Search PubMed⌕ Search

Biomedical subjects

R J Cook

Publications and source records attributed to R J Cook.

At least 55 records · Page 3Linked to original sources
PubMed1999

The utility of mixed-form likelihoods.

We highlight a feature of likelihood-based methods that provides flexibility in model formulation and inference. In particular, overall likelihoods that consist of likelihood contributions with different forms are considered. The particular forms may be predetermined by design criteria or may be selected based on features of the data. Inferences based on such mixed-form likelihoods are valid provided standard regularity conditions hold and the parameters of interest have the same interpretation in the various forms. The advantages of constructing overall likelihoods in this way are illustrated by applications involving the analysis of 2 x 2 x K tables and left-censored water quality data.

Biometry↗
PubMed1999

A mixed model for two-state Markov processes under panel observation.

Many chronic medical conditions can be meaningfully characterized in terms of a two-state stochastic process. Here we consider the problem in which subjects make transitions among two such states in continuous time but are only observed at discrete, irregularly spaced time points that are possibly unique to each subject. Data arising from such an observation scheme are called panel data, and methods for related analyses are typically based on Markov assumptions. The purpose of this article is to present a conditionally Markov model that accommodates subject-to-subject variation in the model parameters by the introduction of random effects. We focus on a particular random effects formulation that generates a closed-form expression for the marginal likelihood. The methodology is illustrated by application to a data set from a parasitic field infection survey.

Biometry↗
PubMed1999

International developments in abortion law from 1988 to 1998.

OBJECTIVES: In 2 successive decades since 1967, legal accommodation of abortion has grown in many countries. The objective of this study was to assess whether liberalizing trends have been maintained in the last decade and whether increased protection of women's human rights has influenced legal reform. METHODS: A worldwide review was conducted of legislation and judicial rulings affecting abortion, and legal reforms were measured against governmental commitments made under international human rights treaties and at United Nations conferences. RESULTS: Since 1987, 26 jurisdictions have extended grounds for lawful abortion, and 4 countries have restricted grounds. Additional limits on access to legal abortion services include restrictions on funding of services, mandatory counseling and reflection delay requirements, third-party authorizations, and blockades of abortion clinics. CONCLUSIONS: Progressive liberalization has moved abortion laws from a focus on punishment toward concern with women's health and welfare and with their human rights. However, widespread maternal mortality and morbidity show that reform must be accompanied by accessible abortion services and improved contraceptive care and information.

Abortion, Legal↗
PubMed1999

Validity assessment of the disabilities of arm, shoulder, and hand questionnaire (DASH) for patients with psoriatic arthritis.

OBJECTIVE: To determine whether patients' perception of their functional ability, as measured by the disabilities of arm, shoulder. and hand (DASH) questionnaire, correlates with clinical measures of articular status in patients with psoriatic arthritis (PsA). METHODS: Patients attending the University of Toronto Psoriatic Arthritis Clinic between June and August 1997 were asked to complete a DASH questionnaire during their visits. Clinical assessments were performed according to a standard protocol including number of actively inflamed joints, total number of damaged joints, and grip strength. Spearman rank correlations were used to examine the relationship between clinical measures and the DASH questionnaire. RESULTS: Fifty consecutive patients, 28 men and 22 women, (mean age 49.2 yrs, mean disease duration 13 yrs) were included. DASH scores correlated with clinical measures of upper extremity function including right grip strength (r = -0.47, CI -0.67, -0.21) and number of active joints in the upper limbs (r = 0.65, CI 0.46, 0.79). As expected, the correlation between DASH scores and total number of active joints (r = 0.40, CI 0.14, 0.61) was lower than that between DASH scores and number of active joints in the upper limbs. The DASH was unrelated to clinical damage. CONCLUSION: DASH is a valid instrument for assessing upper extremity function and inflammatory disease activity in patients with PsA.

Arm↗
PubMed1998

Identification of protein-arginine N-methyltransferase as 10-formyltetrahydrofolate dehydrogenase.

