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Results for “reference databases”

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PubMed1991

Non-categorical problem lists in a primary-care information system.

An ambulatory-care patient-tracking system has been implemented that records non-categorical problem descriptions in the outpatient problem list. The system does not restrict physicians to the use of predefined diagnostic categories. Instead, the system stores patient problems in a database as free-text records. Subsequent diagnostic categorization and coding is accomplished through prompted free-text input and appropriate reference databases. This system design allows an outpatient problem-list summary to reflect non-categorical health-status information in addition to coded medical diagnoses.

Ambulatory Care Information Systems↗

PubMed2000

Mass spectrometry of the human pituitary proteome: identification of selected proteins.

The field of proteomics involves the combined application of advanced separation techniques, mass spectrometry, and bioinformatics tools to characterize proteins in complex biological mixtures. Here we report the identification of nine proteins from the human pituitary proteome, using the proteomics approach. The pituitary proteins were separated by two-dimensional electrophoresis, and were visualized by silver staining. The proteins of interest were subjected to in-gel digestion with trypsin, and the masses of the resulting peptides were determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This tryptic mass map was used to identify the proteins through a search of a protein-sequence database. The identified proteins include important hormones, and enzymes with various catalytic activities. These proteins will be used to construct a two-dimensional reference database of the human pituitary. This database will be employed to study changes in the pituitary proteome that are associated with the formation of pituitary tumors.

Databases, Factual↗

PubMed1986

Standardizing clinical laboratory data for the development of transferable computer-based diagnostic programs.

The existence of systematic differences between test results obtained at different laboratories can compromise the development of generally accessible reference databases for interpretive pathology. We review approaches to the elimination of inter-laboratory bias from pathology test results through the use of standard unit transformations. A general transform procedure is described that will permit laboratories serving a common population to make use of reference data, decision rules, and computer-based interpretive programs developed around a larger clinical database than each of these test centers could amass for themselves.

Clinical Laboratory Techniques↗

PubMed1997

An Internet service for manipulating 3D models of human organs reconstructed from computer tomography and magnetic resonance imaging.

Our paper describes an integrated methodology addressing the development of an Internet service for medical professionals, medical students and generally, people interested in medicine. The service (currently developed in the framework of IAEVA, a Telematics Application Programme project of the European Union), incorporates a mechanism for retrieving from a relational database (reference library) 3D volumetric models of human organs reconstructed from computer tomography (CT) and/or magnetic resonance imaging (MRI). Retrieval is implemented in a way transparent to the actual physical location of the database. Prospective users are provided with a Solid Object Viewer that offers them manipulation (rotation, zooming, dissection etc.) of 3D volumetric models. The service constitutes an excellent foundation of understanding for medical professionals/students and a mechanism for broad and rapid dissemination of information related to particular pathological conditions; although pathological conditions of the knee and skin are supported currently, our methodology allows easy service extension into other human organs ultimately covering the entire human body. The service accepts most Internet browsers and supports MS-Windows 32 platforms; no graphics accelerators or any specialised hardware are necessary, thereby allowing service availability to the widest possible audience. Nevertheless, the service operates in near real-time not only over high speed expensive network lines but also over low/medium network connections.

Computer Communication Networks↗

PubMed2000

Information systems: the key to evidence-based health practice.

Increasing prominence is being given to the use of best current evidence in clinical practice and health services and programme management decision-making. The role of information in evidence-based practice (EBP) is discussed, together with questions of how advanced information systems and technology (IS&T) can contribute to the establishment of a broader perspective for EBP. The author examines the development, validation and use of a variety of sources of evidence and knowledge that go beyond the well-established paradigm of research, clinical trials, and systematic literature review. Opportunities and challenges in the implementation and use of IS&T and knowledge management tools are examined for six application areas: reference databases, contextual data, clinical data repositories, administrative data repositories, decision support software, and Internet-based interactive health information and communication. Computerized and telecommunications applications that support EBP follow a hierarchy in which systems, tasks and complexity range from reference retrieval and the processing of relatively routine transactions, to complex "data mining" and rule-driven decision support systems.

Decision Support Systems, Clinical↗

PubMed1995

[Studies on biological indicator values in diagnosis for lead poisoning].

Blood lead levels, urine lead levels, indicators of porphyrin metabolism and other biological indicators were determined in 330 workers exposed to lead and 100 unexposed controls with national standardized methods for quality assurance. Data were analyzed with modern statistical methods in a microcomputer with SAS software. Criteria values for blood lead and urine lead were formulated with curve fitting and discriminant analysis, and local normal upper limit values were 1.43 and 0.25 mumol/L for blood lead and urine lead, respectively, acceptable upper limit values 1.93 and 0.35 mumol/L, respectively, and diagnostic values for poisoning 3.02 and 0.56 mumol/L, respectively. Correlation between workplace air lead concentrations and biological indicators, between blood lead levels and other indicators, and their specificity, sensitivity, accuracy and underdiagnosis and misdiagnosis were evaluated at the same time to provide a reference database for revising the national diagnostic criteria for lead poisoning.

