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PubMed1989

Construction of a database to identify Staphylococcus species.

A database was constructed for the routine identification of Staphylococcus species, isolated from man. The method comprised 15 conventional characterisation tests using substrates incorporated into agar plates and a multipoint inoculation system. The database was constructed from results of 125 reference strains and 1567 clinical isolates. In an evaluation trial, using a probability profile index generated from the database, 529 of 559 (94.6%) further clinical isolates were identified to species level. A further 20 (3.6%) gave low discrimination between two species. The proposed scheme was rapid, reliable, and inexpensive.

Bacteriological Techniques↗
PubMed1995

Management of alternate level of care patients using a computerized database.

The term "alternate level of care" (ALC) refers to the status of hospitalized patients who are no longer acutely ill but cannot be discharged because posthospital plans are not yet in place. ALC is a major problem for patients, families, and hospitals. This article describes the experiences of an urban teaching hospital with ALC and the development of a computerized database to better manage the ALC population. Among the findings were that age, waiting for a nursing home placement, family-related discharge problems, and pending Medicaid eligibility all significantly contributed to length of stay beyond the acute phase of the illness. Using these data, the hospital developed an innovative program in which the preparation of Medicaid applications was transferred from the Department of Finance to the Department of Social Work Services.

Aged↗
PubMed1994

Common variable immunodeficiency: diagnosis and management.

OBJECTIVE: Common variable immunodeficiency is a heterogeneous syndrome characterized by humoral immunodeficiency, recurrent bacterial infections, and a variety of immunologic abnormalities. The goal of this article is to review the pathogenesis, clinical manifestations, diagnosis, and management of common variable immunodeficiency. DATA SOURCES: References are limited to the English language literature. Sources include computerized databases and bibliographies of recent articles and books. STUDY SELECTION: References that made important contributions to our understanding of the pathogenesis, clinical manifestations, diagnosis, and treatment of this disease were selected for inclusion in this review. RESULTS AND CONCLUSION: Common variable immunodeficiency is an idiopathic state of immune dysregulation that results in impaired antibody synthesis and the development of recurrent bacterial infections. This syndrome is also associated with a variety of autoimmune and neoplastic disorders. Effective management of these patients includes intravenous immunoglobulin replacement, vigorous treatment of infections, and readiness to promptly evaluate and treat unusual autoimmune and neoplastic complications should they appear.

Common Variable Immunodeficiency↗
PubMed1993

Diversity of ribosomal DNA fingerprints of Leptospira serovars provides a database for subtyping and species assignation.

Ribosomal DNA fingerprints from 103 pathogenic Leptospira strains were examined using EcoRI restriction and fragment length polymorphisms of rRNA genes. Sixty-nine new leptospiral ribotypes were described, in addition to 49 previously observed. Except for 5 strains, a good correlation between DNA homology data and ribotyping was observed. The genospecies of 31 reference strains could be presumed, since they shared 13 ribotypes with strain(s) previously studied by DNA homology. Furthermore, the definition of common rRNA hybridization fragments in each recognized DNA hybridization group provides information about the status of Leptospira reference strains yet to be classified. With 118 ribotypes now defined among the validated serovar reference strains, rRNA fingerprints constitute a database for subtyping Leptospira species.

DNA Fingerprinting↗
PubMed1993

Spine and total body bone mineral density in amenorrheic endurance athletes.

Lumbar spine, total body, and regional bone mineral densities (BMDs) were measured in eumenorrheic and amenorrheic runners and triathletes by using dual-energy X-ray absorptiometry (Lunar DPX). Values were also compared with age- and weight-matched reference data from the Lunar British database. The amenorrheic group had significantly lower lumbar spine (P = 0.003), arm (P = 0.018), trunk (P = 0.014), and total spine (P < 0.0001) BMDs compared with the eumenorrheic group and significantly lower lumbar (P = 0.002) and total spine (P < 0.001) values compared with the reference controls. Leg (P = 0.009) and arm (P < 0.001) densities were significantly higher than controls. All regions, apart from the lumbar spine, were significantly higher in the eumenorrheic group compared with the reference group. There were no within-group differences for the runners and triathletes. Compared with the eumenorrheic athletes, the amenorrheic women had significantly later age of menarche (P = 0.0032). The type of physical activity undertaken by these athletes can compensate for the loss of menses at the majority of skeletal sites with the exception of the spine.

Adult↗
PubMed1996

MHCPEP--a database of MHC-binding peptides: update 1995.

MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding affinity, source protein, anchor positions, as well as publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using Gopher, FTP or WWW.

Computer Communication Networks↗
PubMed1994

Generation of reference values for cardiac enzymes from hospital admission laboratory data.

