Scalable and expressive medical terminologies

The K-Rep system, based on description logic, is used to represent and reason with large and expressive controlled medical terminologies. Expressive concept descriptions incorporate semantically precise definitions composed using logical operators, together with important non-semantic information such as synonyms and codes. Examples are drawn from our experience with K-Rep in modeling the InterMed laboratory terminology and also developing a large clinical terminology now in production use at Kaiser-Permanente. System-level scalability of performance is achieved through an object-oriented database system which efficiently maps persistent memory to virtual memory. Equally important is conceptual scalability-the ability to support collaborative development, organization, and visualization of a substantial terminology as it evolves over time. K-Rep addresses this need by logically completing concept definitions and automatically classifying concepts in a taxonomy via subsumption inferences. The K-Rep system includes a general-purpose GUI environment for terminology development and browsing, a custom interface for formulary term maintenance, a C+2 application program interface, and a distributed client-server mode which provides lightweight clients with efficient run-time access to K-Rep by means of a scripting language.

Prevalence of self-reported physician-diagnosed systemic lupus erythematosus in the USA

The objective of this study was to estimate the prevalence of self-reported physician-diagnosed systemic lupus erythematosus (SLE) in the USA. During the conduct of an epidemiologic study of systemic sclerosis (scleroderma), 16 607 randomly selected telephone numbers in the continental USA were called to recruit controls. All potentially eligible women were asked 'Have you ever been told by a doctor that you have lupus or SLE'? Of 4034 women aged 18 and above who completed telephone screening, 15 stated they had a physician diagnosis of SLE, corresponding to a prevalence of 372 cases per 100 000 (95% confidence intervals: 208, 614). After review of available medical records in six cases, however, the prevalence of 'validated' SLE was revised to 124 cases per 100 000 (95% confidence intervals: 40, 289). In conclusion, these data suggest that the prevalence of SLE in the USA may be up to three to 10-fold greater than previously estimated. Based on 1990 census data, we would project that over 275 000 women aged 18 and above have SLE in the USA.

Immunologic aspects of scleroderma

Activation of both cellular and humoral immunity are early events in systemic sclerosis (SSc) that appear to contribute to disease pathogenesis. Recent reports suggest that CD4+ and CD8+ T cells and a subset of gamma delta T cells each may play a role in the disease. Interest in potential profibrotic effects of transforming growth factor-beta in SSc continues. Expression of a variety of adhesion molecules is increased on fibroblasts and endothelial cells in SSc patients, as are circulating levels of the same molecules. Different autoantibody specificities are generated in B cells from tight-skin mice by use of identical VH genes, with similar V kappa genes but different J kappa segments. Centromeric proteins, topoisomerase I, RNA polymerases I, II, and III, fibrillarin, and upstream binding factor may become autoantibody targets in SSc because they are presented to the immune system as part of larger multiunit complexes. Homology between target autoantigens and infectious agents suggests that molecular mimicry initiates some autoantibody responses in SSc patients. Genetic factors influence the pattern of autoantibodies produced in different populations. Exogenous agents can induce autoantibodies in humans and mice that are similar to those seen in spontaneous SSc.

Oligoclonal expansion of V delta 1+ gamma/delta T-cells in systemic sclerosis patients

Systemic sclerosis (SSc) is a multisystem disease characterized by T-cell infiltration of involved tissues, fibrosis, and small vessel vasculopathy. Using flow cytometric analyses, we found an increased percentage of gamma/delta T-cells expressing the T-cell antigen receptor variable (V) delta 1 gene segment in the peripheral blood and bronchoalveolar lavage fluid of patients with SSc. To estimate clonality of these V delta 1+ T-cells, the diversity of V delta 1 junctional regions (V-Diversity-Joining gene segments) was examined using a reverse transcriptase-polymerase chain reaction to amplify T-cell antigen receptor delta chain transcripts isolated from peripheral blood mononuclear cells, lung, esophagus, stomach, or skin of patients and controls. Limited diversity of V delta 1-J delta junctional regions in SSc patients was demonstrated by the finding of greater restriction in the nucleotide lengths of junctional region cDNAs in individual SSc patients than in controls. Sequence analyses confirmed that V delta 1-J delta junctional regions from the blood of SSc patients had less diversity than those from controls, in that a significantly higher proportion of sequences were repeated in patients (54.4% vs. 19.4% in controls). Evidence for selection of the V delta 1+ T-cells in tissues of individual SSc patients came from the findings that the same V delta 1-J delta junctional sequences could be isolated from the same tissue over time and that identical V delta 1-J delta junctional sequences could be isolated from multiple tissues. These data suggest that expansion of V delta 1+ gamma/delta T cells may be antigen driven in SSc patients.

