Genetic Analysis of Victorin Sensitivity and Identification of a Causal Nucleotide-Binding Site Leucine-Rich Repeat Gene in Phaseolus vulgaris.

Cochliobolus victoria, the causal agent of Victoria blight, is pathogenic due to its production of a toxin called victorin. Victorin sensitivity in oats, barley, Brachypodium spp., and Arabidopsis has been associated with nucleotide-binding site leucine-rich repeat (NLR) genes, a class of genes known for conferring disease resistance. In this work, we investigated the sensitivity of Phaseolus vulgaris to victorin. We found that victorin sensivity in Phaseolus vulgaris is a developmentally regulated, quantitative trait. A single quantitative trait locus (QTL) accounted for 34% of the phenotypic variability in victorin sensitivity among Stampede × Red Hawk (S×R) recombinant inbred lines. We cloned two NLR-encoding genes within this QTL and showed one, Phvul05G031200 (PvLOV), confers victorin-dependent cell death when overexpressed in Nicotiana benthamiana. Protein sequences of PvLOV from victorin-sensitive and the victorin-resistant bean parents differ by two amino acids in the leucine-rich repeat region, but both proteins confer victorin-dependent cell death when overexpressed in N. benthamiana.

Precision and reproducibility of quantitative coronary angiography with applications to controlled clinical trials. A sampling study.

Most computer methods that quantify coronary artery disease from angiograms are designed to analyze frames recorded during the end-diastolic portion of the cardiac cycle. The purpose of this study was to determine if end diastole is the best portion of the cardiac cycle to sample, or if other sampling schemes produce more precise and/or reproducible estimates of coronary disease. 20 cinecoronary angiograms were selected at random from a controlled clinical trial testing the effects of plasma lipid lowering on atherosclerosis. Sampling schemes included sequential and random sampling of two to five frames within the complete cardiac cycle, systole, and diastole. Three vessel measures and percent stenosis were evaluated for each sampling scheme. From the sampling experiment, it was determined that sampling sequentially end diastole yielded the most precise estimates (i.e., exhibiting minimum variability within a cycle) of the vessel measures. With regard to reproducibility (i.e., similar values across cycles), sampling randomly within the cycle was best. Overall, the average diameter of a vessel segment was the most precise and the most reproducible of the measures. Sample size calculations are given for each of these measures under the best sampling scheme.

Cortical blindness after correction of symptomatic hyponatremia: dynamic cerebral dysfunction visualized using serial SPECT scanning.

A 70-yr-old woman developed cortical blindness after correction of hyponatremia. Regional hyperperfusion was noted on SPECT scans obtained in the acute phase. One month later when symptoms had largely resolved, a repeat examination was normal. This regional hyperperfusion, which was not associated with any apparent structural damage, may have represented either luxury perfusion or a transient increased metabolic requirement of the dysfunctional cortical area. SPECT scanning may be a useful method to study cerebral dysfunction resulting from an osmotic disturbance.

Immunopathology of acute experimental histoplasmic choroiditis in the primate.

The immunopathologic features of experimental acute histoplasmic choroiditis were studied in the nonhuman primate. Using an indirect immunoperoxidase technique, a panel of hybridoma-derived anti-human monoclonal antibodies, recognizing distinct lymphoid cell and macrophage surface antigens, have been adapted for use in the primate system. Twenty-two individual foci of histoplasmic choroiditis from five eyes were studied at time periods from 20 to 60 days post intracarotid injection of yeast phase Histoplasma capsulatum. A mononuclear and granulocytic cell infiltration was seen in all lesions. The predominant cell type was the CAPPEL+ T lymphocyte (suppressor/cytotoxic subset). Other cell types found in smaller numbers were OKT4+ T cells (helper/inducer subset), OK7+ (peripheral B lymphocytes), IgD+ (mantle B cells) and OKM1+ cells (macrophages and polymorphonuclear leukocytes). Herein, we present immunopathologic data on the acute phase of experimental ocular histoplasmosis.

Optimizing recovery of cytomegalovirus in the shell vial culture procedure.