An approach is described for using patient databases of a hospital information system as a source of reference values for cardiac enzymes. Of a total of 2029 emergency admission patients with serial cardiac enzyme data, 538 patients were considered "healthy" (having no damage in myocardium) because their discharge diagnoses suggested neither myocardial damage nor any other condition that could lead to elevated enzyme activities, and because their serially collected cardiac enzyme activities remained stable. Enzyme activities of creatine kinase (EC 2.7.3.2), creatine kinase isoenzyme MB, lactate dehydrogenase (EC 1.1.1.28), and lactate dehydrogenase isoenzyme 1 of these patients at admission to hospital were considered as suitable health related reference values. The upper (97.5%) reference limits of activities, measured at 37 degrees C according to Scandinavian recommendations, were as follows (age dependent limits given at 25 and at 75 years of age, U/l): creatine kinase men 268, 192; creatine kinase women 200 (no age effect); creatine kinase-MB 16, 24; lactate dehydrogenase 497, 603; lactate dehydrogenase isoenzyme 1 103, 140. For comparison, reference values were also produced conventionally from a group of 246 healthy subjects. Observed effects of age on enzyme activities were quite similar to those in the selected patient group. Calculated reference limits for isoenzymes creatine kinase-MB and lactate dehydrogenase isoenzyme 1 were also similar but reference limits for less cardiospecific total enzyme activities, creatine kinase and lactate dehydrogenase, were more variable between these two groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMedDate not supplied

Current Contents on Diskette and Reference Update.

Both Current Contents on Diskette and Reference Update provide an excellent mechanism for keeping abreast of the biomedical literature with a personal computer. Both systems are compatible with the two major database management programs for manipulating reprint files. Reference Update exports directly to Reference Manager (a choice on the main menu). Exporting to a file can also be done with one of four formats: Table of Contents, MEDLINE, Full, and One Line. To export Reference Update records into Pro-Cite, for example, the records must first be downloaded into MEDLINE format. Current Contents on Diskette also exports in four different formats: MEDLINE, Comma Delimited, Screen Image, and DIALOG. MEDLINE corresponds to Reference Manager format, and Comma Delimited corresponds to Pro-Cite format. Both products include reprint request systems that can be used directly from the programs. The two products share many features and differ primarily in terms of journal coverage. Current Contents on Diskette provides document delivery by means of the Genuine Article service, and Reference Update offers a synonym feature. Both programs are attractive alternatives to manual or on-line searching of the biomedical literature.

Information Systems↗
PubMed1989

Computerization of academic vascular surgery.

Academic surgical units have a combination of computer needs, including access to the surgical literature, storage and retrieval of patient registry data, laboratory, and research data, generation of reports; statistical analysis of data; and word processing. A system that fulfills these requirements was developed for an academic vascular surgical unit. The system integrates these functions in a multi-user environment and is accessed from menus on multiple terminals in laboratories and offices in three hospitals and in staff members' homes. Databases currently include more than 7000 references to published articles in vascular surgery, a vascular registry consisting of more than 7500 patients, patient data from three integrated noninvasive vascular laboratories, data generated from both clinical and basic research, and a log of resident, fellow, and faculty operative experience. Statistical analysis, using essentially all modern statistical methods including sophisticated log-rank, proportional hazards, and multivariant analyses, can be performed on all databases, either separately or in any combination, without the need to reenter data. An electronic mail and messaging system provides for paperless communication between surgeons, research personnel, and clerical staff.

Academic Medical Centers↗
PubMed2026

Metagenomics indicates new taxa in Candidatus Saccharimonadia and proposal of Parviradicicola hetaonensis gen. nov. sp. nov. and Parviputeicola dengkouensis gen. nov. sp. nov. following the rules of the SeqCode.

Candidatus Saccharimonadia is a core lineage within the phylum Patescibacteriota (formerly the bacterial candidate phyla radiation, CPR), yet the class has long lacked a standardized, complete taxonomic framework. This nomenclatural gap severely hinders consistent academic exchange and global research into its diversity, evolutionary history, and ecological roles. Here, we recovered 29 medium- to high-quality Ca. Saccharimonadia metagenome-assembled genomes (MAGs) from groundwater, rhizosphere soil, and saline-alkali soil in the Hetao Irrigation District, Inner Mongolia, China, and performed integrated phylogenomic, genome size evolution, and metabolic analyses alongside reference genomes from the GTDB r220 database. Based on robust polyphasic taxonomic evidence (multi-dimensional phylogenetic analyses, widely accepted genome-wide ANI/AAI thresholds) and SeqCode rules, we formally propose two novel taxa: Parviradicicola hetaonensis gen. nov., sp. nov. (type material: txb011_bin.8.strictTS) and Parviputeicola dengkouensis gen. nov., sp. nov. (type material: sgl022_bin.19.origTS), plus two novel families and one novel order. We further identified potential drivers and important associations related to Ca. Saccharimonadia genome size evolution and adaptive metabolic traits. This work refines the Ca. Saccharimonadia taxonomic framework, providing critical genomic references for follow-up research.