Inter and intraobserver variability of total skin thickness score (modified Rodnan TSS) in systemic sclerosis

OBJECTIVE

Assessment of the inter and intraobserver variability of the modified Rodnan (m-Rodnan) total skin thickness score by clinical palpation [a commonly used outcome measure in trials of systemic sclerosis (SSc)].

METHODS

Skin thickness was assessed by clinical palpation of 17 body areas on 0 to 3 scale (normal, mild, moderate, severe). The m-Rodnan total skin thickness score was derived by summation of the scores from all 17 body areas. Using the m-Rodnan, 6-7 investigators assessed skin thickness in 5-6 patients with SSc (22 patients and 23 examiners total) at each of 4 sessions for the determination of interobserver variability (accuracy). In addition 21 of the investigators then assessed m-Rodnan in 2-3 patients each (60 patients total) 3 times over a 2-8 week period to quantitate intraobserver variability (reliability).

RESULTS

Interobserver and intraobserver mean +/- within patient standard deviations (SD) for the m-Rodnan were found to be 17.7 +/- 4.6 and 20.7 +/- 2.45, respectively.

CONCLUSION

The m-Rodnan total skin thickness score is at least as reliable for measuring skin thickness in SSc as are the ARA and Ritchie joint tenderness counts for assessing joint disease in rheumatoid arthritis. These data are useful for the determination of sample size and for the definitions of clinically meaningful response. Assessment of skin score is sufficiently reproducible to include as a measure of disease outcome, especially if patients are serially evaluated by the same investigator.

Human adenovirus serotypes 3 and 5 bind to two different cellular receptors via the fiber head domain

The adenovirus fiber protein is responsible for attachment of the virion to cell surface receptors. The identity of the cellular receptor which mediates binding is unknown, although there is evidence suggesting that two distinct adenovirus receptors interact with the group C (adenovirus type 5 [Ad5]) and the group B (Ad3) adenoviruses. In order to define the determinants of adenovirus receptor specificity, we have carried out a series of competition binding experiments using recombinant native fiber polypeptides from Ad5 and Ad3 and chimeric fiber proteins in which the head domains of Ad5 and Ad3 were exchanged. Specific binding of fiber to HeLa cell receptors was assessed with radiolabeled protein synthesized in vitro, and by competition analysis with baculovirus-expressed fiber protein. Fiber produced in vitro was found as both monomer and trimer, but only the assembled trimers had receptor binding activity. Competition data support the conclusion that Ad5 and Ad3 interact with different cellular receptors. The Ad5 receptor distribution on several cell lines was assessed with a fiber binding flow cytometric assay. HeLa cells were found to express high levels of receptor, while CHO and human diploid fibroblasts did not. A chimeric fiber containing the Ad5 fiber head domain blocked the binding of Ad5 fiber but not Ad3 fiber. Similarly, a chimeric fiber containing the Ad3 fiber head blocked the binding of labeled Ad3 fiber but not Ad5 fiber. In addition, the isolated Ad3 fiber head domain competed effectively with labeled Ad3 fiber for binding to HeLa cell receptors. These results demonstrate that the determinants of receptor binding are located in the head domain of the fiber and that the isolated head domain is capable of trimerization and binding to cellular receptors. Our results also show that it is possible to change the receptor specificity of the fiber protein by manipulation of sequences contained in the head domain. Modification or replacement of the fiber head domain with novel ligands may permit adenovirus vectors with new receptor specificities which could be useful for targeted gene delivery in vivo to be engineered.

Guidelines for clinical trials in systemic sclerosis (scleroderma). I. Disease-modifying interventions. The American College of Rheumatology Committee on Design and Outcomes in Clinical Trials in Systemic Sclerosis

OBJECTIVE

To develop guidelines for therapeutic trials designed to improve the overall course of systemic sclerosis (SSc), that is, to reduce the development of significant organ damage or death.

METHODS

A committee developed general guidelines for patient inclusion and exclusion criteria, randomization, blinding of patients and physicians, controls, duration of the trial, investigator training, responses, samples size, study dropouts, statistical analyses, data management, and safety monitoring. Delphi and nominal group techniques were used.

