women were eligible. DATA EXTRACTION: Reviewers working independently in pairs abstracted data and assessed validity according to six quality criteria. DATA SYNTHESIS: Each trial yielded differences in blood pressure change between calcium supplementation and control groups that we weighted by the inverse of the variance. The pooled analysis showed a reduction in systolic blood pressure of -5.40 mm Hg (95% confidence interval [CI], -7.81 to -3.00 mm Hg; P<.001) and in diastolic blood pressure of -3.44 mm Hg (95% CI, -5.20 to -1.68 mm Hg; P<.001). The odds ratio for preeclampsia in women with calcium supplementation compared with placebo was 0.38 (95% CI, 0.22 to 0.65). CONCLUSIONS: Calcium supplementation during pregnancy leads to an important reduction in systolic and diastolic blood pressure and preeclampsia. While pregnant women at risk of preeclampsia should consider taking calcium, many more patient events are needed to confirm calcium's impact on maternal and fetal morbidity.

Blood Pressure↗
PubMed1996

Effects of dietary calcium supplementation on blood pressure. A meta-analysis of randomized controlled trials.

OBJECTIVE: To review the effect of supplemental calcium on blood pressure. DATA SOURCE: We searched MEDLINE and EMBASE for 1996 to May 1994. We contacted authors of eligible trials to ensure accuracy and completeness of data and to identify unpublished trials. STUDY SELECTION: We included any study in which investigators randomized people to calcium supplementation or placebo and measured blood pressure for at least 2 weeks. Fifty-six articles met the inclusion criteria, and 33 were eligible for analysis, involving a total of 2412 patients. DATA EXTRACTION: Two pairs of independent reviewers abstracted data and assessed validity according to six quality criteria. DATA SYNTHESIS: We calculated the differences in blood pressure change between the calcium supplementation group and the control group and pooled the estimates, with each trial weighted with the inverse of the variance using a random-effects model. Predictors of blood pressure reduction that we examined included method of supplementation, baseline blood pressure, and the methodological quality of the studies. The pooled analysis showed a reduction in systolic blood pressure of -1.27 mm Hg (95% confidence interval [CI], -2.25 to -0.29 mm Hg; P=.01) and in diastolic blood pressure of -0.24 mm Hg (95% CI, -0.92 to 0.44 mm Hg; P=.49). None of the possible mediators of blood pressure reduction explained differences in treatment effects. CONCLUSIONS: Calcium supplementation may lead to a small reduction in systolic but not diastolic blood pressure. The results do not exclude a larger, important effect of calcium on blood pressure in subpopulations. In particular, further studies should address the hypothesis that inadequate calcium intake is associated with increased blood pressure that can be corrected with calcium supplementation.

Blood Pressure↗
PubMed1996

Criteria for the evaluation of treatment planning systems.

Radiation treatment planning systems (RTPS) are evolving on a rapid and continual basis. After the evaluation of several commercial systems, we have developed a list of features we consider desirable in a product. The goal in the compilation of these criteria was a comprehensive worksheet which categorized the characteristics of RTPS into hardware (computer and peripheral devices), 2-D planning tools, 3-D planning tools, irregular field planning tools, and brachytherapy planning. With these distinctions, one can evaluate a system conforming to the specific planning needs, e.g., conformal therapy, dynamic therapy capabilities, or optimized remote afterloading brachytherapy, of a department. The rationales of the special requirements are provided for justification.

Brachytherapy↗
PubMed1996

Conservation of the 2,4-diacetylphloroglucinol biosynthesis locus among fluorescent Pseudomonas strains from diverse geographic locations.