Phylogeny↗
PubMed2025

eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA.

Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across nearly all eukaryotic organisms. In humans, eccDNAs are widely distributed in normal tissues, cancerous tissues, and body fluids, where they play important roles in tumorigenesis and are often associated with poor clinical outcomes. Given their biological and clinical significance, a well-integrated and high-quality database is essential for advancing eccDNA-related research. To address this need, we developed eccDNABase, a comprehensive and curated resource for browsing, searching, and analyzing eccDNAs across multiple species. The database systematically catalogs eccDNA-disease associations from diverse tissues and organisms. Currently, eccDNABase contains 1,875,452 eccDNA-disease associations, encompassing 8,398 ecDNA entries across nine species, 63 diseases, and healthy individuals. Each entry provides detailed information, including eccDNA ID, type, chromosomal localization, species, tissue or cell line source, disease name and Disease Ontology ID, overlap length and percentage with genes, oncogene overlap, detection method, and links to literature and source databases. Given its extensive and curated datasets, eccDNABase serves as a valuable resource for both basic and translational research, offering deeper insights into the role of eccDNA in health and disease. The database is publicly accessible at http://cgga.org.cn/eccDNABase/.

Humans↗
PubMed1991

The gene-protein database of Escherichia coli: edition 4.

The gene-protein database of Escherichia coli has as its core an index that links each of the protein spots from a two-dimensional polyacrylamide gel to the gene that encodes the protein. Additional information about each protein and its gene is generated from two-dimensional gel analysis or collated from the literature to form the database. Earlier editions of the database have provided periodic updates of information. The current edition does this, but also introduces a new reference gel image produced by an electrophoresis system recently adopted in this laboratory. The new gel system was chosen because it offers an improved opportunity for other investigations to produce close replicas of the reference gel pattern, thereby allowing easier access to the information of the database and encouraging independent contribution to the database. The new gel format also is larger and hence more compatible with computer assisted image analysis, which has become essential for a project of this magnitude. This edition continues the use of the former reference gel images, but adds a reference image of an equilibrium gel of E. coli strain W3110 produced by the new standardized gel system. At this time, 55% of the protein spots annotated on the previous equilibrium reference gel for this organism have been located on the new reference image, and these identifications are included in the tables of the database.

Bacterial Proteins↗
PubMed1989

Electrocardiographic quantitation of ventricular repolarization.

Quantification of the electrocardiographic ventricular repolarization involving the T-U wave complex is usually performed with reference to the axis of the T wave and the QT interval duration. A novel quantitative approach to improve the description of ventricular repolarization was applied to the digitized electrocardiograms of 423 normal subjects. Six electrocardiographic repolarization characteristics were identified: duration, rate, area, symmetry, late phenomena, and interlead heterogeneity. A computer algorithm was designed to automatically interpret the electrocardiographic repolarization segment and measure 11 variables that quantified these repolarization characteristics. The application of redundancy-reduction techniques selected a final set of seven variables that were used in the statistical analysis. The QT interval, which was included in the initial group of variables, was replaced by the time interval between S wave offset and T wave maximum. All selected electrocardiographic variables were independent of age (r2 less than 0.11) and body surface area (r2 less than 0.03); all except the early duration variable were heart rate- and QT interval-independent (r2 less than 0.2, r2 less than 0.13, respectively; and most were uncorrelated to each other. A comparison of repolarization characteristics by gender revealed that repolarization duration was significantly more prolonged (p less than 0.0001) in women than in men. This multidimensional quantitative approach conveys a new and more complete description of the repolarization process and provides an electrocardiographic repolarization database in normal subjects as a reference standard for identifying patients with disordered repolarization.

Adult↗
PubMed1995

A standards-based clinical information system for HIV/AIDS.