We have investigated three factors that may be related to the recovery of cytomegalovirus (CMV) using the shell vial culture procedure. First, we compared fluorescent-antibody staining of shell vial cultures using a monoclonal antibody to a CMV immediate early antigen at 16 vs 40 hr after inoculation. Of 332 routinely submitted specimens cultured in duplicate and stained at the different times, 25 (7.5%) were positive at 16 hr and 32 (9.6%) were positive at 40 hr. The increased yield was 28%. Second, we analyzed the effect of using duplicate shell vials (both stained at 40 hr) for all routinely submitted CMV cultures. During a 6-month period, 272 (12.5%) of the 2157 cultures processed with duplicate shell vials were positive, including 222 positive in both vials and 50 positive in only one. Assuming that a single-vial setup would have detected 50% of those positive in only one of the two vials, the increased yield attributable to the duplicate vial was estimated at 10% (25/(222 + 25)). Third, we investigated the effects of seeding density and culture age on the shell vial assay. Cell age of greater than 1 day was associated with a decrease in sensitivity both in cultures that were confluent and in those that were subconfluent at the time of inoculation. Incorporating these findings in the routine shell vial culture procedure used in our Clinical Virology Laboratory has resulted in a greater overall detection of CMV in shell vial cultures than in conventional 6-week tube cultures.

Comparative laboratory diagnosis of experimental herpes simplex keratitis.

We compared two commercially available tests, a direct immunofluorescence assay and an enzyme-linked immunosorbent assay (ELISA), to viral isolation in tissue culture for the laboratory diagnosis of untreated and partially treated experimental herpes simplex virus keratitis. New Zealand albino rabbits were inoculated bilaterally with herpes simplex virus-1 McKrae strain after corneal scarification. One eye of each rabbit was treated with a 1% trifluorothymidine solution daily, starting on the third day after inoculation. The direct immunofluorescence assay showed lower sensitivity for herpes simplex virus detection than viral isolation in tissue culture for both untreated and partially treated eyes. The Herpchek ELISA demonstrated similar sensitivity to tissue culture in detecting herpes simplex virus in untreated eyes. In the treated group, however, the Herpchek ELISA showed a higher percentage of eyes positive for herpes simplex virus than did viral isolation in tissue culture. After the initiation of antiviral therapy, eyes that no longer harbor infectious virus that can be isolated in tissue culture may remain herpes simplex virus antigen-positive and thus be more amenable to laboratory diagnosis using the rapid ELISA method.

An architecture for knowledge-based construction of decision models.

Clinical application of decision analysis has been limited by unfamiliarity of clinicians with the technique, large data requirements, and the length of time needed to construct models. In order to make decision modeling more accessible to clinicians, the authors developed a computer program to construct decision models automatically. The system contains two separate knowledge bases. One contains frames encoding knowledge of the medical domain, the evaluation of pulmonary disease in patients infected with the human immunodeficiency virus (HIV). The other contains rules of correct decision model construction that guide the selection of items from the domain knowledge base and their insertion into the decision model. The system can create either a tree or an influence diagram that satisfies previously published critiquing rules. The system has the potential to enable novices to construct useful decision models and to provide individualized decision-analytic advice to clinicians in real time.

Distributed decision support using a web-based interface: prevention of sudden cardiac death.

Although decision models can provide a formal foundation for guideline development and clinical decision support, their widespread use is often limited by the lack of platform-independent software that geographically dispersed users can access and use easily without extensive training. To address these limitations the authors developed a World Wide Web-based interface for previously developed decision models. They describe the use and functionality of the interface using a decision model that evaluates the cost-effectiveness of strategies for preventing sudden cardiac death. The system allows an analyst to use a web browser to interact with the decision model and to change the values of input variables within pre-specified ranges, to specify sensitivity or threshold analyses, to evaluate the decision model, and to view the results generated dynamically. The web site also provides linkages to an explanation of the model, and evidence tables for input variables. The system demonstrates a method for providing distributed decision support to remote users such as guideline developers, decision analysts, and potentially practicing physicians. The web interface provides platform-independent and almost universal access to a decision model. This approach can make distributed decision support both practical and economical, and has the potential to increase the usefulness of decision models by enabling a broader audience to incorporate systematic analyses into both policy and clinical decisions.

Costs and net health effects of contraceptive methods.