The broad-spectrum antibiotic 2,4-diacetylphloroglucinol (PHL) is a major determinant in the biological control of a range of plant pathogens by many fluorescent Pseudomonas spp. A 4.8-kb chromosomal DNA region from Pseudomonas fluorescens Q2-87, carrying PHL biosynthetic genes, was used as a probe to determine if the PHL biosynthetic locus is conserved within PHL-producing Pseudomonas strains of worldwide origin. The phl gene probe hybridized with the genomic DNA of all 45 PHL-producing Pseudomonas strains tested, including well-characterized biocontrol strains from the United States and Europe and strains isolated from disease-suppressive soils from Switzerland, Washington, Italy, and Ghana. The PHL producers displayed considerable phenotypic and genotypic diversity. Two phenotypically distinct groups were detected. The first produced PHL, pyoluteorin, and hydrogen cyanide and consisted of 13 strains from almost all locations sampled in the United States, Europe, and Africa. The second produced only PHL and HCN and consisted of 32 strains from the U.S. and European soils. Analysis of restriction patterns of genomic DNA obtained after hybridization with the phl gene probe and cluster analysis of restriction patterns of amplified DNA coding for 16S rRNA (ARDRA) and randomly amplified polymorphic DNA (RAPD) markers indicated that the strains that produced both PHL and pyoluteorin were genetically highly similar. In contrast, there was more diversity at the genotypic level in the strains that produced PHL but not pyoluteorin. ARDRA analysis of these strains indicated two clusters which, on the basis of RAPD analysis, split into several subgroups with additional polymorphisms. In general, the occurrence of phenotypically and genotypically similar groups of PHL producers did not correlate with the geographic origin of the isolates, and highly similar strains could be isolated from diverse locations worldwide.

Antifungal Agents↗
PubMed1996

Coupled error spending functions for parallel bivariate sequential tests.

Sequential procedures are developed to facilitate marginal monitoring of bivariate response vectors in clinical trials. The general approach is based on an extension of the error spending function methodology of Lan and DeMets (1983, Biometrika 70, 659-663) and is sufficiently flexible that one may elect to fix the experimental type I error rate (Cook, 1994, Controlled Clinical Trials 15(3), 187-200) or the marginal type I error rates. Sample size calculations are described to ensure power requirements are satisfied for marginal tests of significance. Reformulating the procedures in terms of repeated confidence intervals (Jennison and Turnbull, 1989, Journal of the Royal Statistical Society, Series B 51, 305-361) lends added flexibility to the monitoring process. The developments are discussed in the context of responses with a bivariate normal distribution. Data from an asthma intervention trial are used for illustrative purposes.

Asthma↗
PubMed1996

Robust tests for treatment comparisons based on recurrent event responses.

Robust nonparametric tests are considered for use in longitudinal studies in which the response of interest is a recurrent event. The tests are robust in the sense that they do not rely on distributional assumptions regarding the processes generating the events. The methods we describe are presented in the context of a clinical trial with attention initially directed at the two-sample problem in which a single experimental treatment is compared to a control. We investigate a family of generalized pseudo-score statistics (Lawless and Nadeau, 1995, Technometrics 37, 158-168) in which weight functions may be chosen to generate tests sensitive to various types of departure from the null hypothesis that the mean functions for the treatment and control groups are identical. All tests we consider are evaluated by simulation with respect to the type I error rate and power under a variety of practical scenarios. An application involving data from a kidney transplant study illustrates these procedures. For trials with multiple treatment arms, we generalize these approaches and indicate test statistics appropriate for unstructured alternatives and tests based on linear contrasts of the treatment-specific mean functions. Extensions of this methodology for stratified designs are also indicated.

Antibodies↗
PubMed1996

Design considerations in crossover trials with a single interim analysis and serial patient entry.

A two-stage sequential design is presented to facilitate a single interim analysis in crossover trials with serial patient entry. The interim analysis is based on a linear statistic that combines data from individuals observed for only one treatment period with data from those observed for both periods (Cook, R. J., 1995, Biometrics 51, 932-945). The final analysis is based on the usual test statistic used in crossover trials. The size of this procedure is controlled by partitioning the experimental type I error rate over the two analyses and deriving the appropriate critical values. We investigate the design implications of adopting this procedure over the usual analysis for crossover trials by examining the necessary sample size inflation factors to maintain power, and indicate the expected savings in terms of the number of responses required. Data from a study designed to compare two antiemetic therapies for previously untreated chemotherapy patients (Osaba, D., et al., 1986, Clinical and Investigative Medicine 9, 225-231) are used to illustrate the procedure.