RESULTS

Briefly, patients with diffuse cutaneous SSc of less than 24 months' duration should be included because they are at greatest risk for the development of severe organ damage and death. Patients should be excluded if they have other connective tissue diseases, SSc-like illnesses related to exposures or ingestions, severe existing internal organ damage, an unacceptable risk of side effects, or concurrent therapies that might independently influence the outcome. Randomized, double-blind, placebo-controlled trials are preferred. The treatment and followup period must be long enough to permit observation of any disease modification, which is likely to require 18-36 months, unless an extraordinarily effective therapy is identified. Responses selected should be quantitative, consistently and accurately reflect activity of SSc in major target organs (not solely the skin), be sensitive to change, and be standardized, with limited variability. An example of a set of responses is given. Surrogate responses are desirable, but none have been validated as correlating with organ damage.

CONCLUSION

Guidelines have been established for trials of disease-modifying interventions in SSc. These guidelines will need to be altered as additional information becomes available. Any given protocol will be individualized based on the nature of the intervention and objectives of the study. Nonetheless, each study team should develop a protocol that meets the spirit of these guidelines.

T cell repertoire in systemic sclerosis

An increase of certain T cell subsets in systemic sclerosis patients, particularly of V delta 1+ gamma delta T cells in the blood and lungs and CD8+ alpha beta T cells in the lungs, has been shown. The diversity of T cell antigen receptor (TCR) V delta 1, V alpha, and V beta gene repertoires was examined using reverse transcriptase-polymerase chain reaction to amplify rearranged TCR transcripts across the junctional region. This was followed by two methods of analysis. First, the relative expression of V alpha and V beta genes was determined in the blood and bronchoalveolar lavage fluid of the patients. Second, we looked for evidence of restricted diversity of the junctional regions in TCR V delta 1 transcripts and in different V alpha and V beta gene families. Limited V delta 1-C delta junctional region lengths were observed in the patients compared to controls. This was confirmed by sequence analysis of V delta 1-C delta junctional regions after subcloning amplified products in a bacterial vector. A restricted diversity of the junctional region lengths was also detected in a number of V alpha and V beta gene families, particularly within bronchoalveolar CD8+ T cell subset. These data suggest that the oligoclonal expansion of the corresponding alpha beta and gamma delta T cells is antigen-driven and may be important in the pathogenesis of systemic sclerosis.

Immunologic aspects of scleroderma

Many distinct areas of investigation contribute to the understanding of immune abnormalities in systemic sclerosis. Recent immunohistochemical studies question the causal relationship of increased transforming growth factor-beta expression to dermal fibrosis. RNA polymerase I, II, and III have been identified as autoantigens specific for systemic sclerosis. Anti-RNA polymerase antibodies are directed against both unique and shared subunits of the multiprotein complexes. The targeting of several subunits suggests that the entire complexes are processed and presented by antigen-presenting cells. Genetic studies show that both HLA-DR and HLA-DQ genes control the antitopoisomerase response in Japanese patients. The null allele of the complement component C4 and HLA-DQA2 have been identified as two independent disease susceptibility genes.

Analysis of diversity of T cell antigen receptor genes using polymerase chain reaction and sequencing gel electrophoresis

A sensitive, highly resolvable, and quantitative method was designed to analyse the diversity of polymerase chain reaction (PCR)-amplified transcripts which possess length polymorphism. A reverse transcriptase-PCR technique was used to amplify rearranged T cell antigen receptor (TCR) transcripts isolated from human blood. Oligonucleotide primers specific for conserved TCR V and C region sequences were used in PCR, with one of the primers end-labeled with 32P. Amplified cDNA products were analysed by polyacrylamide sequencing gel electrophoresis with an M13mp18 sequencing ladder as a size marker. 32P-labeled products were detected by either autoradiography or PhosphorImager. The method allowed determination of the sizes of PCR products with the precision of one nucleotide. The resolution using this technique was much higher than by electrophoresis in agarose gel with ethidium bromide staining. The sizes of PCR products determined by sequencing gel electrophoresis were consistent with the lengths of nucleotide sequences obtained after subcloning PCR products in competent bacterial cells. Analysis of PCR products by sequencing gel electrophoresis was more rapid and as accurate as nucleotide sequence analysis in determining the relative ratios of TCR mRNA in mixtures of T cell clones. The method is applicable for analysis of both rearranged TCR and immunoglobulin genes.

A controlled study of danazol for the treatment of karyotypically normal spontaneous premature ovarian failure

OBJECTIVE

To determine if the immunomodulatory and gonadotropin-suppressing properties of danazol would improve follicle function or ovulation rates in patients with karyotypically normal spontaneous premature ovarian failure.

DESIGN

Prospective, double-blind, crossover trial.

SETTING

Tertiary care research institution.

INTERVENTIONS

Two intervention phases lasting 4 months each: one phase during which patients received a standardized estrogen and progestin replacement regimen and one phase during which each patient received a twice daily 400 mg oral dose of danazol.