BACKGROUND: Pregnancy and contraceptive methods both have important health effects that include risks and benefits. The net impact of contraception on women's health has not been reported previously. STUDY DESIGN: This is a cost-utility analysis using a Markov model evaluated by Monte Carlo simulation using the societal perspective for costs. The analysis compared 13 methods of contraception to nonuse of contraception with respect to healthcare costs and quality-adjusted life years (QALYs). Discounting was applied for future costs and health effects. The base-case analysis applies to women of average health and fertility, ranging from 15 to 50 years of age, who are sexually active in a mutually monogamous relationship; smoking rates observed in women of reproductive age were used. Sensitivity analysis extended the analysis to nonmonogamous status and smoking status. RESULTS: Compared with use of no contraception, contraceptive methods of all types result in substantial cost savings over 2 years, ranging from US$5907 per woman for tubal sterilization to US$9936 for vasectomy and health gains ranging from 0.088 QALYs for diaphragm to 0.147 QALYs for depot medroxyprogesterone acetate. Compared with nonuse, even with a time horizon as short as 1 year, use of any method other than sterilization results in financial savings and health gains. Most of the financial savings and health gains were due to contraceptive effects. In a population of patients, even modest increases in the use of the most effective methods result in financial savings and health gains. CONCLUSIONS: Every method of contraception dominates nonuse in most clinical settings. Increasing the use of more effective methods even modestly at the expense of less effective methods will improve health and reduce costs. Methods that require action by the user less frequently than daily are both less costly and more effective than methods requiring action on a daily basis.

Multiplex immunoassay for Lyme disease using VlsE1-IgG and pepC10-IgM antibodies: improving test performance through bioinformatics.

The Centers for Disease Control and Prevention currently recommends a 2-tier serologic approach to Lyme disease laboratory diagnosis, comprised of an initial serum enzyme immunoassay (EIA) for antibody to Borrelia burgdorferi followed by supplementary IgG and IgM Western blotting of EIA-positive or -equivocal samples. Western blot accuracy is limited by subjective interpretation of weakly positive bands, false-positive IgM immunoblots, and low sensitivity for detection of early disease. We developed an objective alternative second-tier immunoassay using a multiplex microsphere system that measures VlsE1-IgG and pepC10-IgM antibodies simultaneously in the same sample. Our study population comprised 79 patients with early acute Lyme disease, 82 patients with early-convalescent-phase disease, 47 patients with stage II and III disease, 34 patients post-antibiotic treatment, and 794 controls. A bioinformatic technique called partial receiver-operator characteristic (ROC) regression was used to combine individual antibody levels into a single diagnostic score with a single cutoff; this technique enhances test performance when a high specificity is required (e.g., ≥ 95%). Compared to Western blotting, the multiplex assay was equally specific (95.6%) but 20.7% more sensitive for early-convalescent-phase disease (89.0% versus 68.3%, respectively; 95% confidence interval [95% CI] for difference, 12.1% to 30.9%) and 12.5% more sensitive overall (75.0% versus 62.5%, respectively; 95% CI for difference, 8.1% to 17.1%). As a second-tier test, a multiplex assay for VlsE1-IgG and pepC10-IgM antibodies performed as well as or better than Western blotting for Lyme disease diagnosis. Prospective validation studies appear to be warranted.

Computer-interpretable clinical practice guidelines. Where are we and where are we going ?

OBJECTIVES: To provide a comprehensive overview of computer-interpretable guideline (CIG) systems aimed at non-experts. The overview includes the history of efforts to develop CIGs, features of and relationships among current major CIG systems, current status of standards developments pertinent to CIGs and identification of unsolved problems and needs for future research. METHODS: Literature review based on PubMed, AMIA conference proceedings and key references from publications identified. Search terms included practice guidelines, decision support, controlled vocabulary and medical record systems. Papers were reviewed by both authors and summarized narratively. RESULTS: There is a consensus that guideline delivery systems must be integrated with electronic health records (EHRs) to be most effective. Several evolving CIG formalisms have in common, use of a task network model. There is currently no dominant CIG system. The major challenge in development of interoperable CIGs, is agreement on a standard controlled vocabulary. Such standards are under development, but not widely used, particularly in commercial EHR systems. The Virtual Medical Record (VMR) concept has been proposed as a standard that would serve as an intermediary between guideline vocabulary and that used in EHR implementation. CONCLUSION: CIG systems are in a state of evolution. Standards efforts promise to improve interoperability without compromising innovation. The VMR concept can assist guideline development even before clinical systems routinely adhere to standards. Frontiers for future work include using the principles learned by computer implementation of guidelines to improve the guideline development process and evaluation methods that isolate the effects of specific CIG features.

