Publications

Randomized controlled trials (RCTs) are one of the least biased sources of clinical research evidence, and are therefore a critical resource for the practice of evidence-based medicine. With over 10,000 new RCTs indexed in Medline each year, knowledge systems are needed to help clinicians translate evidence into practice. Common ontologies for RCTs and other domains would facilitate the development of these knowledge systems. However, no standard method exists for developing domain ontologies. In this paper, we describe a new systematic approach to specifying and evaluating the conceptual content of ontologies. In this method, called competency decomposition, the target task for an ontology is hierarchically decomposed into subtasks and methods, and the ontology content is specified by identifying the domain information required to complete each of the subtasks. We illustrate the use of this competency decomposition approach for the content specification and evaluation of an RCT ontology for evidence-based practice.

Platelet binding by Streptococcus gordonii strain M99 is strongly correlated with the expression of the large surface glycoprotein GspB. A 14 kb chromosomal region downstream of gspB was previously shown to be required for the expression of this protein. The region encodes SecA2 and SecY2, which are components of an accessory secretion system dedicated specifically to the export of GspB. The region also includes three genes (gly, nss and gtf) that encode proteins likely to function in carbohydrate metabolism, and four genes (orf1-4) that encode proteins of unknown function. In this report, we have investigated the role of these genes in GspB expression. We found that disruption of orf1, orf2 or orf3 resulted in a loss of GspB export and the intracellular accumulation of GspB. As they are apparently essential components of the accessory secretion system, these genes were renamed asp1-3 (for accessory secretory protein). In gtf and orf4 mutants, gspB was transcribed, but no GspB was detected. These results suggest that Gtf and Orf4 are required for the translation or for the stability of GspB. In contrast, gly and nss mutants were able to express and export GspB. However, disruption of these genes appeared to affect the carbohydrate composition of this glycoprotein. As asp1-3, gtf and orf4, but not gly and nss, are conserved in the accessory sec loci of several staphylococcal and streptococcal species, these genes may also have crucial roles in the expression and export of GspB homologues in the other Gram-positive bacteria.

Invasive fungal infections carry significant morbidity and mortality. Candida species have become one of the most frequent causes of bloodstream infections, and infections caused by molds such as Aspergillus are becoming more frequent in immunocompromised patients. As this population grows, more invasive fungal infections can be anticipated. In the past, treatment options have been limited for many of these infections due to toxicity and efficacy concerns with the available antifungals. Fortunately, the past few years have brought exciting developments in antifungal pharmacotherapy. Lipid-based formulations of amphotericin B were introduced in the 1990s to attenuate adverse effects caused by amphotericin B deoxycholate (Fungizone, Bristol-Myers Squibb). Most recently, the echinocandins have been added to our antifungal regimen with the introduction of caspofungin (Cancidas, Merck and Co.) and voriconazole (Vfend, Pfizer), a new triazole, has come to market. The introduction of the echinocandins has invigorated the discussion about combination antifungal therapy. Evidence-based studies using these new agents are accumulating, and they are assuming important roles in the pharmacotherapy of invasive fungal infections in seriously ill and complex patients.

The API 20 Strep system was used to speciate 46 enterococcal isolates with vancomycin MICs between 16-32 microg/mL. All were identified as Enterococcus faecium. Further testing revealed that 42/46 isolates had been identified incorrectly. Enterococci with low-level vancomycin resistance should not be speciated solely with the API 20 Strep system.

Although loricrin is the predominant protein of the cornified envelope (CE) in keratinocytes, loss or gain of loricrin function in mouse models produces only modest skin phenotypes. In contrast, insertional mutations resulting in a frameshift in the C-terminal domain of loricrin produce the characteristic ichthyosis of loricrin keratoderma in mouse and man. To ascertain the basis for the loricrin keratoderma phenotype, we assessed epidermal structure and stratum corneum (SC) function in a previously genotyped human loricrin keratoderma kindred. Our studies revealed abnormal corneocyte fragility and basal permeability barrier function, but accelerated repair kinetics. Despite fragility, increased water loss occurred predominantly via extracellular domains, which correlated with disorganized lamellar bilayers that were linked spatially to discontinuities of the CE. Accelerated barrier recovery was explicable by amplified lamellar body secretion, while partial normalization of the CE in the outer SC correlated with persistence of abundant calcium in the extracellular spaces (positioned to activate transglutaminase-1). These results show that the barrier abnormality in loricrin keratoderma is linked to a defective CE scaffold, resulting in increased extracellular permeability, as shown previously for another "scaffold disorder", lamellar ichthyosis. But in contrast to lamellar ichthyosis, the CE scaffold partially normalizes in the outer SC in loricrin keratoderma.