S-Adenosylmethionine:protein-arginine N-methyltransferase (EC 2.1.1. 23; protein methylase I) transfers the methyl group of S-adenosyl-L-methionine to an arginine residue of a protein substrate. The homogeneous liver protein methylase I was subjected to tryptic digestion followed by reverse phase high performance liquid chromatography (HPLC) separation and either "on-line" mass spectrometric fragmentation or "off-line" Edman sequencing of selected fractions. Data base searching of both the mass spectrometric and Edman sequencing data from several peptides identified the protein methylase as 10-formyltetrahydrofolate dehydrogenase (EC 1.5.1.6; Cook, R. J., Lloyd, R. S., and Wagner, C. (1991) J. Biol. Chem. 266, 4965-4973; Swiss accession number). This identification was confirmed by comparative HPLC tryptic peptide mapping and affinity chromatography of the methylase on the 5-formyltetrahydrofolate-Sepharose affinity gel used to purify the dehydrogenase. The purified rat liver methylase had approximately 33% of the 10-formyltetrahydrofolate dehydrogenase and 36% of the aldehyde dehydrogenase activity as compared with the recombinant dehydrogenase, which also had protein methylase I activity. Polyclonal antibodies against recombinant dehydrogenase reacted with protein methylase I purified either by polyacrylamide gel electrophoresis or 5-formyltetrahydrofolate affinity chromatography. In each instance there was only a single immunoreactive band at a molecular weight of approximately 106,000. Together, these results confirm the co-identity of protein-arginine methyltransferase and 10-formyltetrahydrofolate dehydrogenase.

Amino Acid Sequence↗
PubMed1998

Incidence of and risk factors for ventilator-associated pneumonia in critically ill patients.

BACKGROUND: Understanding the risk factors for ventilator-associated pneumonia can help to assess prognosis and devise and test preventive strategies. OBJECTIVE: To examine the baseline and time-dependent risk factors for ventilator-associated pneumonia and to determine the conditional probability and cumulative risk over the duration of stay in the intensive care unit. DESIGN: Prospective cohort study. SETTING: 16 intensive care units in Canada. PATIENTS: 1014 mechanically ventilated patients. MEASUREMENTS: Demographic and time-dependent variables reflecting illness severity, ventilation, nutrition, and drug exposure. Pneumonia was classified by using five methods: adjudication committee, bedside clinician's diagnosis, Centers for Disease Control and Prevention definition, Clinical Pulmonary Infection score, and positive culture from bronchoalveolar lavage or protected specimen brush. RESULTS: 177 of 1014 patients (17.5%) developed ventilator-associated pneumonia 9.0 +/- 5.9 days (median, 7 days [interquartile range, 5 to 10 days]) after admission to the intensive care unit. Although the cumulative risk increased over time, the daily hazard rate decreased after day 5 (3.3% at day 5, 2.3% at day 10, and 1.3% at day 15). Independent predictors of ventilator-associated pneumonia in multivariable analysis were a primary admitting diagnosis of burns (risk ratio, 5.09 [95% CI, 1.52 to 17.03]), trauma (risk ratio, 5.00 [CI, 1.91 to 13.11]), central nervous system disease (risk ratio, 3.40 [CI, 1.31 to 8.81]), respiratory disease (risk ratio, 2.79 [CI, 1.04 to 7.51]), cardiac disease (risk ratio, 2.72 [CI, 1.05 to 7.01]), mechanical ventilation in the previous 24 hours (risk ratio, 2.28 [CI, 1.11 to 4.68]), witnessed aspiration (risk ratio, 3.25 [CI, 1.62 to 6.50]), and paralytic agents (risk ratio, 1.57 [CI, 1.03 to 2.39]). Exposure to antibiotics conferred protection (risk ratio, 0.37 [CI, 0.27 to 0.51]). Independent risk factors were the same regardless of the pneumonia definition used. CONCLUSIONS: The daily risk for pneumonia decreases with increasing duration of stay in the intensive care unit. Witnessed aspiration and exposure to paralytic agents are potentially modifiable independent risk factors. Exposure to antibiotics was associated with low rates of early ventilator-associated pneumonia, but this effect attenuates over time.

Adult↗
PubMed1998

A role for jasmonate in pathogen defense of Arabidopsis.

To investigate the role of jasmonate in the defense of plants against fungal pathogens, we have studied a mutant of Arabidopsis, fad3-2 fad7-2 fad8, that cannot accumulate jasmonate. Mutant plants were extremely susceptible to root rot caused by the fungal root pathogen Pythium mastophorum (Drechs.), even though neighboring wild-type plants were largely unaffected by this fungus. Application of exogenous methyl jasmonate substantially protected mutant plants, reducing the incidence of disease to a level close to that of wild-type controls. A similar treatment with methyl jasmonate did not protect the jasmonate-insensitive mutant coi1 from infection, showing that protective action of applied jasmonate against P. mastophorum was mediated by the induction of plant defense mechanisms rather than by a direct antifungal action. Transcripts of three jasmonate-responsive defense genes are induced by Pythium challenge in the wild-type but not in the jasmonate-deficient mutant. Pythium species are ubiquitous in soil and root habitats world-wide, but most (including P. mastophorum) are considered to be minor pathogens. Our results indicate that jasmonate is essential for plant defense against Pythium and, because of the high exposure of plant roots to Pythium inoculum in soil, may well be fundamental to survival of plants in nature. Our results further indicate that the fad3-2 fad7-2 fad8 mutant is an appropriate genetic model for studying the role of this important signaling molecule in pathogen defense.