Adult↗

PubMed1994

As assessment of habitat pressure, oxygen fraction, and EVA suit design for space operations.

At high cabin pressure [e.g. 1013 hPa (14.7 psi) 21% O2] there are serious issues relative to specification of suit pressure and the need for prebreathing. A high pressure suit will be costly but use of the existing, flexible suit requires up to 6 h of prebreathing. Or one could use a cabin pressure of 700 hPa (10.2 psi) prior to extravehicular activity (EVA) in order to use the existing suit with only 1 h of prebreathing. If these normal cabin pressures and O2 levels are utilized, existing physiological and medical databases apply, providing a known basis for evaluating effects of long duration space missions. If a 345 hPa (5 psi), 70-100% O2 atmosphere is adopted the existing suit can be used with no prebreathing required. However, there is no reference database on physiological effects under the conditions of lower pressure and higher O2 concentration. This paper considers the major issues involved in defining habitat pressure, O2 fraction, and EVA suit design for operations in space. A preliminary model for evaluating habitat/suit pressure and O2% strategies is presented.

Aerospace Medicine↗

PubMed2026

Meta2DB: curated shotgun metagenomic feature sets and metadata for health state prediction.

SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health. AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.

Metadata↗

PubMed2026

resLens: genomic language models to enhance antibiotic resistance gene detection.

The rise of antibiotic resistance necessitates advanced tools to detect and analyze antibiotic resistance genes (ARGs). We present resLens, a family of genomic language models that leverage latent genomic representations to enhance ARG detection and analysis. Unlike alignment-based methods constrained by reference databases, resLens fine-tunes a pre-trained DNA language model on curated ARG datasets, achieving competitive or superior performance in classifying resistance genes across multiple evaluation scenarios, including when ARGs exhibit sequences and mechanisms of resistance dissimilar to those in reference datasets.

Journal Article↗

PubMed2001

Identification of Mycobacterium species by multiple-fluorescence PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene.

Identification of mycobacteria to the species level by growth-based methodologies is a process that has been fraught with difficulties due to the long generation times of mycobacteria. There is an increasing incidence of unusual nontuberculous mycobacterial infections, especially in patients with concomitant immunocompromised states, which has led to the discovery of new mycobacterial species and the recognition of the pathogenicity of organisms that were once considered nonpathogens. Therefore, there is a need for rapid and sensitive techniques that can accurately identify all mycobacterial species. Multiple-fluorescence-based PCR and subsequent single-strand conformation polymorphism (SSCP) analysis (MF-PCR-SSCP) of four variable regions of the 16S rRNA gene were used to identify species-specific patterns for 30 of the most common mycobacterial human pathogens and environmental isolates. The species-specific SSCP patterns generated were then entered into a database by using BioNumerics, version 1.5, software with a pattern-recognition capability, among its multiple uses. Patient specimens previously identified by 16S rRNA gene sequencing were subsequently tested by this method and were identified by comparing their patterns with those in the reference database. Fourteen species whose SSCP patterns were included in the database were correctly identified. Five other test organisms were correctly identified as unique species or were identified by their closest relative, as they were not in the database. We propose that MF-PCR-SSCP offers a rapid, specific, and relatively inexpensive identification tool for the differentiation of mycobacterial species.

DNA Primers↗

PubMed1995

Large scale database experiments to assess the significance of matching DNA profiles.

Over 5,700 three-probe VNTR DNA profiles collected by several United Kingdom (UK) laboratories have been compared to examine the probability of randomly matching 2 samples from different individuals. In over 16 million comparisons, using a matching rule corresponding to the matching guideline employed by the UK Forensic Science Service, no profiles were found to match at the 3 loci D1S7 (MS1), D7S21(MS31) and D12S11 (MS43a). The frequency of occurrence of a set of Caucasian profiles have been estimated with 6 reference databases. The results show that there were greater differences in the frequency estimates when using a database of Afro-Caribbean or Asian profiles, rather than a different Caucasian database. The results further demonstrate the power and robustness of the VNTR DNA profiling technique for forensic casework.

Bayes Theorem↗

PubMed1995

A database for estimating normal spinal motion derived from noninvasive measurements.

STUDY DESIGN: A database for estimated normal spinal motion was derived using a noninvasive, high-resolution, computer-aided system, which tracks the motion of skin markers strategically placed on the spine. Forty normal subjects, selected from hundreds of possible subjects according to rigorous inclusion/exclusion criteria, were tested on the system. OBJECTIVES: Patterns of estimated spinal motion were analyzed as a function of load, age, and sex, confirming a correlation between the movement of spinal segments and the motion of skin markers. SUMMARY OF BACKGROUND DATA: The Workers Compensation Board of Quebec funded and supervised the experiments necessary to establish a normative reference database for a high-resolution motion analysis system that permits a noninvasive assessment of spinal function. A previous study examined the correlation between the movements of the skin markers and the underlying bony structures for trunk flexion. Skin movement cannot be random and contains information characterizing both the spine and its surrounding soft tissues. METHODS: A noninvasive dynamic imaging system was used to measure normal spinal function under free movement. A high-resolution three-dimensional camera system collected basic kinematic data from strategically placed skin markers over the lumbar spine while the activity of paraspinal muscles was being recorded with surface electromyography. The measurements were analyzed for consistent, specific patterns recognizable as normal lumbar spine skin motion and reflecting normal lumbar spine function. A comparison was made with previous radiographic studies to confirm the correlation between the motion of skin markers and lumbar spine function. RESULTS: Lumbar skin marker motion patterns in normal subjects were consistent and varied little with load; gender had no effect except in the initial phase of a movement. There was less mobility but similar coordination in older subjects. No inconsistencies with previous radiologic investigations were found for sagittal and lateral plane movement.