PATIENTS

Fifty-two patients with karyotypically normal spontaneous premature ovarian failure ranging in age from 21 to 39 years.

MAIN OUTCOME MEASURES

We measured serum E2 and P levels weekly during the 2 months after each intervention. We defined a serum E2 > 50 pg/mL (184 pmol/L) as evidence of ovarian follicle function and a P > 3.0 ng/mL (9.5 nmol/L) as evidence for ovulation.

RESULTS

Of the 46 patients who completed the study, danazol did not significantly enhance ovarian follicle function or the chance of ovulation. Eight patients ovulated after danazol and four patients ovulated after estrogen and progestin. The power to detect a 30% and a 5% ovulation success rate with therapy was 0.80 and 0.90, respectively. Overall, 30 of 46 women (65%) demonstrated ovarian follicle function and 10 women (21%) ovulated.

CONCLUSION

We were unable to demonstrate a statistically significant benefit from the immunomodulatory and gonadotropin-suppressing effects of danazol in patients with karyotypically normal spontaneous premature ovarian failure. These patients often have spontaneous remission. Thus, controlled studies are required to determine the effectiveness of treatments for this condition.

Expansion of selected V delta 1+ gamma delta T cells in systemic sclerosis patients

We have previously shown an increased percentage of gamma delta T cells expressing the TCR V delta 1 gene segment in the peripheral blood and bronchoalveolar lavage fluid of patients with systemic sclerosis (SSC). To estimate clonality of these V delta 1+ T cells, the diversity of V delta 1 junctional regions (V-D-J) was examined using a reverse transcriptase-PCR to amplify TCR delta-chain transcripts isolated from PBMC, lung, esophagus, stomach, or skin of patients and controls. Limited diversity of V delta 1-J delta junctional regions in SSC patients was demonstrated by comparing the size distribution of PCR-amplified junctional region cDNA from patients with that of controls. Sequence analyses confirmed that V delta 1-J delta junctional regions from the blood of SSc patients had less diversity than those from controls, in that a significantly higher proportion of sequences were repeated in patients (54.4 vs 19.4% in controls). Evidence for selection of the V delta 1+ T cells in the tissues of SSC patients came from the findings that the same V delta 1-J delta junctional sequences persisted in an individual patient over time and that identical junctional sequences were isolated from multiple sites. Analysis of deduced amino acid sequences revealed two clusters of similarities among the junctional regions from patients. These data suggest that expansion of V delta 1+ gamma delta T cells may be Ag driven in SSC patients.

Expansion of selected V delta 1+ gamma delta T cells in systemic sclerosis patients

We have previously shown an increased percentage of gamma delta T cells expressing the TCR V delta 1 gene segment in the peripheral blood and bronchoalveolar lavage fluid of patients with systemic sclerosis (SSC). To estimate clonality of these V delta 1+ T cells, the diversity of V delta 1 junctional regions (V-D-J) was examined using a reverse transcriptase-PCR to amplify TCR delta-chain transcripts isolated from PBMC, lung, esophagus, stomach, or skin of patients and controls. Limited diversity of V delta 1-J delta junctional regions in SSC patients was demonstrated by comparing the size distribution of PCR-amplified junctional region cDNA from patients with that of controls. Sequence analyses confirmed that V delta 1-J delta junctional regions from the blood of SSc patients had less diversity than those from controls, in that a significantly higher proportion of sequences were repeated in patients (54.4 vs 19.4% in controls). Evidence for selection of the V delta 1+ T cells in the tissues of SSC patients came from the findings that the same V delta 1-J delta junctional sequences persisted in an individual patient over time and that identical junctional sequences were isolated from multiple sites. Analysis of deduced amino acid sequences revealed two clusters of similarities among the junctional regions from patients. These data suggest that expansion of V delta 1+ gamma delta T cells may be Ag driven in SSC patients.

Preferential adherence of human gamma delta, CD8+, and memory T cells to fibroblasts

Fibroblasts and extracellular matrix produced by fibroblasts provide a framework within solid tissues to which lymphocytes can adhere. Lymphocyte adherence to this framework under basal and inflammatory conditions should contribute to retention of cells involved in innate and specific immunity. The purpose of this work was to determine whether all T cell subsets bind equally well to fibroblast cultures. T cells from healthy humans were co-cultured with autologous or allogenic dermal fibroblast cultures and adherent cells evaluated for surface markers. T cells adherent to untreated autologous fibroblast cultures were enriched for gamma delta T cells, with a striking increase in the V delta 1+ subpopulation. Exposure of the fibroblast cultures to rhIFN-gamma increased the number of adherent T cells and changed the pattern of adherence. Adherent T cells were further enriched for gamma delta T cells but not the V delta 1+ subset, and enriched for CD8+ and memory T cells. These findings suggest that T cell populations that bind to basal and stimulated fibroblast cultures are distinct. There were no qualitative differences in the binding of T cells to autologous and allogeneic fibroblast cultures.