Journal Article↗
PubMed1998

Toward a successful multinational crop plant genome initiative.

Plant genome research is needed as the foundation for an entirely new level of efficiency and success in the application of genetics and breeding to crop plants and products from crop plants. Genetic improvements in crop plants beyond current capabilities are needed to meet the growing world demand not only for more food, but also a greater diversity of food, higher-quality food, and safer food, produced on less land, while conserving soil, water, and genetic resources. Plant biology research, which is poised for dramatic advances, also depends fundamentally on plant genome research. The current Arabidopsis Genome Project has proved of immediate value to plant biology research, but a much greater effort is needed to ensure the full benefits of plant biology and especially plant genome research to agriculture. International cooperation is critical, both because genome projects are too large for any one country and the information forthcoming is of benefit to the world and not just the countries that do the work. Recent research on grass genomes has revealed that, because of extensive senteny and colinearity within linkage groups that make up the chromosomes, new information on the genome of one grass can be used to understand the genomes and predict the location of genes on chromosomes of the other grasses. Genome research applied to grasses as a group thereby can increase the efficiency and effectiveness of breeding for improvement of each member of this group, which includes wheat, corn, and rice, the world's three most important sources of food.

Animals↗
PubMed1998

von Willebrand disease and its management in oral and maxillofacial surgery.

von Willebrand disease (vWD) is the most common of the hereditary disorders of coagulation. We describe the pathophysiology, diagnosis and the new simplified classification of the disorder and discuss the management of patients about to undergo dental procedures and maxillofacial surgery. Close collaboration between oral and maxillofacial surgeons and haematologists in the management of patients with vWD is essential.

Blood Loss, Surgical↗
PubMed1998

Radiological assessment in psoriatic arthritis.

Our objective was to compare the reliability and responsiveness of the original Steinbrocker's (OS), our modified Steinbrocker's (MS) and Larsen's (L) radiological scoring methods for detecting radiological change in psoriatic arthritis over time. Two sets of radiographs of the hands and feet at least 2 yr apart were selected from 68 patients. Films were randomly presented and scored independently by a rheumatologist (DDG) and a radiologist (DS), in a blinded fashion using all methods. The index of reliability was the intraclass coefficient (ICC) and the responsiveness was assessed using plots and regression analyses. All three radiological scoring methods have excellent interobserver and good intra-observer reliability. L and MS are equally responsive and superior to OS in detecting change in joint damage over time. Thus, the L or MS radiological scoring methods can be used to monitor disease progression in psoriatic arthritis.

Adult↗
PubMed1998

A seven-gene locus for synthesis of phenazine-1-carboxylic acid by Pseudomonas fluorescens 2-79.

Pseudomonas fluorescens 2-79 produces the broad-spectrum antibiotic phenazine-1-carboxylic acid (PCA), which is active against a variety of fungal root pathogens. In this study, seven genes designated phzABCDEFG that are sufficient for synthesis of PCA were localized within a 6.8-kb BglII-XbaI fragment from the phenazine biosynthesis locus of strain 2-79. Polypeptides corresponding to all phz genes were identified by analysis of recombinant plasmids in a T7 promoter/polymerase expression system. Products of the phzC, phzD, and phzE genes have similarities to enzymes of shikimic acid and chorismic acid metabolism and, together with PhzF, are absolutely necessary for PCA production. PhzG is similar to pyridoxamine-5'-phosphate oxidases and probably is a source of cofactor for the PCA-synthesizing enzyme(s). Products of the phzA and phzB genes are highly homologous to each other and may be involved in stabilization of a putative PCA-synthesizing multienzyme complex. Two new genes, phzX and phzY, that are homologous to phzA and phzB, respectively, were cloned and sequenced from P. aureofaciens 30-84, which produces PCA, 2-hydroxyphenazine-1-carboxylic acid, and 2-hydroxyphenazine. Based on functional analysis of the phz genes from strains 2-79 and 30-84, we postulate that different species of fluorescent pseudomonads have similar genetic systems that confer the ability to synthesize PCA.

Amino Acid Sequence↗
PubMed1998

HLA markers and progression in psoriatic arthritis.