Adolescent↗

PubMed1989

Automatic analysis of heart rate variation: I. Method and reference values in healthy controls.

Many patients referred to an electrophysiological laboratory may have autonomic dysfunction. Some parasympathetic tests are based on the assessment of heart rate variation induced by breathing, Valsalva maneuver, and standing. We have developed fast and practical computer-based methods to analyze heart rate variation using standard EMG equipment and a personal computer. For quantitative description we have evaluated different algorithms, both earlier described and new ones. Findings in patients with diabetes have been compared with those obtained from healthy subjects in order to determine the diagnostic utility of the various algorithms. The optimal algorithm has been chosen by this and other criteria, and a reference database from healthy subjects has been developed.

Adolescent↗

PubMed2000

Suitability of the T-score for establishing bone mineral density categories.

The use of different reference ranges may give rise to different T-score values for the same bone mineral density (BMD) value. This study was designed to quantify the differences in the classification of a particular population on the basis of normal ranges obtained from other reference databases. The T-scores obtained in a sample of 148 women by applying the Spanish normal range were compared with the normal range obtained in NHANES III for femoral neck. Significant differences were found when T-scores were compared, but there were no differences in categorizations using the WHO criteria. The application of these reference ranges to a female population aged older than 45 years with known BMD showed significant differences in classification. In conclusion, the T-score can vary according to the normal range used as reference, but it has little influence on the categorization of individual patients. However, it may be important when applied to a general population.

Adult↗

PubMed2026

nf-core/magmap: Map metatranscriptomes to large collections of genomes.

SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes. AVAILABILITY AND IMPLEMENTATION: The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

Software↗

PubMed1999

Acoustic characteristics of /s/ in adolescents.

The goal of the current study was to construct a reference database against which misarticulations of /s/ can be compared. Acoustic data for 26 typically speaking 9- to 15-year-olds were examined to resolve measurement issues in acoustic analyses, including alternative sampling points within the /s/ frication; the informativeness of linear versus Bark transformations of each of the 4 spectral moments of /s/ (Forrest, Weismer, Milenkovic, & Dougall, 1988); and measurement effects associated with linguistic context, age, and sex. Analysis of the reference data set indicates that acoustic characterization of /s/ is appropriately and optimally (a) obtained from the midpoint of /s/, (b) represented in linear scale, (c) reflected in summary statistics for the 1 st and 3rd spectral moments, (d) referenced to individual linguistic-phonetic contexts, (e) collapsed across the age range studied, and (f) described individually by sex.

Adolescent↗

PubMed1998

Plasma apolipoproteins A-I and B in survivors of myocardial infarction and in a control group.

The values of apolipoproteins (apo) A-I and B were determined in a population sample of hospital outpatients with a standardized method to verify if the cutpoints calculated in a cross-sectional study in the US are usable with other populations. We also tested the apolipoproteins' ability to discriminate between healthy people and survivors of myocardial infarction. In the studied population the apo A-I value corresponding to the HDL-cholesterol decisional centile is 1.12 g/L for males and 1.17 g/L for females; the apo B value corresponding to the LDL-cholesterol decisional centile is 1.23 g/L for males and 1.14 g/L for females. These values are quite close to the cutpoints proposed for the American population (1.20 g/L for both apolipoproteins). In comparison with the LDL- and HDL-cholesterol decisional concentrations, the cutpoints for apolipoproteins allow a correct classification of a greater percentage of postmyocardial infarction patients (16% higher for apo B and 5% for apo A-I). Standardized assays coupled with a reference database allow a better clinical use of apolipoprotein measurements.

Adult↗

PubMed1996

Are convenience DNA samples significantly different?

In this paper, the issue of whether DNA databases collected by different convenience sampling methods are significantly different statistically is investigated. Testing the null hypothesis that the population probability or frequency distributions of DNA profiles under different sampling methods are the same is of interest in this investigation. Some statistical analyses are conducted on the single-locus VNTR databases collected from different sources by the Hong Kong Government Laboratory. The bootstrap, Monte Carlo simulation and significance tests including the Pearson's chi-squared, likelihood ratio, and Kolmogorov-Smirnov two-sample statistics are employed for testing the hypothesis. The results are promising that no probability values of the tests are smaller than 5%. In other words, there is not enough evidence to reject the null hypothesis at the 5% level, which provides more confidence for using the VNTR reference databases commonly collected by convenience sampling.

DNA↗