Antineoplastic Agents↗
PubMed1996

Interim monitoring of longitudinal comparative studies with recurrent event responses.

A method of interim monitoring is described for longitudinal comparative studies in which the outcome of interest is a recurrent event and treatment comparisons are based on expected numbers of events. The nonparametric methods described by Cook, Lawless, and Nadeau (1996, Biometrics 52, 116-130) are generalized to provide a robust estimate of the covariance matrix for a sequence of test statistics calculated over time. The error spending function methodology of Lan and DeMets (1983, Biometrika 70, 659-663) is adopted to control the experimental type I error rate. A simulation study indicates satisfactory frequency properties of this procedure for the moderate to large scale trials for which it is intended. Extensions of this approach to handle stratified designs and studies with multitype recurrent events are indicated. Data from a kidney transplant study (Cole et al., 1994, Transplantation 57, 60-67) are used for illustrative purposes.

Antilymphocyte Serum↗
PubMed1995

The design and analysis of randomized trials with recurrent events.

This paper describes a method for planning the duration of a randomized parallel group study in which the response of interest is a potentially recurrent event. At the design stage we assume patients accrue at a constant rate, we model events via a homogeneous Poisson process, and we utilize an independent exponential censoring mechanism to reflect loss to follow-up. We derive the appropriate study duration to ensure satisfaction of power requirements for the effect size of interest under a Poisson regression model. An application to a kidney transplant study illustrates the potential savings of the Poisson-based design relative to a design based on the time to the first event. Revised design criteria are also derived to accommodate overdispersed Poisson count data. We examine the frequency properties of two non-parametric tests recently proposed by Lawless and Nadeau for trials based on the above design criteria. In simulation studies involving homogeneous and non-homogeneous Poisson processes they performed well with respect to their type I error rate and power. Results from supplementary simulation studies indicate that these tests are also robust to extra-Poisson variation and to clustering in the event times, making these tests attractive in their generality. We illustrate both tests by application to data from a completed kidney transplant study.

Algorithms↗
PubMed1995

Enzymatic activities of rat liver cytosol 10-formyltetrahydrofolate dehydrogenase.

10-Formyltetrahydrofolate dehydrogenase (10-FTH-FDH: EC 1.5.1.6) catalyzes the NADP(+)-dependent oxidation of 10-formyltetrahydrofolate (10-HCO-H4PteGlu) to tetrahydrofolate (H4PteGlu) and CO2 and the NADP(+)-independent hydrolytic cleavage of 10-HCO-H4PteGlu to H4PteGlu and formate. 10-FTHFDH has a 485 amino acid domain at the C-terminus which is 46% identical to aldehyde dehydrogenase (ALDH: EC 1.2.1.3) and contains a conserved active site cysteine (Cys-707). 10-FTHFDH catalyzed NADP(+)-dependent oxidation of propanal and the hydrolysis of p-nitrophenyl acetate (pNPA) in a similar fashion to ALDH. Initial rate studies gave Km values of 46 and 636 microM, respectively, for NADP+ and propanal, while pNPA had a Km of 220 microM. Propanal was able to compete with 10-HCO-H4PteGlu for NADP(+)-dependent oxidation but had no effect on the NADP(+)-independent hydrolase reaction. N-Ethylmaleimide inhibited NADP(+)-dependent 10-HCO-H4PteGlu oxidation but only partially inhibited (65%) hydrolase activity. Disulfiram, a potent inhibitor of cytosolic ALDH, inhibited NADP(+)-dependent propanal oxidation by 10-FTHFDH. We propose that the dehydrogenase reaction of 10-FTHFDH has a mechanism which proceeds through thiohemiacetal and thioester intermediates, similar to that described for aldehyde dehydrogenase. 10-FTHFDH hydrolase activity was dependent on 2-mercaptoethanol and is probably an artifact of the assay system. The N-terminal domain of 10-FTHFDH shows identity to glycinamide ribonucleotide transformylase (EC 2.1.2.2) and contains a putative 10-HCO-H4PteGlu binding site but shows no GAR-TF activity. NADP(+)-dependent oxidation of 10-HCO-H4PteGlu by 10-FTHFDH was inhibited by the folate anti-metabolite, 5,10-dideazatetrahydrofolate, a known GAR-TF inhibitor.

