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PubMed2000

Bone densitometry.

Assessment of BMD has become the essential part of evaluation of patients at risk of osteoporosis. It is likely that different BMD technologies will coexist in clinical practice in the future depending on varying clinical needs. DXA is currently the leading bone density technique because it has the capacity to measure axial and appendicular sites, superior monitoring capabilities, and more sophisticated reference databases and quality control procedures. More rapid and portable peripheral devices, such as peripheral DXA, peripheral instantaneous x-ray imager, and QUS, will likely be used for screening. This large variety of available bone densitometry techniques will provide a wide selection for clinicians to choose from. It may also add confusion, however, about which devices should be used and how to interpret data from different techniques. It is critical for clinicians to have a basic understanding of the technology being used, and the clinical advantages and disadvantages of each instrument, to choose properly which test to perform and interpret the obtained results. When combined with other major risks for fracture, such as age and prior fragility fractures, knowledge of the BMD is an invaluable tool in the assessment of patients with known or suspected osteoporosis.

Absorptiometry, Photon↗

PubMed2000

A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males.

A 9-locus microsatellite framework (minimal haplotype), previously developed for forensic purposes so as to facilitate stain analysis, personal identification and kinship testing, has been adopted for the establishment of a large reference database of male European Y-chromosomal haplotypes. The extent of population stratification pertaining to this database, an issue crucial for its practical forensic application, was assessed through analysis of molecular variance (AMOVA) of the 20 regional samples included. Despite the notion of some significant haplotype frequency differences, which were found to correlate with known demographic and historic features of Europeans, AMOVA generally revealed a high level of genetic homogeneity among the populations analyzed. Owing to their high diversity, however, accurate frequency estimation is difficult for Y-STR haplotypes when realistic (i.e. moderately sized) datasets are being used. As expected, strong pair-wise and higher order allelic associations were found to exist between all markers studied, implying that haplotype frequencies cannot be estimated as products of allele frequencies. A new extrapolation method was therefore developed which treats haplotype frequencies as random variables and generates estimates of the underlying distribution functions on the basis of closely related haplotypes. This approach, termed frequency 'surveying', is based upon standard population genetics theory and can in principle be applied to any combination of markers located on the Y-chromosome or in the mitochondrial genome. Application of the method to the quality assured reference Y-STR haplotype database described herein will prove very useful for the evaluation of positive trace-donor matches in forensic casework.

Alleles↗

PubMed1997

A suggested methodology for the construction of national bone densitometry reference ranges: 1372 Caucasian women from four UK sites.

This paper presents a simple methodology for combining bone densitometry data from different sites in the UK, having instruments from the same manufacturer (LUNAR Radiation). Additive normalization factors were used on all data prior to inclusion in a reference database which ultimately included data on 1372 Caucasian women, aged 20-70 years, of whom 749 were post-menopausal. Reference data for spine (L2-L4) and femoral neck bone mineral density are given in tabular form as 3 year moving averages for: (1) all women; (2) perimenopausal women grouped by menopausal status; and (3) post-menopausal women with respect to years since menopause. These data may be used to construct Z-score. T-score or percentile reporting ranges and may be adopted as the core for a UK reference range.

Adult↗

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↗

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↗

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↗

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↗