OBJECTIVE: To investigate whether the addition of all serologically defined HLA antigens to a baseline model further influences the predisposition to disease progression in psoriatic arthritis (PsA). METHODS: Patients with PsA followed prospectively over 19 years were studied. Clinical and laboratory assessments of both active inflammation and clinical damage were performed at 6 month intervals according to a standard protocol. Progression of damage was defined as transition to higher damage states defined by the number of damaged joints. A model that provides estimates of the ratio of transition rates for an individual with the antigen versus one without, and examines the antigen effect on each of the 3 transition rates, was used. HLA antigens were examined in groups by loci under the assumption of common effects across transitions when added to the basic model. The significance levels were examined in comparison with Bonferroni type corrections. Likelihood ratio chi-squared statistics were used as a basis for the significance levels. In total, 292 patients with PsA were included in the study. RESULTS: Only HLA-B22 was added to the original model, which includes HLA-B39, providing risk for progression in early stages, HLA-B27 in the presence of HLA-DR7 providing risk for progression through all states, and DQw3 providing increased risk in the absence of DR7, while in the presence of DR7 it provides "protection." HLA-B22 provides protection from disease progression through all states. CONCLUSION: This study extends our report that HLA antigens serve as markers for disease progression in PsA.

Adolescent↗
PubMed1998

The use of sulfasalazine in psoriatic arthritis: a clinic experience.

OBJECTIVE: To assess the tolerability of sulfasalazine in a clinic setting and determine its longterm effectiveness with respect to articular disease and prevention of radiographic progression in patients with psoriatic arthritis (PsA). METHODS: Patients who were given sulfasalazine during their attendance at the University of Toronto Psoriatic Arthritis Clinic were enrolled in the study. For patients that were able to tolerate sulfasalazine for at least 3 months a matched control was identified who did not receive sulfasalazine. The primary outcome measures were the tolerability of sulfasalazine, clinical response of the actively inflamed joints at 6 and 12 months, and the change in radiographic score at 24 months. RESULTS: Thirty-six patients received sulfasalazine. Fourteen of 16 patients discontinued sulfasalazine due to one or more side effects occurring within 3 months of treatment initiation. For the remaining 20 patients, a 50% reduction in actively inflamed joint count was noted in 7/20 patients at 6 months and 11/15 patients at 12 months, compared to 7/19 patients in the control group at 6 months and 10/20 patients at 12 months. The mean change in the radiographic score at 24 months between the 2 groups was not statistically significant. CONCLUSION: Sulfasalazine was not well tolerated in patients with PsA in our clinic. For those able to tolerate sulfasalazine, there was no evidence of a treatment effect with respect to articular involvement. In addition, sulfasalazine does not appear to halt radiographic progression in PsA.

Adolescent↗
PubMed1998

Responsiveness of health status instruments to changes in articular status and perceived health in patients with psoriatic arthritis.

OBJECTIVE: To compare the responsiveness of the Health Assessment Questionnaire (HAQ), Arthritis Impact Measurement Scale 2 (AIMS2), and Medical Outcome Study Short Form Health Survey (SF-36) to changes in articular status and perceived health in outpatients with psoriatic arthritis (PsA). METHODS: The 3 health status instruments were administered in random order on 2 occasions, about 12-18 months apart, to 70 patients attending the University of Toronto psoriatic arthritis clinic. Standardized assessments of disease activity, disease severity, and general health perceptions were also performed at each clinic visit. To assess responsiveness we used: (1) linear regression analyses to relate change scores for perceived health, the number of actively inflamed, and damaged joints to change scores for selected dimensions of the HAQ, AIMS2, and SF-36; (2) logistic regression analyses to relate both improvement in disease activity and disease progression to health status change scores; and (3) standardized response means (SRM). RESULTS: There were 43 men and 27 women with a mean age of 46 years and arthritis duration of 13 years. Univariate regression analyses showed that the individual instruments were responsive to perceived changes in health, but relatively insensitive to detect changes in articular status. Multivariate regression analyses, in which the common dimensions of the instruments were jointly entered, indicated the SF-36 was equally or more responsive to changes in number of actively inflamed joints, clinical improvement in disease activity, and perceived health than the HAQ and AIMS2. The SRM analysis also suggested that the SF-36 was the most responsive. CONCLUSION: The SF-36 proved equally or more responsive to short term changes in perceived health and inflammatory disease activity; however, none of the instruments showed responsiveness to disease progression.

Adult↗
PubMed1997

Marginal analysis of recurrent events and a terminating event.

Chronic medical conditions are often manifested by the incidence of recurrent adverse clinical events. In clinical trials designed to investigate therapeutic interventions for such conditions it is natural to make treatment comparisons on the basis of event occurrence. However, when there is a more serious, possibly related, event that terminates the occurrence of the recurrent events, the problem of dependent censoring arises. Here, we consider robust modelling strategies for expressing covariate effects on the recurrent event process that address the possible dependence between the recurrent and terminal events. The various methods differ in the way the dependence is addressed, and hence in the interpretation of covariate effects. The methods are applied to a data set from a kidney transplant study and simulated data chosen for illustrative purposes.

Chronic Disease↗