Aldehydes↗
PubMed1995

Molecular mechanisms of defense by rhizobacteria against root disease.

Genetic resistance in plants to root diseases is rare, and agriculture depends instead on practices such as crop rotation and soil fumigation to control these diseases. "Induced suppression" is a natural phenomenon whereby a soil due to microbiological changes converts from conducive to suppressive to a soilborne pathogen during prolonged monoculture of the susceptible host. Our studies have focused on the wheat root disease "take-all," caused by the fungus Gaeumannomyces graminis var. tritici, and the role of bacteria in the wheat rhizosphere (rhizobacteria) in a well-documented induced suppression (take-all decline) that occurs in response to the disease and continued monoculture of wheat. The results summarized herein show that antibiotic production plays a significant role in both plant defense by and ecological competence of rhizobacteria. Production of phenazine and phloroglucinol antibiotics, as examples, account for most of the natural defense provided by fluorescent Pseudomonas strains isolated from among the diversity of rhizobacteria associated with take-all decline. There appear to be at least three levels of regulation of genes for antibiotic biosynthesis: environmental sensing, global regulation that ties antibiotic production to cellular metabolism, and regulatory loci linked to genes for pathway enzymes. Plant defense by rhizobacteria producing antibiotics on roots and as cohabitants with pathogens in infected tissues is analogous to defense by the plant's production of phytoalexins, even to the extent that an enzyme of the same chalcone/stilbene synthase family used to produce phytoalexins is used to produce 2,4-diacetylphloroglucinol. The defense strategy favored by selection pressure imposed on plants by soilborne pathogens may well be the ability of plants to support and respond to rhizosphere microorganisms antagonistic to these pathogens.

Journal Article↗
PubMed1995

Recombinant 10-formyltetrahydrofolate dehydrogenase catalyses both dehydrogenase and hydrolase reactions utilizing the synthetic substrate 10-formyl-5,8-dideazafolate.

10-Formyltetrahydrofolate dehydrogenase (EC 1.5.1.6) is a bifunctional enzyme, displaying both NADP(+)-dependent dehydrogenase activity for the formation of tetrahydrofolate and CO2, and NADP(+)-independent hydrolase activity for the formation of tetrahydrofolate and formate. A previous report [Case, Kaisaki and Steele (1988) J. Biol. Chem. 263, 1024-1027] claimed that dehydrogenase and hydrolase activities were products of separate cytosolic and mitochondrial forms of this enzyme. Here we report that recombinant 10-formyltetrahydrofolate dehydrogenase carries out both enzymic reactions, proving that a product of a single gene, i.e. one protein, not two, has both activities. The stable synthetic analogue 10-formyl-5,8-dideazafolate can substitute for the labile natural substrate, 10-formyltetrahydrofolate, in both reactions. This was shown with both native and recombinant rat liver enzyme. The Km values for 10-formyl-5,8-dideazafolate were half of those for 10-formyltetrahydrofolate in both the dehydrogenase and hydrolytic reactions. The Vmax, values were similar for both substrates. Both dehydrogenase and hydrolase reactions were dependent on the presence of 2-mercaptoethanol. The pH optima were 7.8 and 5.6 for the dehydrogenase and hydrolase reactions respectively, consistent with the presence of two active sites in the enzyme.

Enzyme Activation↗
PubMed1995

The number needed to treat: a clinically useful measure of treatment effect.

The relative benefit of an active treatment over a control is usually expressed as the relative risk, the relative risk reduction, or the odds ratio. These measures are used extensively in both clinical and epidemiological investigations. For clinical decision making, however, it is more meaningful to use the measure "number needed to treat." This measure is calculated on the inverse of the absolute risk reduction. It has the advantage that it conveys both statistical and clinical significance to the doctor. Furthermore, it can be used to extrapolate published findings to a patient at an arbitrary specified baseline risk when the relative risk reduction associated with treatment is constant for all levels of risk.

Cerebrovascular Disorders↗