OBJECTIVE: To create a clinical data repository to interface the Veteran's Administration (VA) Decentralized Hospital Computer Program (DHCP) and a departmental clinical information system for the management of HIV patients. This system supports record-keeping, decision-making, reporting, and analysis. The database development was designed to overcome two impediments to successful implementations of clinical databases: (i) lack of a standard reference data model, and; (ii) lack of a universal standard for medical concept representation. BACKGROUND: Health Level Seven (HL7) is a standard protocol that specifies the implementation of interfaces between two computer applications (sender and receiver) from different vendors or sources of electronic data exchange in the health care environment. This eliminates or substantially reduces the custom interface programming and program maintenance that would otherwise be required. HL7 defines the data to be exchanged, the timing of the interchange, and the communication of errors to the application. The formats are generic in nature and must be configured to meet the needs of the two applications involved. The standard conceptually operates at the seventh level of the ISO model for Open Systems Interconnection (OSI). The OSI simply defines the data elements that are exchanged as abstract messages, and does not prescribe the exact bit stream of the messages that flow over the network. Lower level network software developed according to the OSI model may be used to encode and decode the actual bit stream. The OSI protocols are not universally implemented and, therefore, a set of encoding rules for defining the exact representation of a message must be specified. The VA has created an HL7 module to assist DHCP applications in exchanging health care information with other applications using the HL7 protocol. The DHCP HL7 module consists of a set of utility routines and files that provide a generic interface to the HL7 protocol for all DHCP applications. SETTING: The VA's DHCP core modules are in standard use at 169 hospitals, and the role of the VA system in health care delivery has been discussed elsewhere. This development was performed at the Miami VA Medical Center Special Immunology Unit, where a database was created for an HIV patient registry in 1987. Over 2,300 patient have been entered into a database that supports a problem-oriented summary of the patient's clinical record. The interface to the VA DHCP was designed and implemented to capture information from the patient treatment file, pharmacy, laboratory, radiology, and other modules. RESULTS: We obtained a suite of programs for implementing the HL7 encoding rules from Columbia-Presbyterian Medical Center in New York, written in ANSI C. This toolkit isolates our application programs from the details of the HL7 encoding rules, and allows them to deal with abstract messages and the programming level. While HL7 has become a standard for healthcare message exchange, SQL (Structured Query Language) is the standard for database definition, data manipulation, and query. The target database (Stitt F.W. The Problem-Oriented Medical Synopsis: a patient-centered clinical information system. Proc 17 SCAMC. 1993:88-93) provides clinical workstation functionality. Medical concepts are encoded using a preferred terminology derived from over 15 sources that include the Unified Medical Language System and SNOMed International ( Stitt F.W. The Problem-Oriented Medical Synopsis: coding, indexing, and classification sub-model. Proc 18 SCAMC, 1994: in press). The databases were modeled using the Information Engineering CASE tools, and were written using relational database utilities, including embedded SQL in C (ESQL/C). We linked ESQL/C programs to the HL7 toolkit to allow data to be inserted, deleted, or updated, under transaction control. A graphical format will be used to display the entity-rel

Acquired Immunodeficiency Syndrome↗
PubMed1995

Comprehensive ultrasound examination in a private perinatal practice.

A retrospective review of the types of patients seen and the accuracy of the diagnosis made was undertaken for patients referred for comprehensive ultrasound examination in a large private perinatal practice. A review of the perinatal ultrasound database, neonatal intensive care database, and hospital charts was done in 1338 patients referred to the perinatal ultrasound laboratory for comprehensive ultrasound examination during a 2-year period. Accuracy of the ultrasound diagnosis and relationships between structural anomalies seen on ultrasound examination and perinatal outcome was undertaken. Positive and negative predictive values for the ultrasonic diagnosis were 82% and 98%, respectively. There were 19 (1.4%) false-positive diagnoses and 38 (2.8%) false-negative diagnoses. There was a high correlation between structural anomalies and chromosomal anomalies, with 15 of the 87 infants (17.2%) with structural anomalies also having chromosomal anomalies. The accuracy of ultrasonic diagnosis for comprehensive examinations in a large private perinatal practice compared favorably with previous reports in the literature. The information presented in this study should be helpful to obstetric centers with similar patient populations.

Congenital Abnormalities↗
PubMed1994

Reference intervals developed from data for hospitalized patients: computerized method based on combination of laboratory and diagnostic data.

We utilized the databases of a hospital information system to select for determination of reference values various individual hospitalized patients on the basis of their diagnoses at discharge. The nonparametric 2.5-97.5% "health-related" reference intervals were calculated for hemoglobin concentration, mean corpuscular volume (MCV), and erythrocyte count for both sexes. After excluding patients with diseases possibly affecting erythrocyte variables, we obtained a final group of 1786 women and 1450 men, ages 20-65 years, who were studied in age groups of 20-30, 30-45, 45-55, and 55-65 years. The upper reference limits of the MCV results obtained from hospitalized patients were higher than those produced conventionally from healthy individuals, as would be intuitively suggested by clinical experience. This method, based on selection by diagnosis, could be applicable to various analytes measured in hospital laboratories, provided sufficient data are available as databases.

Adult↗
PubMed1993

Human liver protein map: update 1993.

This publication updates the reference human liver protein map. By microsequencing, 27 spots or 34 polypeptide chains were identified. The most abundant polypeptides detected on the silver stained liver map were key elements in major hepatic biochemical pathways. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing the 1993 reference human liver SWISS-2DPAGE database. SWISS-2DPAGE and the SWISS-PROT protein sequence databases are closely linked together through the use of common accession numbers.

Amino Acid Sequence↗