Preferential adherence of human gamma delta, CD8+, and memory T cells to fibroblasts

Fibroblasts and extracellular matrix produced by fibroblasts provide a framework within solid tissues to which lymphocytes can adhere. Lymphocyte adherence to this framework under basal and inflammatory conditions should contribute to retention of cells involved in innate and specific immunity. The purpose of this work was to determine whether all T cell subsets bind equally well to fibroblast cultures. T cells from healthy humans were co-cultured with autologous or allogenic dermal fibroblast cultures and adherent cells evaluated for surface markers. T cells adherent to untreated autologous fibroblast cultures were enriched for gamma delta T cells, with a striking increase in the V delta 1+ subpopulation. Exposure of the fibroblast cultures to rhIFN-gamma increased the number of adherent T cells and changed the pattern of adherence. Adherent T cells were further enriched for gamma delta T cells but not the V delta 1+ subset, and enriched for CD8+ and memory T cells. These findings suggest that T cell populations that bind to basal and stimulated fibroblast cultures are distinct. There were no qualitative differences in the binding of T cells to autologous and allogeneic fibroblast cultures.

Cloning and genetic characterization of the human kinesin light-chain (KLC) gene

We report the isolation, sequence, and identification of a cDNA encoding the human kinesin light-chain (KLC) protein. The cDNA molecule consisted of 276 nucleotides of 5' untranslated region, the complete coding sequence of 1,710 nucleotides, and 322 nucleotides of 3' untranslated region. It encoded a polypeptide of 569 amino acids and a deduced molecular mass of 64,789 daltons. The predicted secondary internal structure of the KLC molecule consisted of about 27 contiguous repeats, each of approximately 21 amino acid residues, and could be divided into three domains. The amino-terminal domain consisted of heptad repeats typical of the rod domain of several cytoskeletal proteins. The central and carboxy-terminal domains consist of 21-mer repeats. KLC mRNA was expressed in most tissues analyzed. The gene, which was expressed in bacteria and Chinese hamster ovary cells, was provisionally assigned to the long arm of human chromosome 14.

Regional mapping of human DNA excision repair gene ERCC4 to chromosome 16p13.13-p13.2

Mitomycin C (MMC)-resistant interspecific somatic cell hybrids made between human cells and the MMC-sensitive, Chinese hamster ovary (CHO) excision repair-deficient UV41 cells generally contained human chromosome 16, while other human chromosomes were randomly present. MMC-sensitive and -resistant subclones were isolated from resistant clones, and resistance generally segregated concordantly with human chromosome 16 markers. UV radiation survival analysis of subclones indicated that MMC and UV resistance were correlated. Therefore, the complementing gene, Excision Repair Cross Complementing 4 (ERCC4), was assigned to human chromosome 16. Complementation of UV41 by human cells derived from patients with xeroderma pigmentosum groups A, C, D and F excluded ERCC4 from involvement in those disease syndromes. Resistant hybrids containing only portions of chromosome 16 were identified by the lack of concordance of multiple chromosome 16 markers. When such hybrids were used as a source of probe for fluorescent in situ hybridization onto normal human metaphases, the only region of chromosome 16 identified as being consistently present was 16p13.1-p13.3. Genetic marker analysis of informative hybrids with mapped probes refined the position of ERCC4 to 16p13.13-p13.2 and allowed the following order of markers within the region to be established: pter--(PRM1, D16S215)-D16S213-D16S53-(D16S214,ERCC4) -D16S3-D16S96-cen.

Growth hormone and physiological responses to clonidine in depression

Clonidine (1.3 micrograms/kg) was administered to 62 control and 55 depressed patients free of psychoactive drugs for at least 7 days and fasted overnight. Growth hormone (GH), pulse, blood pressure and sedation were measured every 15 min for 1 h before and 2 h after clonidine infusion. GH response did not differ significantly between control and depressed subjects overall or when divided by sex. The systolic hypotensive and sedative responses were blunted in depressed subjects compared with controls; these effects appeared to be secondary to residual antidepressant drugs since the differences were only significant for those depressed subjects with short drug-free intervals. No differences between depressed subjects and controls were seen in diastolic hypotensive or bradycardic responses and no differences in GH, cardiovascular or sedative responses were found between endogenous and non-endogenous depressed subjects.