Peroxisome proliferator-activated receptor (PPAR) are nuclear hormone receptors that are activated by endogenous lipid metabolites. Previous studies have demonstrated that PPAR-alpha activation stimulates keratinocyte differentiation in vitro and in vivo, is anti-inflammatory, and improves barrier homeostasis. Recent studies have shown that PPAR-beta/delta activation induces keratinocyte differentiation in vitro. This study demonstrated that topical treatment of mice with a selective PPAR-beta/delta agonist (GW1514) in vivo had pro-differentiating effects, was anti-inflammatory, improved barrier homeostasis, and stimulated differentiation in a disease model of epidermal hyperproliferation [corrected]. In contrast to PPAR-alpha activation, PPAR-beta/deltain vivo did not display anti-proliferative or pro-apoptotic effects. The pro-differentiating effects persisted in mice lacking PPAR-alpha, but were decreased in mice deficient in retinoid X receptor-alpha, the major heterodimerization partner of PPAR. Furthermore, in vitro PPAR-beta/delta activation, aside from stimulating differentiation-related genes, additionally induced adipose differentiation-related protein (ADRP) and fasting induced adipose factor (FIAF) mRNA in cultures keratinocytes, which was paralleled by increased oil red O staining indicative of lipid accumulation, the bulk of which were triglycerides (TG). Comparison of differentially expressed genes between PPAR-beta/delta and PPAR-alpha activation revealed distinct profiles. Together, these studies indicate that PPAR-beta/delta activation stimulates keratinocyte differentiation, is anti-inflammatory, improves barrier homeostasis, and stimulates TG accumulation in keratinocytes.

STUDY OBJECTIVES

To compare kinds and amounts of health care used by adults with asthma in managed care and fee-for-service settings.

DESIGN

Cross-sectional structured telephone survey of Northern California adults with asthma from random samples of pulmonologists, allergist-immunologists, family practitioners, and from a random sample of the non-institutionalized population.

MEASUREMENTS

Validated measures of kind of health insurance plans, kinds and amounts of services used for asthma and other reasons, demographic characteristics, severity of asthma, comorbidity, and overall health and functional status.

RESULTS

Eighty one percent of the 416 adults with asthma studied were in some form of managed care (75% in HMOs and 6% in PPOs). Those in managed care (MC) and fee-for-service (FFS) did not differ substantively in the proportion with a regular source or principal provider of asthma care, with a peak flow meter or action plan, having received instructions in the use of an inhaler, reporting current use of inhaled beta-agonists, home nebulized beta-agonists, or inhaled steroids, or reporting ER visits or flu shots in the year prior to interview. Persons with asthma in MC reported significantly fewer total physician visits (after adjustment, 4.3 MC, 7.1 FFS, difference = 2.8, 95% CI -5.4, -0.1), principally because those in MC had many fewer visits to allergist-immunologists (after adjustment 4.9 MC, 21.4 FFS, difference = -16.5, 95% CI -27.8, -5.3). The two groups did not differ significantly in the proportion with asthma-related or nonasthma hospital admissions.

CONCLUSIONS

Persons with asthma in fee-for-service settings reported a greater number of certain kinds of ambulatory visits, particularly visits to allergist-immunologists, for their asthma than those in managed care, but did not differ in the use of the hospital for their asthma and in nonasthma care.

Proper management of chemotoxicity in transplant patients requires detailed knowledge of the biochemical mechanisms underlying immunosuppressant toxicity. Neurotoxicity is one of the most significant clinical side effects of the immunosuppressive undecapeptide cyclosporine, occurring at some degree in up to 60% of transplant patients. The clinical symptoms of cyclosporine-mediated neurotoxicity consist of decreased responsiveness, hallucinations, delusions, seizures, cortical blindness, and stroke-like episodes that mimic those clinical symptoms of mitochondrial encephalopathy. Clinical computed tomography (CT) and magnetic resonance imaging (MRI) studies have revealed a correlation between clinical symptoms of cyclosporine-mediated neurotoxicity and morphological changes in the brain, such as hypodensity of white matter, cerebral edema, metabolic encephalopathy, and hypoxic damages. Paradoxically, in animal models cyclosporine protects the brain from ischemia-reperfusion (I/R) injury. Interestingly, cyclosporine appears to mediate both neurotoxicity (under normoxic conditions) and I/R protection across the same range of drug concentration. Both toxicity and protection might arise from the intersection of cyclosporine with mitochondrial energy metabolism. This review addresses basic biochemical mechanisms of: 1) cyclosporine toxicity in normoxic brain, and 2) its protective effects in the same organ during I/R. The marked and unparallel potential of magnetic resonance spectroscopy (MRS) as a novel quantitative approach to evaluate metabolic drug toxicity is described.