Prediction in annotation based guideline encoding.

The encoding of clinical practice guidelines into machine operable representations poses numerous challenges and will require considerable human intervention for the foreseeable future. To assist and potentially speed up this process, we have developed an incremental approach to guideline encoding which begins with the annotation of the original guideline text using markup techniques. A modular and flexible sequence of subtasks results in increasingly inter-operable representations while maintaining the connections to all prior source representations and supporting knowledge. To reduce the encoding bottleneck we also employ a number of machine-assisted learning and prediction techniques within a knowledge-based software environment. Promising results with a straightforward incremental learning algorithm illustrate the feasibility of such an approach.

Vocabulary requirements for implementing clinical guidelines in an electronic medical record: a case study.

As part of a larger effort to automate guidelines we determined the number and types of clinical variables required to implement two complex clinical guidelines and the adequacy of the electronic medical record (EMR) to capture them. 178 unique variables were required by both guidelines. Variables were classified as simple (existing observation terms in the EMR), calculated (transformations of simple variables), and complex (requiring multiple simple variables and logical rules for combining them). Many variables are unlikely to be instantiated in an EMR without focused efforts to collect them. In addition, many variables required knowledge that was neither provided in the guideline nor referenced. We conclude that, although the EMR contains the necessary variables to implement these guidelines, successful automated implementation requires unambiguous definition of required terms, incorporation of additional knowledge not provided in the guideline and modification of workflow to collect variables not normally captured in routine clinical care.

Cost-effectiveness and contraceptive effectiveness of the transdermal contraceptive patch.

OBJECTIVE: The purpose of this study was to examine implications of increased perfect use on the cost-effectiveness of the contraceptive patch compared with combination oral contraceptives (COCs). STUDY DESIGN: This study compared the patch with low-estrogen-dose COCs. It assumes that the risks of developing a medical condition during use are the same for both the patch and COCs. Differences in net cost and pregnancies avoided during use were modeled. With the use of a pharmacoeconomic model, both methods were compared with a hypothetical reference case of contraception nonuse. The base-case model considered women, ages 15 to 50, in average health in a long-term, mutually monogamous, heterosexual relationship. RESULTS: The base-case analysis showed that use of the patch resulted in a savings of 249 US dollars and 0.03 pregnancies per woman over 2 years compared with COCs. CONCLUSION: This analysis demonstrated that patch use would be cost saving compared with COC use, resulting in a net avoidance of pregnancy for this population. The cost savings are attributed to reduced costs of pregnancy.

HGML: a hypertext guideline markup language.

Existing text-based clinical practice guidelines can be difficult to put into practice. While a growing number of such documents have gained acceptance in the medical community and contain a wealth of valuable information, the time required to digest them is substantial. Yet the expressive power, subtlety and flexibility of natural language pose challenges when designing computer tools that will help in their application. At the same time, formal computer languages typically lack such expressiveness and the effort required to translate existing documents into these languages may be costly. We propose a method based on the mark-up concept for converting text-based clinical guidelines into a machine-operable form. This allows existing guidelines to be manipulated by machine, and viewed in different formats at various levels of detail according to the needs of the practitioner, while preserving their originally published form.

A microcomputer-based distributed data management system for a large cooperative study of transfusion associated acquired immunodeficiency syndrome.

This paper describes the details of a microcomputer-based, distributed data management system in the acquisition of data collected in a large multicentered cooperative investigation of transfusion-transmitted acquired immunodeficiency syndrome (AIDS). Clinical, virological, and immunological data are obtained from six clinical centers and six central laboratories using a variety of hardware components and software packages. Data are merged and processed on a mainframe computer at the Biostatistics Office at the University of Southern California. The advantages and disadvantages of this system are discussed relative to the dynamics of the study, the magnitude and nature of the database, and the organization of the distributed centers involved.